Time filter

Source Type

Qin Z.,Chinese Academy of Agricultural Sciences | Li C.,Peking University | Mao L.,Chinese Academy of Agricultural Sciences | Wu L.,Chinese Academy of Agricultural Sciences
Frontiers in Plant Science | Year: 2014

Plant microRNAs (miRNAs), a class of small non-coding regulatory RNAs, are canonically 20-24 nucleotides in length and bind to complementary target RNA sequences, guiding target attenuation via mRNA degradation or translation inhibition. Of the annotated miRNA families, evolutionarily conserved families have been well known to extensively regulate analogous targets and play critical roles in plant development and adaptation to adverse environments. By contrast, majority of these families that are merely present in a specific lineage or in a few closely related species have not been well functionally explored until recently. The fast-growing progresses being made in the actions of non-conserved miRNAs nowadays in diverse plant species may represent a highly promising research field in future. This review thereby summarizes the emerging advances in our understanding of the biogenesis, associated effectors, modes to targets, and biological functions of plant non-conserved miRNAs. In addition, it outlines the regulatory units recently discovered between conserved miRNAs and their alternative targets. © 2014 Qin, Li, Mao and Wu.


Wang K.,Chinese Academy of Agricultural Sciences | Wang Z.,BGI Shenzhen | Li F.,Chinese Academy of Agricultural Sciences | Ye W.,Chinese Academy of Agricultural Sciences | And 26 more authors.
Nature Genetics | Year: 2012

We have sequenced and assembled a draft genome of G. raimondii, whose progenitor is the putative contributor of the D subgenome to the economically important fiber-producing cotton species Gossypium hirsutum and Gossypium barbadense. Over 73% of the assembled sequences were anchored on 13 G. raimondii chromosomes. The genome contains 40,976 protein-coding genes, with 92.2% of these further confirmed by transcriptome data. Evidence of the hexaploidization event shared by the eudicots as well as of a cotton-specific whole-genome duplication approximately 13-20 million years ago was observed. We identified 2,355 syntenic blocks in the G. raimondii genome, and we found that approximately 40% of the paralogous genes were present in more than 1 block, which suggests that this genome has undergone substantial chromosome rearrangement during its evolution. Cotton, and probably Theobroma cacao, are the only sequenced plant species that possess an authentic CDN1 gene family for gossypol biosynthesis, as revealed by phylogenetic analysis. © 2012 Nature America, Inc. All rights reserved.


Guo J.-J.,Soochow University of China | Guo J.-J.,Qiqihaer Medical College | Zheng H.-J.,Chinese National Human Genome Center at Shanghai | Xu J.,Soochow University of China | And 3 more authors.
PLoS Neglected Tropical Diseases | Year: 2012

Background: Schistosomiasis japonica is a serious debilitating and sometimes fatal disease. Accurate diagnostic tests play a key role in patient management and control of the disease. However, currently available diagnostic methods are not ideal, and the detection of the parasite DNA in blood samples has turned out to be one of the most promising tools for the diagnosis of schistosomiasis. In our previous investigations, a 230-bp sequence from the highly repetitive retrotransposon SjR2 was identified and it showed high sensitivity and specificity for detecting Schistosoma japonicum DNA in the sera of rabbit model and patients. Recently, 29 retrotransposons were found in S. japonicum genome by our group. The present study highlighted the key factors for selecting a new perspective sensitive target DNA sequence for the diagnosis of schistosomiasis, which can serve as example for other parasitic pathogens. Methodology/Principal Findings: In this study, we demonstrated that the key factors based on the bioinformatic analysis for selecting target sequence are the higher genome proportion, repetitive complete copies and partial copies, and active ESTs than the others in the chromosome genome. New primers based on 25 novel retrotransposons and SjR2 were designed and their sensitivity and specificity for detecting S. japonicum DNA were compared. The results showed that a new 303-bp sequence from non-long terminal repeat (LTR) retrotransposon (SjCHGCS19) had high sensitivity and specificity. The 303-bp target sequence was amplified from the sera of rabbit model at 3 d post-infection by nested-PCR and it became negative at 17 weeks post-treatment. Furthermore, the percentage sensitivity of the nested-PCR was 97.67% in 43 serum samples of S. japonicum-infected patients. Conclusions/Significance: Our findings highlighted the key factors based on the bioinformatic analysis for selecting target sequence from S. japonicum genome, which provide basis for establishing powerful molecular diagnostic techniques that can be used for monitoring early infection and therapy efficacy to support schistosomiasis control programs. © 2012 Guo et al.


Ali A.,Chinese Academy of Agricultural Sciences | Ahmad F.,University of Agriculture at Faisalabad | Biondi A.,University of Catania | Biondi A.,French National Institute for Agricultural Research | And 2 more authors.
Journal of Pest Science | Year: 2012

Various plants are well known for their insecticidal activity and their use was maintained for millennia throughout all the agricultural regions of the world. In a current context, the use of Botanical insecticides represents one of the best alternatives to chemicals for the development of environmental-friendly strategies for stored grain pest control. Datura alba Nees is a plant found extensively in the warmer regions of the world and it is used as a medicinal plant. This study aims to assess the contact toxicity and the trans-generational effect of D. alba leaf extract (DLE) against two important insect pests on stored rice, Trogodermagranarium and Sitophilus oryzae, under laboratory conditions. Filter papers were soaked in three DLE concentration solutions and in two control treatments: water and acetone. The survivor specimens (F 0) were transferred to a new untreated feeding substrate and the population build up of the two following generations (F 1 and F 2) were counted after 30 and 60 days, respectively. The highest DLE concentration (2. 5 %) induced the significantly highest mortality with 33. 5 and 45 % mortality in T. granarium and S. oryzae after 7 days of exposure, respectively. The DLE long-term effect toward both tested species was also proved by the high demographic decrease in the F 2 generations, when compared to control groups. This study is the first step toward establishing a scientific basis for the effective application of D. alba plant materials as biorational tools to control stored grain pests. © 2012 Springer-Verlag.


Huang S.,Jiangxi Agricultural University | Huang S.,Nanjing Agricultural University | Sun Y.,Jiangxi Agricultural University | Sun Y.,Nanjing Agricultural University | And 2 more authors.
Climatic Change | Year: 2012

Great uncertainties remain in the impact of cropping systems on soil organic carbon (SOC) stocks in paddy fields that hold a large potential for carbon (C) sequestration. In this study, a meta-analysis was performed to examine trends on SOC stocks in unfertilized and fertilized fields from three of the most common rice cropping systems in China. Results showed that rice cropping without any nutrient application (Control) significantly increased SOC stocks by 9% compared to the initial level in double rice cropping systems (DR), whereas no significant effects were observed in single rice cropping systems (SR) and rice-upland crop rotation systems (RU). Paddy soils sequestered C in all the three cropping systems under inorganic NPK fertilization, and the magnitude of the increase in SOC stocks was in the order DR & RU & SR. Soil C stocks increased with the increasing cropping duration. Continuous rice cropping for more than 20 years led to average SOC gains of 15% and 23% in the control and NPK treatments, respectively. Furthermore, it seems that C sequestration was still occurring in the longest fields from the included studies. Thus, no SOC saturation trend was found over the investigated cropping duration. However, the negative relationship between SOC changes and their initial C stocks suggests indirectly the possibility of SOC saturation in paddy fields. © 2011 Springer Science+Business Media B.V.


Cheng G.,Chinese Academy of Agricultural Sciences | Luo R.,Chinese Academy of Agricultural Sciences | Hu C.,Chinese Academy of Agricultural Sciences | Cao J.,Chinese Academy of Agricultural Sciences | Jin Y.,Shanghai University
Parasitology | Year: 2013

Circulating microRNAs (miRNAs) have received considerable attention as a novel class of biomarkers for the diagnosis of cancer and as signalling molecules in mediating intercellular communication. Schistosomes, the causative agents of schistosomiasis, live in the blood vessels of a mammalian host in the adult stage. In the present study, we characterized schistosome-specific small RNA populations in the plasma of rabbits infected with Schistosoma japonicum (S. japonicum) using a deep sequencing method and then identified five schistosome-specific miRNAs, including four known miRNAs (Bantam, miR-3479, miR-10 and miR-3096), and one novel miRNA (miR-0001, miRBase ID: sja-miR-8185). Four of the five schistosome-specific miRNAs were also detected by real-time RT-PCR in the plasma of S. japonicum-infected mice. In addition, our study indicated that schistosome Argonaute 2/3 may be an excretory-secretory (ES) protein. In summary, our findings are expected to provide useful information for further development of novel biomarkers for the diagnosis of schistosomiasis and also for deeper understanding of the mechanism of host-parasite interaction. © Cambridge University Press 2013.


Tian S.,Chinese Academy of Agricultural Sciences | Tian S.,Sichuan Agricultural University | Mao X.,Chinese Academy of Agricultural Sciences | Zhang H.,Chinese Academy of Agricultural Sciences | And 4 more authors.
Journal of Experimental Botany | Year: 2013

Environmental stresses such as drought, salinity, and cold are major adverse factors that significantly affect agricultural productivity. Protein phosphorylation/dephosphorylation is a major signalling event induced by osmotic stress in higher plants. Sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family members play essential roles in the response to hyperosmotic stresses in plants. In this study, the TaSnRK2.3 gene, a novel SnRK2 member was cloned, and three copies located on chromosomes 1A, 1B, and 1D were identified in common wheat. TaSnRK2.3 was strongly expressed in leaves, and responded to polyethylene glycol, NaCl, abscisic acid, and cold stresses. To characterize its function, transgenic Arabidopsis overexpressing TaSnRK2.3-GFP controlled by the cauliflower mosaic virus 35S promoter was generated and subjected to severe abiotic stresses. Overexpression of TaSnRK2.3 resulted in an improved root system and significantly enhanced tolerance to drought, salt, and freezing stresses, simultaneously demonstrated by enhanced expression of abiotic stress-responsive genes and ameliorative physiological indices, including a decreased rate of water loss, enhanced cell membrane stability, improved photosynthetic potential, and significantly increased osmotic potential and free proline content under normal and/or stressed conditions. These results demonstrate that TaSnRK2.3 is a multifunctional regulator, with potential for utilization in transgenic breeding for improved abiotic stress tolerance in crop plants. © The Author(s) [2013].


Qiao W.,Chinese Academy of Agricultural Sciences | Li C.,Peking University | Fan L.-M.,Peking University
Environmental and Experimental Botany | Year: 2014

Nitric oxide (NO) and hydrogen peroxide (H2O2) are two signaling molecules, which play roles in diverse organisms. In the past two decades, evidence has been accumulating to address their involvements in stress responses in plants, but how these two molecules interact with each other and how the signals are integrated in biological processes remain fragmentary and far from clear in the literature. This review brings together the knowledge obtained so far on these two molecules and their cross-talk in plant stress responses, particularly abiotic stresses including drought, salinity, extreme temperatures, UV light, and heavy metals. We tentatively discuss, in the context of abiotic stresses, how NO and H2O2 interact with each other at two levels, biosynthesis, and regulation of gene expression or protein activities. The cross-talk between NO and H2O2 with other signaling pathways in the regulation of abiotic stress responses in plants is also discussed. © 2014 Elsevier B.V.


Zhang R.,French National Institute for Agricultural Research | Zhang R.,Chinese Academy of Agricultural Sciences | Murat F.,French National Institute for Agricultural Research | Li A.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Plant Cell | Year: 2012

The recent availability of plant genome sequences, combined with a robust evolutionary scenario of the modern monocot and eudicot karyotypes from their diploid ancestors, offers an opportunity to gain insights into microRNA (miRNA) gene paleohistory in plants. Characterization and comparison of miRNAs and associated protein-coding targets in plants allowed us to unravel (1) contrasted genome conservation patterns of miRNAs in monocots and eudicots after whole-genome duplication (WGD), (2) an ancestral miRNA founder pool in the monocot genomes dating back to 100 million years ago, (3) miRNA subgenome dominance during the post-WGD diploidization process with selective miRNA deletion complemented with possible transposable element-mediated return flows, and (4) the miRNA/target interaction-directed differential loss/ retention of miRNAs following the gene dosage balance rule. Together, our data suggest that overretained miRNAs in grass genomes may be implicated in connected gene regulations for stress responses, which is essential for plant adaptation and useful for crop variety innovation. © © American Society of Plant Biologists. All rights reserved.


Xu Y.,Chinese Academy of Agricultural Sciences | Lu Y.,Sichuan Agricultural University | Xie C.,Chinese Academy of Agricultural Sciences | Gao S.,Sichuan Agricultural University | And 2 more authors.
Molecular Breeding | Year: 2012

Molecular breeding for complex traits in crop plants requires understanding and manipulation of many factors influencing plant growth, development and responses to an array of biotic and abiotic stresses. Molecular marker-assisted breeding procedures can be facilitated and revolutionized through whole-genome strategies, which utilize full genome sequencing and genome-wide molecular markers to effectively address various genomic and environmental factors through a representative or complete set of genetic resources and breeding materials. These strategies are now increasingly based on understanding of specific genomic regions, genes/alleles, haplotypes, linkage disequilibrium (LD) block(s), gene networks and their contribution to specific phenotypes. Large-scale and high-density genotyping and genome-wide selection are two important components of these strategies. As components of whole-genome strategies, molecular breeding platforms and methodologies should be backed up by high throughput and precision phenotyping and e-typing (environmental assay) with strong support systems such as breeding informatics and decision support tools. Some basic strategies are discussed in this article, including (1) seed DNA-based genotyping for simplifying marker-assisted selection (MAS), reducing breeding cost and increasing scale and efficiency, (2) selective genotyping and phenotyping, combined with pooled DNA analysis, for capturing the most important contributing factors, (3) flexible genotyping systems, such as genotyping by sequencing and arraying, refined for different selection methods including MAS, marker-assisted recurrent selection and genomic selection (GS), (4) marker-trait association analysis using joint linkage and LD mapping, and (5) sequence-based strategies for marker development, allele mining, gene discovery and molecular breeding. © 2012 Springer Science+Business Media B.V.


Li H.,Chinese Academy of Agricultural Sciences | Li H.,Cornell University | Bradbury P.,Robert lley Center For Agriculture And Health | Ersoz E.,Cornell University | And 4 more authors.
PLoS ONE | Year: 2011

Background: Nested association mapping (NAM) is a novel genetic mating design that combines the advantages of linkage analysis and association mapping. This design provides opportunities to study the inheritance of complex traits, but also requires more advanced statistical methods. In this paper, we present the detailed algorithm of a QTL linkage mapping method suitable for genetic populations derived from NAM designs. This method is called joint inclusive composite interval mapping (JICIM). Simulations were designed on the detected QTL in a maize NAM population and an Arabidopsis NAM population so as to evaluate the efficiency of the NAM design and the JICIM method. Principal Findings: Fifty-two QTL were identified in the maize population, explaining 89% of the phenotypic variance of days to silking, and nine QTL were identified in the Arabidopsis population, explaining 83% of the phenotypic variance of flowering time. Simulations indicated that the detection power of these identified QTL was consistently high, especially for large-effect QTL. For rare QTL having significant effects in only one family, the power of correct detection within the 5 cM support interval was around 80% for 1-day effect QTL in the maize population, and for 3-day effect QTL in the Arabidopsis population. For smaller-effect QTL, the power diminished, e.g., it was around 50% for maize QTL with an effect of 0.5 day. When QTL were linked at a distance of 5 cM, the likelihood of mapping them as two distinct QTL was about 70% in the maize population. When the linkage distance was 1 cM, they were more likely mapped as one single QTL at an intermediary position. Conclusions: Because it takes advantage of the large genetic variation among parental lines and the large population size, NAM is a powerful multiple-cross design for complex trait dissection. JICIM is an efficient and specialty method for the joint QTL linkage mapping of genetic populations derived from the NAM design.


Zhou M.-L.,Sichuan Agricultural University | Zhou M.-L.,Chinese Academy of Agricultural Sciences | Zhou M.-L.,Leiden University | Zhu X.-M.,Sichuan Agricultural University | And 3 more authors.
Applied Microbiology and Biotechnology | Year: 2011

In the past three decades, hairy roots research for the production of valuable biological active substances has received a lot of attention. The addition of knowledge to enhance the yields of desired substances and the development of novel tools for biomass engineering offer new possibilities for large-scale cultivation of the plant hairy root. Hairy roots can also produce recombinant proteins through the transfer of Agrobacterium T-DNA into the plant genome, and thereby hold immense potential for the pharmaceutical industry. This review highlights some of the significant progress made in the past few years and outlines future prospects for exploiting the potential utility of hairy root cultures as "chemical factories" for producing bioactive substances. © 2011 Springer-Verlag.


Zhao M.,China Agricultural University | Zhao M.,Chinese Academy of Agricultural Sciences | Ding H.,China Agricultural University | Zhu J.-K.,University of California at Riverside | And 2 more authors.
New Phytologist | Year: 2011

Recent studies have revealed that microRNAs (miRNAs) regulate plant adaptive responses to nutrient deprivation. However, the functional significance of miRNAs in adaptive responses to nitrogen (N) limitation remains to be explored. The Arabidopsis miR169 was strongly down-regulated, whereas its targets, NFYA (Nuclear Factor Y, subunit A) family members, were strongly induced by nitrogen N starvation. Analysis of the expression of miR169 precursors showed that MIR169a was substantially down-regulated in both roots and shoots by N starvation. Accumulation of the NFYA family members was suppressed in transgenic Arabidopsis with constitutive expression of MIR169a. Transgenic Arabidopsis plants overexpressing MIR169a accumulated less N and were more sensitive to N stress than the wild type. N sensitivity of 35S::MIR169a might be attributable to impaired uptake systems. These results provide evidence that miRNAs have functional roles in helping plants to cope with fluctuations in N availability in the soil. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.


Bancroft I.,John Innes Center | Morgan C.,John Innes Center | Fraser F.,John Innes Center | Higgins J.,John Innes Center | And 10 more authors.
Nature Biotechnology | Year: 2011

Polyploidy complicates genomics-based breeding of many crops, including wheat, potato, cotton, oat and sugarcane. To address this challenge, we sequenced leaf transcriptomes across a mapping population of the polyploid crop oilseed rape (Brassica napus) and representative ancestors of the parents of the population. Analysis of sequence variation 1 and transcript abundance enabled us to construct twin single nucleotide polymorphism linkage maps of B. napus, comprising 23,037 markers. We used these to align the B. napus genome with that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of its progenitor species, Brassica rapa and Brassica oleracea. We also developed methods to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an interspecific cross. By revealing the genetic consequences of breeding, cost-effective, high-resolution dissection of crop genomes by transcriptome sequencing will increase the efficiency of predictive breeding even in the absence of a complete genome sequence. © 2011 Nature America, Inc. All rights reserved.


Lu Y.,Chinese Academy of Agricultural Sciences | Wu K.,Chinese Academy of Agricultural Sciences | Jiang Y.,National Agro Technical Extension and Service Center | Guo Y.,Chinese Academy of Agricultural Sciences | Desneux N.,French National Institute for Agricultural Research
Nature | Year: 2012

Over the past 16 years, vast plantings of transgenic crops producing insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) have helped to control several major insect pests and reduce the need for insecticide sprays. Because broad-spectrum insecticides kill arthropod natural enemies that provide biological control of pests, the decrease in use of insecticide sprays associated with Bt crops could enhance biocontrol services. However, this hypothesis has not been tested in terms of long-term landscape-level impacts. On the basis of data from 1990 to 2010 at 36 sites in six provinces of northern China, we show here a marked increase in abundance of three types of generalist arthropod predators (ladybirds, lacewings and spiders) and a decreased abundance of aphid pests associated with widespread adoption of Bt cotton and reduced insecticide sprays in this crop. We also found evidence that the predators might provide additional biocontrol services spilling over from Bt cotton fields onto neighbouring crops (maize, peanut and soybean). Our work extends results from general studies evaluating ecological effects of Bt crops by demonstrating that such crops can promote biocontrol services in agricultural landscapes. © 2012 Macmillan Publishers Limited. All rights reserved.


Li X.,Samuel Roberts Noble Foundation | Wei Y.,Samuel Roberts Noble Foundation | Acharya A.,Samuel Roberts Noble Foundation | Jiang Q.,Samuel Roberts Noble Foundation | And 2 more authors.
G3: Genes, Genomes, Genetics | Year: 2014

A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa. © 2014 Li et al.


Li F.,Chinese Academy of Agricultural Sciences | Fan G.,BGI Shenzhen | Wang K.,Chinese Academy of Agricultural Sciences | Sun F.,BGI Shenzhen | And 30 more authors.
Nature Genetics | Year: 2014

The complex allotetraploid nature of the cotton genome (AADD; 2n = 52) makes genetic, genomic and functional analyses extremely challenging. Here we sequenced and assembled the Gossypium arboreum (AA; 2n = 26) genome, a putative contributor of the A subgenome. A total of 193.6 Gb of clean sequence covering the genome by 112.6-fold was obtained by paired-end sequencing. We further anchored and oriented 90.4% of the assembly on 13 pseudochromosomes and found that 68.5% of the genome is occupied by repetitive DNA sequences. We predicted 41,330 protein-coding genes in G. arboreum. Two whole-genome duplications were shared by G. arboreum and Gossypium raimondii before speciation. Insertions of long terminal repeats in the past 5 million years are responsible for the twofold difference in the sizes of these genomes. Comparative transcriptome studies showed the key role of the nucleotide binding site (NBS)-encoding gene family in resistance to Verticillium dahliae and the involvement of ethylene in the development of cotton fiber cells. © 2014 Nature America, Inc.


Darmency H.,French National Institute for Agricultural Research | Picard J.C.,French National Institute for Agricultural Research | Wang T.,French National Institute for Agricultural Research | Wang T.,Chinese Academy of Agricultural Sciences
Heredity | Year: 2011

A mutant Thr-239-Ileu at the α2-tubulin gene was found to confer resistance to dinitroanilines, a family of mitosis-disrupting herbicides. However, mutations affecting microtubule polymerization and cell division are expected to impact growth and reproduction, that is, the fitness of a resistant weed or the yield of a tolerant crop, although it has not been demonstrated yet. This study was designed to test this hypothesis for the growth and reproduction of near-isogenic resistant and susceptible materials that were created in F 2 and F 3 generations after a Setaria viridis x S. italica cross. Differential growth was noticeable at the very onset of seedling growth. The homozygous resistant plants, grown both in a greenhouse cabinet and in the field, were smaller and had lower 1000-grain weight and therefore a lower yield. This fitness penalty is certainly due to modified cell division kinetics. Although the presence of the mutant allele accounted for 20% yield losses, there were also measurable benefits of dinitroaniline resistance, and these benefits are discussed. © 2011 Macmillan Publishers Limited All rights reserved 0018-067X/11.


Tang W.,China Agricultural University | Ding Z.,China Agricultural University | Zhou Z.Q.,Chinese Academy of Agricultural Sciences | Wang Y.Z.,China Institute of Technology | Guo L.Y.,China Agricultural University
Plant Disease | Year: 2012

Apple ring rot and Botryosphaeria canker are severe diseases affecting apple production in China, but there is confusion regarding which pathogens cause these diseases and their similarity to other diseases, such as white rot of apple, and ring rot and Botryosphaeria canker of pear. In this study, the pathogen of apple ring rot in China was compared with the pathogen of apple ring rot in Japan and Korea, the pathogen of Botryosphaeria canker of apple and pear in China, the pathogen of pear ring rot in China, and the pathogen of white rot of apple in the United States. Comparisons were based on morphology, pathogenicity on branches and fruit, and sequences of rDNA in the internal transcribed spacer region and of the β-tubulin and actin genes. Results showed that the causal agent of apple ring rot and Botryosphaeria canker of apple in China was Botryosphaeria dothidea, which has also been reported to be the pathogen of apple ring rot in Korea and Japan. Pathogenicity tests showed that B. dothidea infection on apple and pear branches may induce wart or canker symptoms depending on the conditions. These results are consistent with the hypothesis that the same pathogen causes the wart symptom of apple ring rot and the Botryosphaeria canker symptom on apple branches in China. The results also suggest that apple ring rot and white rot are the same disease and are caused by B. dothidea. Finally, B. dothidea isolates from pear and other fruit or forest trees may serve as inoculum for apple ring rot. © 2012 The American Phytopathological Society.


Liu W.,Chinese Academy of Agricultural Sciences | Yang Y.,Anhui Agricultural University | Zhang J.,Anhui Agricultural University | Gatlin D.M.,Texas A&M University | Zhou Z.,Chinese Academy of Agricultural Sciences
British Journal of Nutrition | Year: 2014

The aim of the present study was to investigate the effects of different dietary sustained-release microencapsulated sodium butyrate (MSB) products (0 (non-supplement), 1·5 and 3·0 h) for a control or oxidised soyabean oil (SBO) diet on fish production, intestinal mucosal condition, immunity and intestinal bacteria in juvenile common carp (Cyprinus carpio). Dietary MSB increased weight gain and reduced the feed conversion ratio within the control and oxidised SBO groups. Gut mucosa was damaged in the oxidised SBO group fed without MSB, in contrast to a normal appearance found in fish fed the MSB1·5 and MSB3·0 diets in the oxidised SBO group. Microvillus density increased in fish fed the MSB1·5 and MSB3·0 diets in the oxidised SBO group (P< 0·001); however, microvillus density was affected by the different pre-fed diets in the midgut (P< 0·001) and by the different sustained-release times of MSB in the distal gut (DG) (P=0·003). The interaction between the pre-fed diets and the sustained-release times of dietary MSB was significant for the relative gene expression levels of gut heat shock protein-70 (HSP70), pro-inflammatory cytokines (IL-1β and TNF-α) and anti-inflammatory cytokines (transforming growth factor-β) within each gut segment, except for HSP70 in the DG and IL-1β in the foregut. Modulation of adherent bacterial communities within each gut segment investigated was not obvious when the common carp were fed the diets with MSB, as similarity coefficients of >0·79 were observed. These results indicated that MSB can be used as a dietary supplement to repair or prevent intestinal damage in carp fed oxidised SBO. Copyright © The Authors 2014.


Qiao W.,Chinese Academy of Agricultural Sciences | Fan L.,Peking University
Frontiers in Biology | Year: 2011

Epigenetics has been becoming a hot topic in recent years. It can be mechanisms that regulate gene expression without changing DNA base sequence. In plants epigenetic regulation has been implicated to be a very important phenomenon and mechanism for the regulation of responses to environmental stresses. Environmental signals induce various epigenetic modifications in the genome, and these epigenetic modifications might likely be inherited to the next generation that behaves with enhanced ability to tolerate stresses. This review highlights recent advances in the study of epigenetics in plant stress responses. © 2011 Higher Education Press and Springer-Verlag Berlin Heidelberg.


Kirby J.K.,CSIRO | McLaughlin M.J.,CSIRO | Ma Y.,CSIRO | Ma Y.,Chinese Academy of Agricultural Sciences | Ajiboye B.,University of Adelaide
Chemosphere | Year: 2012

Aging reactions in soils can influence the lability and hence bioavailability of added metals in soils through their removal from labile pools into pools from which desorption is slow (non-labile pools). The aims of this study were to examine the effect of aging reactions on the lability of soluble molybdate (MoO42-) added into soils with varying physical and chemical properties and develop models to predict changes in the labile pool of MoO42- in soils with incubation time. Soils were spiked with soluble MoO42- at quantities sufficient to inhibit barley root growth by 10% (EC10) or 90% (EC90) and incubated for up to 18months. The labile pool of MoO42- (E value) was observed to decrease in soils with incubation time, particularly in soils with high clay content. A strong relationship was observed between measures of MoO42- lability in soils determined using E and L value techniques (R2=0.98) suggesting E values provided a good measure of the potential plant available pool of MoO42- in soils. A regression model was developed that indicates clay content and incubation time were the most important factors affecting the labile pool of MoO42- in soils with time after addition (R2=0.70-0.75). The aging model developed suggests soluble MoO42- will be removed into non-labile pools more rapidly with time in neutral to alkaline clay soils than in acidic sandy soils. Labile MoO42- concentrations in molybdenum (Mo) contaminated soils was found to be <10% of the total Mo concentrations in soils. © 2012 .


Han P.,Huazhong Agricultural University | Niu C.-Y.,Huazhong Agricultural University | Lei C.-L.,Huazhong Agricultural University | Cui J.-J.,Chinese Academy of Agricultural Sciences | Desneux N.,French National Institute for Agricultural Research
Ecotoxicology | Year: 2010

Transgenic Cry1Ac ? CpTI cotton (CCRI41) is increasingly planted throughout China. However, negative effects of this cultivar on the honey bee Apis mellifera L., the most important pollinator for cultivated ecosystem, remained poorly investigated. The objective of our study was to evaluate the potential side effects of transgenic Cry1Ac ? CpTI pollen from cotton on young adult honey bees A. mellifera L. Two points emphasized the significance of our study: (1) A higher expression level of insecticidal protein Cry1Ac in pollen tissues was detected (when compared with previous reports). In particular, Cry1Ac protein was detected at 300 ± 4.52 ng g -1 [part per billion (ppb)] in pollen collected in July, (2) Effects on chronic mortality and feeding behaviour in honey bees were evaluated using a no-choice dietary feeding protocol with treated pollen, which guarantee the highest exposure level to bees potentially occurring in natural conditions (worst case scenario). Tests were also conducted using imidacloprid-treated pollen at a concentration of 48 ppb as positive control for sublethal effect on feeding behaviour. Our results suggested that Cry1Ac ? CpTI pollen carried no lethal risk for honey bees. However, during a 7-day oral exposure to the various treatments (transgenic, imidacloprid- treated and control), honey bee feeding behaviour was disturbed and bees consumed significantly less CCRI41 cotton pollen than in the control group in which bees were exposed to conventional cotton pollen. It may indicate an antifeedant effect of CCRI41 pollen on honey bees and thus bees may be at risk because of large areas are planted with transgenic Bt cotton in China. This is the first report suggesting a potential sublethal effect of CCRI41 cotton pollen on honey bees. The implications of the results are discussed in terms of risk assessment for bees as well as for directions of future work involving risk assessment of CCRI41 cotton. © The Author(s) 2010.


Yao Y.,Chinese Academy of Agricultural Sciences | Yao Y.,Xinjiang Institute of Ecology and Geography | Sun H.,Chinese Academy of Agricultural Sciences | Xu F.,Huazhong Agricultural University | And 2 more authors.
Planta | Year: 2011

In an attempt to determine the adaptation strategy to phosphorous (Pi) deficiency in oilseed rape, comparative proteome analyses were conducted to investigate the differences of metabolic changes in two oilseed rape genotypes with different tolerance to low phosphorus (LP). Generally in either roots or leaves, there existed few low phosphorus (LP)-induced proteins shared in the two lines. The LP-tolerant genotype 102 maintained higher Pi concentrations than LP-sensitive genotype 105 when growing hydroponically under the 5-μM phosphorus condition. In 102 we observed the downregulation of the proteins related to gene transcription, protein translation, carbon metabolism, and energy transfer in leaves and roots, and the downregulation of proteins related to leaf growth and root cellular organization. But the proteins related to the formation of lateral root were upregulated, such as the auxin-responsive family proteins in roots and the sucrose-phosphate synthase-like protein in roots and leaves. On the other hand, the LP-sensitive genotype 105 maintained the low level of Pi concentrations and suffered high oxidative pressure under the LP condition, and stress-shocking proteins were pronouncedly upregulated such as the proteins for signal transduction, gene transcription, secondary metabolism, universal stress family proteins, as well as the proteins involved in lipid oxygenation and the disease resistance in both leaves and roots. Although the leaf proteins for growth in 105 were downregulated, the protein expressions in roots related to glycolysis and tricarboxylic acid (TCA) cycle were enhanced to satisfy the requirement of organic acid secretion. © 2010 Springer-Verlag.


Periyannan S.,CSIRO | Moore J.,CSIRO | Ayliffe M.,CSIRO | Bansal U.,University of Sydney | And 12 more authors.
Science | Year: 2013

Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as "Ug99" have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea.


Li Z.,Beijing Normal University | Zhang Z.,Chinese Academy of Agricultural Sciences | Yan P.,Beijing Normal University | Huang S.,Chinese Academy of Agricultural Sciences | And 2 more authors.
BMC Genomics | Year: 2011

Background: As more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resources to compute consensus gene structures. However, many newly sequenced genomes have limited resources for gene predictions. In an effort to create high-quality gene models of the cucumber genome (Cucumis sativus var. sativus), based on the EVidenceModeler gene prediction pipeline, we incorporated the massively parallel complementary DNA sequencing (RNA-Seq) reads of 10 cucumber tissues into EVidenceModeler. We applied the new pipeline to the reassembled cucumber genome and included a comparison between our predicted protein-coding gene sets and a published set.Results: The reassembled cucumber genome, annotated with RNA-Seq reads from 10 tissues, has 23, 248 identified protein-coding genes. Compared with the published prediction in 2009, approximately 8, 700 genes reveal structural modifications and 5, 285 genes only appear in the reassembled cucumber genome. All the related results, including genome sequence and annotations, are available at http://cmb.bnu.edu.cn/Cucumis_sativus_v20/.Conclusions: We conclude that RNA-Seq greatly improves the accuracy of prediction of protein-coding genes in the reassembled cucumber genome. The comparison between the two gene sets also suggests that it is feasible to use RNA-Seq reads to annotate newly sequenced or less-studied genomes. © 2011 Li et al; licensee BioMed Central Ltd.


Liu H.,Chinese Academy of Agricultural Sciences | Zhou X.,Chinese Academy of Agricultural Sciences | Zhou X.,Sichuan Agricultural University | Dong N.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Functional and Integrative Genomics | Year: 2011

MYB transcription factors play diverse roles in plant growth, developmental processes and stress responses. A full-length cDNA sequence of a MYB gene, namely TaPIMP1, was isolated from wheat (Triticum aestivum L.). The TaPIMP1 transcript level was significantly up-regulated by inoculation with a fungal pathogen Bipolaris sorokiniana and by drought treatment. TaPIMP1 encodes the MYB protein TaPIMP1 consisting of 323 amino acids. TaPIMP1 contains two MYB DNA binding domains (R2, R3), two putative nuclear localization sites and two putative transcription activation domains. TaPIMP1 is a new member of the R2R3-MYB transcription factor subfamily. Transient expression in onion epidermal cells of GFP fused with TaPIMP1 proved that subcellular localization of TaPIMP1 occurred in the nucleus. The TaPIMP1 gene was transferred into tobacco (Nicotiana tabacum L.) cultivar W38 by Agrobacterium-mediated transformation. After screening through PCR and RT-PCR analyses, transgenic tobacco lines expressing TaPIMP1 were identified and evaluated for pathogen resistance, and drought and salt tolerance. Compared to untransformed tobacco host plants, TaPIMP1 expressing plants displayed significantly enhanced resistance to Ralstonia solanacearum and exhibited improved tolerances to drought and salt stresses. In these transgenic lines, the activities of phenylalanine ammonia-lyase (PAL) and superoxide dismutase (SOD) were significantly increased relative to wild-type tobacco plants. The results suggested that the wheat R2R3-MYB transcription factor plays an important role in modulating responses to biotic and abiotic stresses. © Springer-Verlag 2011.


Guo Z.,Chinese Academy of Agricultural Sciences | Guo Z.,Sichuan Agricultural University | Song Y.,Chinese Academy of Agricultural Sciences | Zhou R.,Chinese Academy of Agricultural Sciences | And 2 more authors.
New Phytologist | Year: 2010

Ppd-D1 is one of the most potent genes affecting the photoperiod response of wheat (Triticum aestivum). Only two alleles, insensitive Ppd-D1a and sensitive Ppd-D1b, were known previously, and these did not adequately explain the broad adaptation of wheat to photoperiod variation. In this study, five diagnostic molecular markers were employed to identify Ppd-D1 haplotypes in 492 wheat varieties from diverse geographic locations and 55 accessions of Aegilops tauschii, the D genome donor species of wheat. Six Ppd-D1 haplotypes, designated I-VI, were identified. Types II, V and VI were considered to be more ancient and types I, III and IV were considered to be derived from type II. The transcript abundances of the Ppd-D1 haplotypes showed continuous variation, being highest for haplotype I, lowest for haplotype III, and correlating negatively with varietal differences in heading time. These haplotypes also significantly affected other agronomic traits. The distribution frequency of Ppd-D1 haplotypes showed partial correlations with both latitudes and altitudes of wheat cultivation regions. The evolution, expression and distribution of Ppd-D1 haplotypes were consistent evidentially with each other. What was regarded as a pair of alleles in the past can now be considered a series of alleles leading to continuous variation. © 2009 New Phytologist.


Qiao Y.,University of California at Riverside | Qiao Y.,Chinese Academy of Agricultural Sciences | Shi J.,University of California at Riverside | Zhai Y.,University of California at Riverside | And 2 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

A broad range of parasites rely on the functions of effector proteins to subvert host immune response and facilitate disease development. The notorious Phytophthora pathogens evolved effectors with RNA silencing suppression activity to promote infection in plant hosts. Here we report that the Phytophthora Suppressor of RNA Silencing 1 (PSR1) can bind to an evolutionarily conserved nuclear protein containing the aspartate-glutamate-alanine-histidine-box RNA helicase domain in plants. This protein, designated PSR1-Interacting Protein 1 (PINP1), regulates the accumulation of both microRNAs and endogenous small interfering RNAs in Arabidopsis. A null mutation of PINP1 causes embryonic lethality, and silencing of PINP1 leads to developmental defects and hypersusceptibility to Phytophthora infection. These phenotypes are reminiscent of transgenic plants expressing PSR1, supporting PINP1 as a direct virulence target of PSR1. We further demonstrate that the localization of the Dicer-like 1 protein complex is impaired in the nucleus of PINP1-silenced or PSR1-expressing cells, indicating that PINP1 may facilitate small RNA processing by affecting the assembly of dicing complexes. A similar function of PINP1 homologous genes in development and immunity was also observed in Nicotiana benthamiana. These findings highlight PINP1 as a previously unidentified component of RNA silencing that regulates distinct classes of small RNAs in plants. Importantly, Phytophthora has evolved effectors to target PINP1 in order to promote infection. © 2015, National Academy of Sciences. All rights reserved.


Cheng G.,Chinese Academy of Agricultural Sciences | Jin Y.,Chinese Academy of Sciences | Jin Y.,Shanghai University
Parasitology | Year: 2012

MicroRNAs (miRNAs) are small, endogenous non-coding RNA molecules that regulate gene expression post-transcriptionally by targeting the 3' untranslated region (3' UTR) of messenger RNAs. Since the discovery of the first miRNA in Caenorhabditis elegans, important regulatory roles for miRNAs in many key biological processes including development, cell proliferation, cell differentiation and apoptosis of many organisms have been described. Hundreds of miRNAs have been identified in various multicellular organisms and many are evolutionarily conserved. Schistosomes are multi-cellular eukaryotes with a complex life-cycle that require genes to be expressed and regulated precisely. Recently, miRNAs have been identified in two major schistosome species, Schistosoma japonicum and S. mansoni. These miRNAs are likely to play critical roles in schistosome development and gene regulation. Here, we review recent studies on schistosome miRNAs and discuss the potential roles of miRNAs in schistosome development and gene regulation. We also summarize the current status for targeting miRNAs and the potential of this approach for therapy against schistosomiasis. © 2012 Cambridge University Press.


Liu S.,Max Planck Institute for Plant Breeding Research | Liu S.,Chinese Academy of Agricultural Sciences | Kracher B.,Max Planck Institute for Plant Breeding Research | Ziegler J.,Leibniz Institute of Plant Biochemistry | And 2 more authors.
eLife | Year: 2015

The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity. © Liu et al.


Wang Z.,Chinese Academy of Agricultural Sciences | Yan H.,Chinese Academy of Agricultural Sciences | Fu X.,Chinese Academy of Agricultural Sciences | Li X.,Samuel Roberts Noble Foundation | Gao H.,Chinese Academy of Agricultural Sciences
Molecular Biology Reports | Year: 2013

Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di - (26.1 %), tetra - (11.5 %), penta - (9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species. © 2012 Springer Science+Business Media Dordrecht.


He Y.,Fujian Academy of Agricultural science | Zhao J.,Fujian Academy of Agricultural science | Zheng Y.,Fujian Academy of Agricultural science | Desneux N.,French National Institute for Agricultural Research | Wu K.,Chinese Academy of Agricultural Sciences
Ecotoxicology | Year: 2012

Neonicotinoid insecticides are widely used for controlling sucking pests, and sublethal effects can be expected in beneficial arthropods like natural enemies. Serangium japonicum is an important predator in many agricultural systems in China, and a potential biological control agent against Bemisia tabaci. We evaluated the toxicity of imidacloprid to S. japonicum and its impact on the functional response to B. tabaci eggs. S. japonicum adults exposed through contact to dried residues of imidacloprid at the recommended field rate on cotton against B. tabaci (4 g active ingredient per 100 l, i.e. 40 ppm [part per million]), and reduced rates (25, 20, 15 and 10 ppm) for 24 h showed high mortality rates. The mortality induced by a lowest rate, 5 ppm, was not significantly different than the control group and thus it was considered as a sublethal rate. The lethal rate 50 and hazard quotient (HQ) were estimated to be 11.54 ppm and 3.47 respectively, indicating a risk for S. japonicum in treated fields (HQ > 2). When exposed to dried residues of imidacloprid at the sublethal rate (5 ppm) on cotton leaves, functional response of S. japonicum to B. tabaci eggs was affected with an increase in handling time and a reduction in peak consumption of eggs. Imidacloprid residues also disturbed predator voracity, the number of B. tabaci eggs consumed on treated leaves being significantly lower than on untreated leaves. All effects disappeared within a few hours after transfer to untreated cotton leaves. Imidacloprid systemically applied at the recommended field rate (for cotton) showed no toxicity to S. japonicum, nor affected the functional response of the predator. Sublethal effects of imidacloprid on S. japonicum observed in our study likely negatively affect S. japonicum development and reproductive capacity and may ultimately reduce predator population growth. These results hint at the importance of assessing potential effects of imidacloprid on S. japonicum for developing effective integrated pest management programs of B. tabaci in China. © Springer Science+Business Media, LLC 2012.


Chen B.,Agricultural Environment and Resources Research Center | Chen B.,Chinese Academy of Forestry | Liu S.,Chinese Academy of Forestry | Ge J.,Beijing Normal University | Chu J.,Chinese Academy of Agricultural Sciences
Soil Biology and Biochemistry | Year: 2010

The annual and seasonal variations in the temperature sensitivity of soil respiration (Rs) were assessed through continuous measurements during the 2004-2006 growing seasons using chamber-based techniques in two sub-alpine forest ecosystems in the Eastern Qinghai-Tibet Plateau, China. The study sites were 40-year-old spruce plantations (Picea asperata) (FSPF) and Faxon Fir Primary Forest (FPF). Our results showed that Q10, regardless of site origin, exhibited a strong seasonal and annual variation pattern, and decreased with soil temperature increase. Estimated Q10 values ranged between 1.16 and 24.3. The maximum, annual, mean Q10 values remained consistent over 3 years, while the highest Q10 values (7.01 in FSPF and 6.39 in FPF) occurred in 2005 (for all sites). There was no significant difference observed among Q10 values between the two forest types in each year (2004-2006) (p=0.07). Q10 values were fitted well with data of soil temperature using linear regression models, while the correlation between Q10 and soil moisture was not significant (p>0.1). This study suggested that soil temperature was the dominant factor influencing Q10 values, while soil moisture was a potential contributor to the annual and seasonal variations of Q10 in a sub-alpine forest. Due to the complexity of correlation between Rs and soil moisture, Q10 values derived from annual and seasonal patterns of RS should be used with caution when predicting future soil CO2 emissions under conditions of global warming. © 2010.


Tang R.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | Tang R.,National Central University | Li Z.-L.,Chinese Academy of Agricultural Sciences | Li Z.-L.,French National Center for Scientific Research | And 4 more authors.
Agricultural and Forest Meteorology | Year: 2013

The Surface Energy Balance Algorithm for Land (SEBAL) has been successfully applied to remote sensing data to estimate surface evapotranspiration (ET) at different spatial and temporal resolutions in more than 30 countries. However, the selection of dry and wet pixels over the area of interest (AOI) makes the SEBAL-estimated ET subject to the sizes of the AOI and the satellite pixels. This paper investigates the effect of the sizes of the AOI and satellite pixels on SEBAL-derived surface energy components by proposing generalized analytical equations. These equations demonstrate how the variations in the intermediate variables, the AOI, and the pixel size affect the resulting surface energy components and under which circumstances the sensible heat flux will be misestimated, without needing to run the SEBAL model. These analytical equations were verified through application to 23 clear-sky MODIS overpasses that cover different soil water contents and crop growth stages from January 2010 to late October 2011. The spatial effects of increasing the size of the AOI for SEBAL can be summarized as follows: (1) if the locations of dry and wet pixels do not vary, the pixel-by-pixel sensible heat flux (HLA) calculated using the larger AOI is equal to that of the smaller AOI (HSA, with HLA/HSA=1), (2) if only the surface temperatures of wet pixels do not vary, the relative variation in H is equal to the relative variation of the slope (a) of the linear equation between the near-surface air temperature difference and the surface temperature (HLA/HSA=1+δHSA/HSA=1+δa/a), and (3) under other circumstances, HLA/HSA decreases with surface temperatures at a slowing pace from ∼∞ at the temperature of the wet pixel (Ts,wet) to a certain value at the temperature of the dry pixel (Ts,dry) (both temperatures are for the small AOI). Analogously, a general analytical equation-a function of the coefficients of the linear equation between the near-surface air temperature difference and surface temperature at the high-resolution, the effective temperature, and the effective momentum roughness length-could be used to quantify the spatial-scale effect of the satellite pixel size. The findings from this study may help determine suitable sizes of the AOIs and the satellite pixels and aid in quantifying uncertainties in the SEBAL-derived surface energy components. © 2013 Elsevier B.V.


Ju H.,Chinese Academy of Agricultural Sciences | Ju H.,Key Laboratory for Agricultural Environment | van der Velde M.,International Institute For Applied Systems Analysis | Lin E.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Climatic Change | Year: 2013

Climate change can bring positive and negative effects on Chinese agriculture, but negative impacts tend to dominate. The annual mean surface temperature has risen about 0.5-0.8 °C. The precipitation trends have not been identified during the past 100 years in China, although the frequency and intensity of extreme weather/climate events have increased, especially of drought. Water scarcity, more frequent and serious outbreaks of insects and diseases, and soil degradation caused by climate change have impacted agro-environmental conditions. However, temperature rise prolonged the crop growth seasons and cold damages have reduced in Northeast China. The projection of climate change indicates that the surface temperature will continue to increase with about 3.9 to 6.0 °C and precipitation is expected to increase by 9 to 11 % at the end of 21st century in China. Climate warming will provide more heat and as a consequence, the boundary of the triple-cropping system (TCS) will extend northwards by as much as 200 to 300 km, from the Yangtze River Valley to the Yellow River Basin, and the current double-cropping system (DCS) will move to the central part of China, into the current single cropping system (SCS) area which will decrease in SCS surface area of 23.1 % by 2050. Climate warming will also affect the optimum location for the cultivation of China's main crop varieties. If no measures are taken to adapt to climate changes, compared with the potential yield in 1961-1990, yields of irrigated wheat, corn and rice are projected to decrease by 2.2-6.7 %, 0.4 %-11.9 % and 4.3-12.4 % respectively in the 2050s. Climate warming will enhance potential evaporation and reduce the availability of soil moisture, thus causing a greater need for agricultural irrigation, intensifying the conflict between water supply and demand, especially in arid and semi-arid areas of China. With adequate irrigation, the extent of the reduction in yield of China's corn and wheat can be improved by 5 % to 15 %, and rice by 5 % or so than the potential yield in 1961-1990. Adaptive measures can reduce the agricultural loss under climate change. If effective measures are taken in a timely way, then climate change in the next 30-50 years will not have a significant influence on China's food security. © 2013 Springer Science+Business Media Dordrecht.


Du H.,Sichuan Agricultural University | Du H.,Chinese Academy of Agricultural Sciences | Yang S.-S.,Sichuan Agricultural University | Liang Z.,Norwegian University of Life Sciences | And 4 more authors.
BMC Plant Biology | Year: 2012

Background: The MYB superfamily constitutes one of the most abundant groups of transcription factors described in plants. Nevertheless, their functions appear to be highly diverse and remain rather unclear. To date, no genome-wide characterization of this gene family has been conducted in a legume species. Here we report the first genome-wide analysis of the whole MYB superfamily in a legume species, soybean (Glycine max), including the gene structures, phylogeny, chromosome locations, conserved motifs, and expression patterns, as well as a comparative genomic analysis with Arabidopsis.Results: A total of 244 R2R3-MYB genes were identified and further classified into 48 subfamilies based on a phylogenetic comparative analysis with their putative orthologs, showed both gene loss and duplication events. The phylogenetic analysis showed that most characterized MYB genes with similar functions are clustered in the same subfamily, together with the identification of orthologs by synteny analysis, functional conservation among subgroups of MYB genes was strongly indicated. The phylogenetic relationships of each subgroup of MYB genes were well supported by the highly conserved intron/exon structures and motifs outside the MYB domain. Synonymous nucleotide substitution (d N/d S) analysis showed that the soybean MYB DNA-binding domain is under strong negative selection. The chromosome distribution pattern strongly indicated that genome-wide segmental and tandem duplication contribute to the expansion of soybean MYB genes. In addition, we found that ~ 4% of soybean R2R3-MYB genes had undergone alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Comparative expression profile analysis of R2R3-MYB genes in soybean and Arabidopsis revealed that MYB genes play conserved and various roles in plants, which is indicative of a divergence in function.Conclusions: In this study we identified the largest MYB gene family in plants known to date. Our findings indicate that members of this large gene family may be involved in different plant biological processes, some of which may be potentially involved in legume-specific nodulation. Our comparative genomics analysis provides a solid foundation for future functional dissection of this family gene. © 2012 Du et al.; licensee BioMed Central Ltd.


Chen C.,Chinese Academy of Agricultural Sciences | Qian Y.,Chinese Academy of Agricultural Sciences | Tao C.,Chinese Institute for the Control of Agrochemicals | Li Y.,Chinese Academy of Agricultural Sciences
Food Control | Year: 2011

In the present study an effort has been made to evaluate the residues of selected insecticides (organophosphorous and pyrethroid) and fungicides (triazoles and chloronitriles) in fruits and vegetables collected from Xiamen, China, during the October 2006 to March 2009 monitoring campaign. Gas chromatography with electron capture detector (GC-ECD) was used to determine the concentrations of 22 pesticide residues among those recommended for pest treatment. Of 1135 samples (37.7%) that contained pesticide residues, pakchoi cabbage, legumes, and leaf mustard were the commodities in which pesticide residues were most frequently detected, with 17.2%, 18.9% and 17.2% of the samples exceeding the maximum residue limits (MRLs), respectively. Concerning the most frequently detected pesticide residues, cypermethrin was found in 18.7% of the samples analyzed. Data obtained were then used for estimating the potential health risks associated with the exposures to these pesticides. The estimated daily intakes (EDIs) range from 0.1% of the ADI for cyfluthrin to 2.61% of the ADI for omethoate and 0.1% of the ADI for omethoate. The most critical commodity is legumes, contributing 2.61% to the hazard index (HI). The results show that despite a high occurrence of pesticide residues in fruits and vegetables from this region, it could not be considered a serious public health problem. Nevertheless, an investigation into continuous monitoring and tighter regulation of pesticide residues in fruits and vegetables is recommended. © 2011 Elsevier Ltd.


Mao X.,Chinese Academy of Agricultural Sciences | Zhang H.,Chinese Academy of Agricultural Sciences | Zhang H.,Northwest University, China | Tian S.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Journal of Experimental Botany | Year: 2010

Osmotic stresses such as drought, salinity, and cold are major environmental factors that limit agricultural productivity worldwide. Protein phosphorylation/dephosphorylation are major signalling events induced by osmotic stress in higher plants. Sucrose non-fermenting 1-related protein kinase2 family members play essential roles in response to hyperosmotic stresses in Arabidopsis, rice, and maize. In this study, the function of TaSnRK2.4 in drought, salt, and freezing stresses in Arabidopsis was characterized. A translational fusion protein of TaSnRK2.4 with green fluorescent protein showed subcellular localization in the cell membrane, cytoplasm, and nucleus. To examine the role of TaSnRK2.4 under various environmental stresses, transgenic Arabidopsis plants overexpressing wheat TaSnRK2.4 under control of the cauliflower mosaic virus 35S promoter were generated. Overexpression of TaSnRK2.4 resulted in delayed seedling establishment, longer primary roots, and higher yield under normal growing conditions. Transgenic Arabidopsis overexpressing TaSnRK2.4 had enhanced tolerance to drought, salt, and freezing stresses, which were simultaneously supported by physiological results, including decreased rate of water loss, enhanced higher relative water content, strengthened cell membrane stability, improved photosynthesis potential, and significantly increased osmotic potential. The results show that TaSnRK2.4 is involved in the regulation of enhanced osmotic potential, growth, and development under both normal and stress conditions, and imply that TaSnRK2.4 is a multifunctional regulatory factor in Arabidopsis. Since the overexpression of TaSnRK2.4 can significantly strengthen tolerance to drought, salt, and freezing stresses and does not retard the growth of transgenic Arabidopsis plants under well-watered conditions, TaSnRK2.4 could be utilized in transgenic breeding to improve abiotic stresses in crops.


Li G.,Chinese Academy of Agricultural Sciences | Wang K.Y.,Northeastern State University | Li D.,Peking University | Wang N.,Chinese Academy of Agricultural Sciences | Liu D.,Chinese Academy of Agricultural Sciences
PLoS ONE | Year: 2012

A lumbrokinase gene encoding a blood-clot dissolving protein was cloned from earthworm (Eisenia fetida) by RT-PCR amplification. The gene designated as CST1 (GenBank No. AY840996) was sequence analyzed. The cDNA consists of 888 bp with an open reading frame of 729 bp, which encodes 242 amino acid residues. Multiple sequence alignments revealed that CST1 shares similarities and conserved amino acids with other reported lumbrokinases. The amino acid sequence of CST1 exhibits structural features similar to those found in other serine proteases, including human tissue-type (tPA), urokinase (uPA), and vampire bat (DSPAα1) plasminogen activators. CST1 has a conserved catalytic triad, found in the active sites of protease enzymes, which are important residues involved in polypeptide catalysis. CST1 was expressed as inclusion bodies in Escherichia coli BL21(DE3). The molecular mass of recombinant CST1 (rCST) was 25 kDa as estimated by SDS-PAGE, and further confirmed by Western Blot analysis. His-tagged rCST1 was purified and renatured using nickel-chelating resin with a recovery rate of 50% and a purity of 95%. The purified, renatured rCST1 showed fibrinolytic activity evaluated by both a fibrin plate and a blood clot lysis assay. rCST1 degraded fibrin on the fibrin plate. A significant percentage (65.7%) of blood clot lysis was observed when blood clot was treated with 80 mg/mL of rCST1 in vitro. The antithrombotic activity of rCST1 was 912 units/mg calculated by comparison with the activity of a lumbrokinase standard. These findings indicate that rCST1 has potential as a potent blood-clot treatment. Therefore, the expression and purification of a single lumbrokinase represents an important improvement in the use of lumbrokinases. © 2012 Li et al.


Qian J.,Shanghai Institute of Digestive Disease | Kong X.,Shanghai Institute of Digestive Disease | Deng N.,National University of Singapore | Tan P.,National University of Singapore | And 8 more authors.
Gut | Year: 2015

Objective: Octamer transcription factor 1 (OCT1) was found to be expressed in intestinal metaplasia and gastric cancer (GC), but the exact roles of OCT1 in GC remain unclear. The objective of this study was to determine the functional and prognostic implications of OCT1 in GC.Design: Expression of OCT1 was examined in paired normal and cancerous gastric tissues and the prognostic significance of OCT1 was analysed by univariate and multivariate survival analyses. The functions of OCT1 on synbindin expression and extracellular signal-regulated kinase (ERK) phosphorylation were studied in vitro and in xenograft mouse models.Results: The OCT1 gene is recurrently amplified and upregulated in GC. OCT1 overexpression and amplification are associated with poor survival in patients with GC and the prognostic significance was confirmed by independent patient cohorts. Combining OCT1 overexpression with American Joint Committee on Cancer staging improved the prediction of survival in patients with GC. High expression of OCT1 associates with activation of the ERK mitogen-activated protein kinase signalling pathway in GC tissues. OCT1 functions by transactivating synbindin, which binds to ERK DEF domain and facilitates ERK phosphorylation by MEK. OCT1-synbindin signalling results in the activation of ERK substrates ELK1 and RSK, leading to increased cell proliferation and invasion. Immunofluorescent study of human GC tissue samples revealed strong association between OCT1 protein level and synbindin expression/ERK phosphorylation. Upregulation of OCT1 in mouse xenograft models induced synbindin expression and ERK activation, leading to accelerated tumour growth in vivo.Conclusions: OCT1 is a driver of synbindin-mediated ERK signalling and a promising marker for the prognosis and molecular subtyping of GC.


Ao D.,Chinese Academy of Agricultural Sciences | Ao D.,Sichuan Agricultural University | Sun S.-Q.,Chinese Academy of Agricultural Sciences | Guo H.-C.,Chinese Academy of Agricultural Sciences
Veterinary Research | Year: 2014

Viroporins are a group of transmembrane proteins with low molecular weight that are encoded by many animal viruses. Generally, viroporins are composed of 50-120 amino acid residues and possess a minimum of one hydrophobic region that interacts with the lipid bilayer and leads to dispersion. Viroporins are involved in destroying the morphology of host cells and disturbing their biological functions to complete the life cycle of the virus. The 2B proteins encoded by enteroviruses, which belong to the family Picornaviridae, can form transmembrane pores by oligomerization, increase the permeability of plasma membranes, disturb the homeostasis of calcium in cells, induce apoptosis, and cause autophagy; these abilities are shared among viroporins. The present paper introduces the structure and biological characteristics of various 2B proteins encoded by enteroviruses of the family Picornaviridae and may provide a novel idea for developing antiviral drugs. © 2014 Ao et al.; licensee BioMed Central Ltd.


Zhang W.J.,Chinese Academy of Agricultural Sciences | Wang X.J.,Xinjiang Institute of Ecology and Geography | Wang X.J.,The Interdisciplinary Center | Xu M.G.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Biogeosciences | Year: 2010

Soil carbon sequestration is a complex process influenced by agricultural practices, climate and soil conditions. This paper reports a study of long-term fertilization impacts on soil organic carbon (SOC) dynamic from six long-term experiments. The experiment sites are located from warm-temperate zone with a double-cropping system of corn (Zea mays L.) - wheat (Triticum Aestivium L.) rotation, to mild-temperate zones with mono-cropping systems of continuous corn, or a three-year rotation of corn-wheat-wheat. Mineral fertilizer applications result in an increasing trend in SOC except in the arid and semi-arid areas with the mono-cropping systems. Additional manure application is important to maintain SOC level in the arid and semi-arid areas. Carbon conversion rate is significant lower in the warm-temperate zone with double cropping system (6.8%-7.7%) than that in the mild-temperate areas with mono-cropping systems (15.8%-31.0%). The conversion rate is significantly correlated with annual precipitation and active accumulative temperature, i.e., higher conversion rate under lower precipitation and/or temperature conditions. Moreover, soil high in clay content has higher conversion rate than soils low in clay content. Soil carbon sequestration rate ranges from 0.07 to 1.461 t ha-1 year -1 in the upland of northern China. There is significantly linear correlation between soil carbon sequestration and carbon input at most sites, indicating that these soils are not carbon-saturated thus have potential to migrate more CO2 from atmosphere.


Gu X.-B.,Chinese Academy of Agricultural Sciences | Gu X.-B.,Sichuan Agricultural University | Liu G.-H.,Chinese Academy of Agricultural Sciences | Song H.-Q.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Parasites and Vectors | Year: 2014

Background: Limited available sequence information has greatly impeded population genetics, phylogenetics and systematics studies in the subclass Acari (mites and ticks). Mitochondrial (mt) DNA is well known to provide genetic markers for investigations in these areas, but complete mt genomic data have been lacking for many Acari species. Herein, we present the complete mt genome of the scab mite Psoroptes cuniculi. Methods. P. cuniculi was collected from a naturally infected New Zealand white rabbit from China and identified by morphological criteria. The complete mt genome of P. cuniculi was amplified by PCR and then sequenced. The relationships of this scab mite with selected members of the Acari were assessed by phylogenetic analysis of concatenated amino acid sequence datasets by Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP). Results: This mt genome (14,247 bp) is circular and consists of 37 genes, including 13 genes for proteins, 22 genes for tRNA, 2 genes for rRNA. The gene arrangement in mt genome of P. cuniculi is the same as those of Dermatophagoides farinae (Pyroglyphidae) and Aleuroglyphus ovatus (Acaridae), but distinct from those of Steganacarus magnus (Steganacaridae) and Panonychus citri (Tetranychidae). Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes, with three different computational algorithms (BI, ML and MP), showed the division of subclass Acari into two superorders, supported the monophylies of the both superorders Parasitiformes and Acariformes; and the three orders Ixodida and Mesostigmata and Astigmata, but rejected the monophyly of the order Prostigmata. Conclusions: The mt genome of P. cuniculi represents the first mt genome of any member of the family Psoroptidae. Analysis of mt genome sequences in the present study has provided new insights into the phylogenetic relationships among several major lineages of Acari species. © 2014 Gu et al.; licensee BioMed Central Ltd.


Cao G.,Chinese Academy of Agricultural Sciences | Feng H.,Henan Academy of Agricultural science | Guo F.,Chinese Academy of Agricultural Sciences | Wu K.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Scientific Reports | Year: 2014

Transgenic Bacillus thuringiensis (Bt) crops play an increasing role in pest control, and resistance management is a major issue in large-scale cultivation of Bt crops. The fitness cost of resistance in targeted pests is considered to be one of the main factors delaying resistance when using the refuge strategy. By comparing 10 resistant Helicoverpa armigera (Hubner) strains, showing various resistance levels to Bt toxin (Cry1Ac), to a susceptible strain, we showed an increasing fitness cost corresponding with increasing levels of resistance. The relationship between overall fitness cost C and the resistance ratio R r could be described by C = 24.47/(1 + exp([1.57 - Log 10 R r ]/0.2)). This model predicted that the maximum overall fitness cost would be ∼24% (±5.22) in the strains with the highest resistance level. The overall fitness cost was closely linked to egg hatching rate, fecundity, emergence rate, larval survival rate, and developmental duration of adults. Among fitness components measured, fecundity was the most sensitive trait linked to the resistance selection. To integrate the results into simulation models would be valuable in evaluating how variation in fitness cost may influence the development of resistance in pest populations, thus helping to develop enhanced refuge strategies.


Li H.,Chinese Academy of Agricultural Sciences | Li H.,Beijing Normal University | Hearne S.,International Institute Of Tropical Agriculture | Banziger M.,International Maize and Wheat Improvement Center | And 2 more authors.
Heredity | Year: 2010

Quantitative trait gene or locus (QTL) mapping is routinely used in genetic analysis of complex traits. Especially in practical breeding programs, questions remain such as how large a population and what level of marker density are needed to detect QTLs that are useful to breeders, and how likely it is that the target QTL will be detected with the data set in hand. Some answers can be found in studies on conventional interval mapping (IM). However, it is not clear whether the conclusions obtained from IM are the same as those obtained using other methods. Inclusive composite interval mapping (ICIM) is a useful step forward that highlights the importance of model selection and interval testing in QTL linkage mapping. In this study, we investigate the statistical properties of ICIM compared with IM through simulation. Results indicate that IM is less responsive to marker density and population size (PS). The increase in marker density helps ICIM identify independent QTLs explaining >5% of phenotypic variance. When PS is >200, ICIM achieves unbiased estimations of QTL position and effect. For smaller PS, there is a tendency for the QTL to be located toward the center of the chromosome, with its effect overestimated. The use of dense markers makes linked QTL isolated by empty marker intervals and thus improves mapping efficiency. However, only large-sized populations can take advantage of densely distributed markers. These findings are different from those previously found in IM, indicating great improvements with ICIM. © 2010 Macmillan Publishers Limited All rights reserved.


Wang T.,French National Institute for Agricultural Research | Wang T.,Chinese Academy of Agricultural Sciences | Picard J.C.,French National Institute for Agricultural Research | Tian X.,French National Institute for Agricultural Research | Darmency H.,French National Institute for Agricultural Research
Heredity | Year: 2010

It is often alleged that mutations conferring herbicide resistance have a negative impact on plant fitness. A mutant ACCase1781 allele endowing resistance to the sethoxydim herbicide was introgressed from a resistant green foxtail (Setaria viridis (L.) Beauv) population into foxtail millet (S. italica (L.) Beauv.). (1) Better and earlier growth of resistant plants was observed in a greenhouse cabinet. (2) Resistant plants of the advanced BC7 backcross generation showed more vigorous juvenile growth in the field, earlier flowering, more tillers and higher numbers of grains than susceptible plants did, especially when both genotypes were grown in mixture, but their seeds were lighter than susceptible seeds. (3) Field populations originating from segregating hybrids had the expected allele frequencies under normal growth conditions, but showed a genotype shift toward an excess of homozygous resistant plants within 3 years in stressful conditions. Lower seed size, lower germination rate and perhaps unexplored differences in seed longevity and predation could explain how the resistant plants have the same field fitness over the whole life cycle as the susceptible ones although they produce more seeds. More rapid growth kinetics probably accounted for higher fitness of the resistant plants in adverse conditions. The likelihood of a linkage with a beneficial gene is discussed versus the hypothesis of a pleiotropic effect of the ACCase resistance allele. It is suggested that autogamous species like Setaria could not develop a resistant population without the help of a linkage with a gene producing a higher fitness. © 2010 Macmillan Publishers Limited All rights reserved.


Jiang H.-H.,Chinese Academy of Agricultural Sciences | Huang S.-Y.,Chinese Academy of Agricultural Sciences | Zhou D.-H.,Chinese Academy of Agricultural Sciences | Zhang X.-X.,Chinese Academy of Agricultural Sciences | And 5 more authors.
Parasites and Vectors | Year: 2013

Abstract. Background: Toxoplasma gondii is a widely prevalent protozoan parasite that causes serious toxoplasmosis in humans and animals. The present study aimed to determine the genetic diversity of T. gondii isolates from pigs in Jiangxi, Sichuan, Guangdong Provinces and Chongqing Municipality in China using multilocous polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. Methods. A total of 38 DNA samples were extracted from hilar lymph nodes of pigs with suspected toxoplasmosis, and were detected for the presence of T. gondii by semi-nested PCR of B1 gene. The positive DNA samples were typed at 11 genetic markers, including 10 nuclear loci, namely, SAG1, 5′-SAG2 and 3′-SAG2, alternative SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and an apicoplast locus Apico. Results: Twenty-five of the 38 DNA samples were T. gondii B1 gene positive. Complete genotyping data for all loci could be obtained for 17 of the 25 samples. Two genotypes were revealed (ToxoDB PCR-RFLP genotypes #9 and #3). Sixteen samples belong to genotype #9 which is the major lineage in mainland China and one sample belongs to genotype #3 which is Type II variant. Conclusions: To our knowledge, this is the first report of genetic typing of T. gondii isolates from pigs in Jiangxi, Sichuan Province and Chongqing Municipality, and the first report of ToxoDB #3 T. gondii from pigs in China. These results have implications for the prevention and control of foodborne toxoplasmosis in humans. © 2013 Jiang et al.; licensee BioMed Central Ltd.


Du H.,Sichuan Agricultural University | Du H.,Chinese Academy of Agricultural Sciences | Wang Y.-B.,Sichuan Agricultural University | Xie Y.,Sichuan Agricultural University | And 5 more authors.
DNA Research | Year: 2013

MYB proteins constitute one of the largest transcription factor families in plants. Recent evidence revealed that MYB-related genes play crucial roles in plants. However, compared with the R2R3-MYB type, little is known about the complex evolutionary history of MYB-related proteins in plants. Here, we present a genome-wide analysis of MYB-related proteins from 16 species of owering plants, moss, Selaginella, and algae. We identified many MYB-related proteins in angiosperms, but few in algae. Phylogenetic analysis classified MYB-related proteins into five distinct subgroups, a result supported by highly conserved intron patterns, consensus motifs, and protein domain architecture. Phylogenetic and functional analyses revealed that the Circadian Clock Associated 1-like/R-R and Telomeric DNA-binding protein-like subgroups are >1 billion yrs old, whereas the I-box-binding factor-like and CAPRICE-like subgroups appear to be newly derived in angiosperms. We further demonstrated that the MYB-like domain has evolved under strong purifying selection, indicating the conservation of MYB-related proteins. Expression analysis revealed that the MYB-related gene family has a wide expression profile in maize and soybean development and plays important roles in development and stress responses. We hypothesize that MYB-related proteins initially diversified through three major expansions and domain shuffling, but remained relatively conserved throughout the subsequent plant evolution. © The Author 2013. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.


Zhou Y.,University of Chinese Academy of Sciences | Wang P.,Chinese Academy of Agricultural Sciences | Su X.,Chinese Academy of Agricultural Sciences | Zhao H.,University of Chinese Academy of Sciences | And 2 more authors.
Talanta | Year: 2013

A highly selective and sensitive method is developed for colorimetric detection of ractopamine and salbutamol using gold nanoparticles (AuNPs) functionalized with melamine (MA), respectively. The presence of these β-agonists induces the aggregation of gold nanoparticles through hydrogen-bonding interaction that was accompanied by a distinct change in color and optical properties, which could be monitored by a UV-vis spectrophotometer or even naked eyes. This process caused a significant decrease in the absorbance ratio (A670 nm/A520 nm) of melamine-gold nanoparticles (MA-AuNPs), and the color changed from wine red to blue. The systems exhibited a wide liner range, from 1×10-10 M to 5×10-7 mol/L with a correlation coefficient of 0.995 for ractopamine, and 1×10-10 M to 1×10-5 mol/L with a correlation coefficient of 0.996 for salbutamol, with measuring the absorbance ratio (A670 nm/A520 nm). The detection limit of these β-agonists is as low as 1×10 -11 mol/L. Particularly, the developed method has been applied to the analysis of real swine feed samples and has achieved satisfactory results. © 2013 Elsevier B.V.


About 2/3 of the rice consumed by European citizens is produced in EU, and its productivity is affected by abiotic and biotic stresses. Of particular concern, global temperature has increased over the last century, especially during the last 50 years (0.13 C / decade). One consequence has been a clear tendency toward salinization, which affects rice as one of the most salt sensitive crop in the region. Associated with changes in temperature and salinity, the biotic stress of the Apple snail species from genus Pomacea now threatens to destroy rice paddy fields eating the sown seed and the rice plantlets, representing one of the worst introduced gastropod crop pest of the recent time. It is calculated that nowadays this pest causes damages in rice fields worldwide that result into losses of tens of billions of Euros a year. Recently, apple snails have been detected in the Ebro river delta (Spain), and now it represents an important thread to Europes wetlands biodiversity and rice production. To date, the measures adopted to combat apple snail have failed, but in the autumn of 2013, 2500 ha of infested fields were flooded with sea water. This treatment proved 100% effective in destroying apple snail infestations, nevertheless residual salt concentrations affected negatively rice productivity. Thus, the general objective of the NEURICE project is to identify and introduce genetic variation in European rice varieties for obtaining commercial varieties tolerant to salinity in order to (i) mitigate the imminent effects of salinization and deterioration of water quality in the Mediterranean basins due to climate change, and (ii) to avoid the decline in production observed after seawater treatments performed in rice paddies that successfully controlled the apple snail pest. The availability of commercial salt tolerant rice lines will prevent the climate change derived abiotic stress while avoiding the dispersion of this devastating pest (biotic stress) all over Europe.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: WASTE-7-2015 | Award Amount: 7.82M | Year: 2016

NoAW : No Agro-Waste. Innovative approaches to turn agricultural waste into ecological and economic assets. Driven by a near zero-waste society requirement, the goal of NoAW project is to generate innovative efficient approaches to convert growing agricultural waste issues into eco-efficient bio-based products opportunities with direct benefits for both environment, economy and EU consumer. To achieve this goal, the NoAW concept relies on developing holistic life cycle thinking able to support environmentally responsible R&D innovations on agro-waste conversion at different TRLs, in the light of regional and seasonal specificities, not forgetting risks emerging from circular management of agro-wastes (e.g. contaminants accumulation). By involving all agriculture chain stakeholders in a territorial perspective, the project will: (1) develop innovative eco-design and hybrid assessment tools of circular agro-waste management strategies and address related gap of knowledge and data via extensive exchange through the Knowledge exchange Stakeholders Platform, (2) develop breakthrough knowledge on agro-waste molecular complexity and heterogeneity in order to upgrade the most widespread mature conversion technology (anaerobic digestion) and to synergistically eco-design robust cascading processes to fully convert agro-waste into a set of high added value bio-energy, bio-fertilizers and bio-chemicals and building blocks, able to substitute a significant range of non-renewable equivalents, with favourable air, water and soil impacts and (3) get insights of the complexity of potentially new, cross-sectors, business clusters in order to fast track NoAW strategies toward the field and develop new business concepts and stakeholders platform for cross-chain valorisation of agro-waste on a territorial and seasonal basis.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2010.4-04 | Award Amount: 1.15M | Year: 2011

The main objective of BIO CIRCLE 2 is to foster the knowledge base about FP7 FAFB & the networking capacities of Third Country researchers in order to reinforce their participation in FP7 projects. 3 project goals are distinguished: 1.Disseminate information effectively to Third Country researchers; 2.Organise information days and training for Third Country researchers; 3.Provide Third Country researchers with efficient networking opportunities. 5 European plus 16 Third Country partners (International Cooperation Partner Countries ICPC and Industrialised Countries) will all be involved in the activities. Apart from Kazakhstan and Thailand all involved countries (and the African continent represented by FARA) have signed a bilateral S&T agreement with the EU. The expected impacts are supported by various activities: Enhanced awareness of the Third Country researchers on the FP7 FAFB: WP2 will develop the regional strategies for the Third Country partners. Increased Third Country researchers participation in EU projects: WP3 will organise at least 2 trainings for Third Country researchers at national and regional level, 3 trainings of Third Country BIO NCPs and the organisation of 1 Regional Event per World Region. Strengthened collaborations with Third Countries signatories of bilateral S&T agreements with the EU: WP4 will implement networking activities for Third Country researchers, including brokerage events and working visits of Third Country researchers to EU research institutes and vice versa. Finally WP5 on dissemination activities will increase the awareness of European researchers about the international cooperation in FP7 FAFB. The impact of the activities will be further maximised by: 1.involving other countries that are not partners through a regional approach; 2.linking the BIO CIRCLE 2 activities to the activities of related INCO projects; 3.involving industrialised countries that are global S&T leaders in FAFB related research.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: SFS-13-2015 | Award Amount: 6.43M | Year: 2016

MycoKey aims to generate innovative and integrated solutions that will support stakeholders in effective and sustainable mycotoxin management along food and feed chains. The project will contribute to reduce mycotoxin contamination mainly in Europe and China, where frequent and severe mycotoxin contaminations occur in crops, and where international trade of commodities and contaminated batches are increasing. MycoKey will address the major affected crops maize, wheat and barley, their associated toxigenic fungi and related mycotoxins (aflatoxins, deoxynivalenol, zearalenone, ochratoxin A, fumonisins). The project will integrate key information and practical solutions for mycotoxin management into a smart ICT tool (MycoKey App), providing answers to stakeholders, who require rapid, customized forecasting, descriptive information on contamination risk/levels, decision support and practical economically-sound suggestions for intervention. Tools and methodologies will be strategically targeted for cost-effective application in the field and during storage, processing and transportation. Alternative and safe ways to use contaminated batches will be also delivered. The focus of Mycokey will be: i) innovating communications of mycotoxin management by applying ICT, providing input for legislation, enhancing knowledge and networks; ii) selecting and improving a range of tools for mycotoxin monitoring; iii) assessing the use of reliable solutions, sustainable compounds/green technologies in prevention, intervention and remediation. The multi-disciplinary consortium, composed by scientific, industrial and association partners (32), includes 11 Chinese institutions and will conduct the 4 years programme in a framework of international networks.


Han P.,Huazhong Agricultural University | Niu C.-Y.,Huazhong Agricultural University | Lei C.-L.,Huazhong Agricultural University | Cui J.-J.,Chinese Academy of Agricultural Sciences | Desneux N.,French National Institute for Agricultural Research
Ecotoxicology | Year: 2010

Transgenic Cry1Ac+CpTI cotton (CCRI41) is a promising cotton cultivar throughout China but side effects and especially sublethal effects of this transgenic cultivar on beneficial insects remain poorly studied. More specifically potential sublethal effects on behavioural traits of the honey bee Apis mellifera L. have not been formally assessed despite the importance of honey bees for pollination. The goal of our study was to assess potential effects of CCRI41 cotton pollen on visual and olfactory learning by honey bees. After a 7-day oral chronic exposure to honey mixed with either CCRI41 pollen, imidaclopridtreated conventional pollen (used as positive sublethal control) or conventional pollen (control), learning performance was evaluated by the classical proboscis extension reflex (PER) procedure as well as a T-tube maze test. The latter assay was designed as a new device to assess potential side effects of pesticides on visual associative learning of honey bees. These two procedures were complementary because the former focused on olfactory learning while the latter was involved in visual learning based on visual orientation ability.Oral exposure to CCRI41 pollen did not affect learning capacities of honey bees in both the T-tube maze and PER tests. However, exposure to imidacloprid resulted in reduced visual learning capacities in T-tube maze evaluation and decreased olfactory learning performances measured with PER. The implications of these results are discussed in terms of risks of transgenic CCRI41 cotton crops for honey bees. © The Author(s) 2010.


Peng Z.,Chinese Academy of Agricultural Sciences | Peng Z.,Sichuan Agricultural University | He S.,Chinese Academy of Agricultural Sciences | Gong W.,Chinese Academy of Agricultural Sciences | And 5 more authors.
BMC Genomics | Year: 2014

Background: Cotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. Results: We investigated two distinct salt stress phases-dehydration (4 h) and ionic stress (osmotic restoration; 24 h)-that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs.Conclusions: Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance. © 2014 Peng et al.; licensee BioMed Central Ltd.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP-SICA | Phase: KBBE-2009-1-3-01 | Award Amount: 4.09M | Year: 2010

Porcine reproductive and respiratory syndrome virus (PRRSV) is the major cause of reproductive and respiratory problems in pigs worldwide. Controlling this disease is a top priority in pig producing countries. Due to mutations at a high frequency, new variants of the virus appear that are no longer effectively controlled by the commercial vaccines. In addition, highly virulent variants emerge, leading to high losses. With regard to animal welfare and agricultural economics, there is an urgent need to control PRRS. Furthermore, the abusive use of antibiotics to control PRRSV-associated respiratory problems may lead to resistance that may endanger public health. PoRRSCon is an initiative of 14 partners originating from Europe and Asia with strong expertises in virology and immunology. They are doing frontline research on PRRSV and/or vaccine development. Two of these partners are leading European pharmaceutical companies that will guide the consortium in the direction of exploitable results. By joining their strengths they have an ideal position to be successful in one of the most difficult challenges in pig health, controlling PRRS. To reach this final goal, the following objectives are forwarded:(i) characterize genetically and antigenically current PRRSV isolates in Europe and Asia, (ii) have a better understanding of the complex pathogenesis of PRRSV infections, immune response against PRRSV and immune modulation by PRRSV, (iii) define the genetic base of PRRSV virulence, (iv) identify PRRSV proteins and domains on these viral proteins that are involved in the induction of the immunity against PRRSV and in the immune modulation of PRRSV, (v) develop new generation, efficacious and safe marker vaccines that can be adapted to temporary changes and geographical differences and (vi) develop DIVA assays that allow to differentiate infected from vaccinated animals. At the end, it will be possible to set up a control strategy by combining marker vaccines with DIVA assays


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: ENV.2009.1.1.6.1 | Award Amount: 4.16M | Year: 2010

CLIMSAVE will develop and apply an integrated methodology for stakeholder-led, climate change impact and vulnerability assessment that explicitly evaluates regional and continental scale adaptation options, and cross-sectoral interactions between the key sectors driving landscape change in Europe (agriculture, forests, biodiversity, coasts/floodplains, water resources, urban development and transport). A range of sectoral meta-models will be linked within a common assessment platform that is user-friendly, interactive and web-based to allow the rapid reproduction of climate change impacts by stakeholders themselves. The meta-models will be derived from detailed state-of-the-art models which represent the latest results on impacts of, and vulnerability to, climate change and which are appropriate for multi-scale spatially explicit impact studies. Indicator metrics, which translate the outputs from the integrated models into ecosystem services outcomes, will create a standardised approach across sectors ensuring comparability in quantifying impacts and vulnerability. The integrated assessment platform will use these metrics to identify hotspots of climate change vulnerability and provide the ability to assess adaptation strategies for reducing these vulnerabilities, in terms of their cost-effectiveness and cross-sectoral benefits and conflicts. Methods for reducing uncertainties and increasing the transparency of model and scenario assumptions will be implemented to inform the development of robust policy responses. A series of professionally facilitated workshops will identify stakeholder needs and test an innovative methodology for participatory scenario development specifically geared towards interactive climate change impact and adaptation assessment. Two sets of three workshops at two levels (European and regional) will ensure that the CLIMSAVE methodologies work at different scales and provide for continuity of engagement and mutual learning.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE-2008-1-2-02 | Award Amount: 1.15M | Year: 2009

BrightAnimal will contribute to economically, socially and environmentally sustainable development by outlining a practical and acceptable methodology for precision livestock farming. To achieve this goal, BrightAnimal has the following mission: To produce a framework for European and non-European small and medium enterprises on effective and acceptable precision livestock farming and to create an international, interdisciplinary network for further development and dissemination. The main activity and achievement of BrightAnimal will be the elaboration of a book on effective Precision Livestock Farming in Europe and world-wide with special consideration of small and medium enterprises. The book aims at describing current and near-future techniques in PLF, especially taking into account both the practicality for SMEs as well as their acceptability (in the broader sense). The book will also try to set the scene for future developments. As the second component of the framework, BrightAnimal will produce best precision livestock farming practices (BPLFP) in a series of problematic areas such as aquaculture, beef, sheep and chicken. These best practice guides will be released to the public domain in the form of booklets. A third deliverable of the project will be a practical showcase activity showing the Good Practices in action in the European Centre of Excellence of Automatic Identification and Data Capture in the UK. BrightAnimal will organise interdisciplinary conferences for opinion exchange and cross-disciplinary discussions. It is of great importance to include opinions from outside Europe. We have been pleased to accept partners from the following ICPC countries: Thailand, Malaysia, South Africa, Brazil and China and from Australia as a third country. Other non-funded partners from third countries will also join the project.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: SFS-01b-2014 | Award Amount: 10.52M | Year: 2015

SAPHIR aims to develop vaccine strategies effective against endemic pathogens responsible for high economic losses in livestock in order to strengthen the profitability of food animal systems, improve animal welfare and reduce xenobiotic usage in farming with a One Health perspective. SAPHIR will bring novel vaccine strategies to the market i) at short term, with several promising vaccines brought to demonstration (RTL6), ii) at long term, with cutting edge strategies brought at proof of concept (RTL3) and iii) in line with socio-economic requirements. SAPHIR has selected two representative pathogens of pigs (Porcine Reproductive and Respiratory Syndrome Virus and Mycoplasma hyopneumoniae), chickens (Eimeria and Clostridium perfringens) and cattle (Bovine Respiratory Syncytial Virus, Mycoplasma bovis) to develop generic vaccine approaches applicable to other pathogens. SAPHIR will issue i) knowledge of immune mechanisms of protection, ii) affordable, safe and multivalent vaccines with DIVA properties, iii) efficient adjuvants targeting dendritic cells, optimal formulations, new mucosal and skin delivery systems, a new generation of DNA vectors and viral replicon platforms for fostering an earlier and longer duration of immunity including the perinatal period, and iv) basal biomarkers of individual immuno-competence for future breeding strategies. The SAPHIR dissemination and training programme includes creation of an integrated health management website, launch of a Global Alliance for Veterinary Vaccines and organization of workshops directed at food animal system stakeholders. This will ensure optimal research translation of SAPHIR outputs to market and field applications. SAPHIR brings together interdisciplinary expertise from fourteen academic institutes including a Chinese partner, five SMEs and two pharmaceutical companies.


Grant
Agency: Cordis | Branch: FP7 | Program: CPCSA | Phase: INFRA-2011-1.2.2. | Award Amount: 4.48M | Year: 2011

agINFRA is an Integrated Infrastructure Initiative (I3) project that will try to introduce the agricultural scientific communities into the vision of open and participatory data-intensive science. In particular, agINFRA aims to design and develop a scientific data infrastructure for agricultural sciences that will facilitate the development of policies and the deployment of services that will promote sharing of data among agricultural scientists and develop trust within and among their communities. agINFRA will try to remove existing obstacles concerning the open access to scientific information and data in agriculture, as well as improve the preparedness of agricultural scientific communities to face, manage and exploit the abundance of relevant data that is (or will be) available and can support agricultural research.\n\nUltimately, agINFRA will demonstrate how a data infrastructure for agricultural scientific communities can be set up to facilitate data generation, provenance, quality assessment, certification, curation, annotation, navigation and management.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2010.1.3-02 | Award Amount: 1.09M | Year: 2011

Animal diseases can cause serious social, economic and environmental damage and in some cases also threaten human health. An increasing number of the major disease problems or threats faced by the livestock industry and zoonoses are of a global nature. The overall aim of the global strategic alliances for the coordination of research on the major infectious diseases of animals is to improve coordination of research activities on the major infectious diseases of livestock and zoonoses so as to hasten the delivery of improved control methods. This will be achieved through the establishment of an international forum of R&D programme owners/managers and international organisations for the purpose of sharing information, improving collaboration on research activities and working towards common research agendas and coordinated research funding on the major animal diseases affecting livestock production and/or human health. It will build on the groundwork established by the SCAR collaborative working group on animal health and welfare research, the EMIDA ERA-NET project and specific INCO-NETs involving partner countries. The scope of the project will include co-ordination of research relevant to emerging and major infectious diseases of livestock, including fish and managed bees, and those infections of livestock that may carry the risk of disease threat to human health. Diseases of wildlife will also be considered where they are identified as reservoirs of infection with emerging and major infectious diseases of humans or production animals. These objectives will be delivered through the following five workpackages: WP1. Project coordination, management, communication and dissemination; WP2. Sharing information on existing research programmes; WP3. Analysis of and responding to global, regional and industry sector priorities; WP4. Networking of ongoing research activities on major issues and WP5. Developing a strategic trans-national animal health research agendas.


News Article | February 22, 2017
Site: www.businesswire.com

DES MOINES, Iowa & DAVIS, Calif.--(BUSINESS WIRE)--Origin (Origin Agritech, LLC, a subsidiary of Origin Agritech Ltd., NASDAQ: SEED), an agricultural biotechnology trait and seed provider, and Arcadia (Arcadia Biosciences, Inc., NASDAQ: RKDA), a California-based company that develops and commercializes agricultural productivity traits and nutritional products, today announced their collaboration to achieve the first-ever export of a key corn biotechnology product developed in China to the United States for completion of global regulatory trials. The successful movement of this corn seed, containing an insect resistance/herbicide tolerance trait discovered and developed in China, to the Arcadia greenhouse represents a key milestone in Origin’s strategic business plan to achieve global regulatory approvals for cultivation and international grain movement. “ This first-of-its-kind export validates Origin’s leading position in China biotech and its close alignment with Chinese ministries leading the transformation of the domestic seed industry. Combining Origin’s robust pipeline of value-added Chinese traits and elite corn germplasm with Arcadia’s research and development infrastructure demonstrates our plan to capture a sizeable piece of China’s estimated billion-dollar corn seed trait market,” said Bill Niebur, Origin chief executive officer. “ As a leader in agtech focused on modernizing the traditional corn seed market, our international team remains focused on accelerating research and development to improve the lives of Chinese farmers.” Arcadia and Origin signed an agreement under which Arcadia will assist Origin in developing information for submission to regulatory authorities in the U.S., China and other countries for the approval of their traits in corn. This project involves production of inbred and hybrid seed lines under quarantine conditions in Arcadia greenhouses. “ Arcadia has the proven expertise to bring traits through the regulatory process successfully and efficiently,” said Raj Ketkar, Arcadia’s president and CEO. “ We have conducted hundreds of studies in the laboratory, greenhouse and field to gain regulatory approvals for various traits in major crops, and we have a strong regulatory team that has developed complete regulatory dossiers in multiple countries. This collaboration with Origin is an example of how our partners can leverage these capabilities to accelerate the commercialization of novel ag biotech traits.” “ Ultimately, this milestone achievement will create more choices and opportunities for farmers,” said Jihong Liang, Origin chief technology officer. “ This is an important achievement, showcasing Origin’s competitive advantage in science and global reach through collaborations inside China and beyond its borders. Origin is leading the way in gaining regulatory approvals for this critical advanced technology globally to drive future business growth.” Origin’s investment and focus aligns tightly with China’s 13th Five Year Plan, which calls for the modernization of agriculture as the foundation for building a prosperous society. The Chinese government, including the Ministry of Agriculture (MOA) and Chinese Academy of Agricultural Sciences (CAAS), has advanced a policy vision to facilitate seed industry innovation, improve the competitiveness of the Chinese ag tech industry and cultivate new seed varieties for farmers around the world. Through these actions, China has shown strong commitment to advancing its ag industry through new advances in biotechnology. Origin anticipates China commercialization of corn biotechnology at the end of this decade. Origin Agritech Limited, founded in 1997 and headquartered in Zhong-Guan-Cun (ZGC) Life Science Park in Beijing, is China’s leading agricultural biotechnology company, specializing in crop seed breeding and genetic improvement, seed production, processing, distribution, and related technical services. Leading the development of crop seed biotechnologies, Origin Agritech’s phytase corn was the first transgenic corn to receive the Bio-Safety Certificate from China's Ministry of Agriculture. Over the years, Origin has established a robust biotechnology seed pipeline including products with glyphosate tolerance and pest resistance (Bt) traits. Origin operates production centers, processing centers and breeding stations nationwide with sales centers located in key crop-planting regions. Product lines are vertically integrated for corn, rice and canola seeds. For further information, please visit the Company’s website at: http://www.originseed.com.cn or http://www.originseed.com.cn/en/. Based in Davis, Calif., Arcadia Biosciences (Nasdaq: RKDA) develops agricultural products that create added value for farmers while benefitting the environment and enhancing human health. Arcadia’s agronomic performance traits, including Nitrogen Use Efficiency, Water Use Efficiency, Salinity Tolerance, Heat Tolerance and Herbicide Tolerance, are all aimed at making agricultural production more economically efficient and environmentally sound. Arcadia’s nutrition traits and products are aimed at creating healthier ingredients and whole foods with lower production costs. For more information, visit www.arcadiabio.com. This communication contains “forward-looking statements” within the meaning of the federal securities laws, including Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. In this context, forward-looking statements often address expected future business and financial performance and financial condition, and often contain words such as “expect,” “anticipate,” “intend,” “plan,” “believe,” “seek,” “see,” “will,” “would,” “target,” similar expressions, and variations or negatives of these words. Forward-looking statements by their nature address matters that are, to different degrees, uncertain, such as statements about the consummation of the proposed transaction and the anticipated benefits thereof. Forward-looking statements are not guarantees of future performance and are based on certain assumptions and expectations of future events which may not be realized. Forward-looking statements also involve risks and uncertainties, many of which are beyond the company’s control. Some of the important factors that could cause the company’s actual results to differ materially from those projected in any such forward-looking statements are: fluctuations in energy and raw material prices; failure to develop and market new products and optimally manage product life cycles; ability to respond to market acceptance, rules, regulations and policies affecting products based on biotechnology and, in general, for products for the agriculture industry; outcome of significant litigation and environmental matters, including realization of associated indemnification assets, if any; failure to appropriately manage process safety and product stewardship issues; changes in laws and regulations or political conditions; global economic and capital markets conditions, such as inflation, interest and currency exchange rates; business or supply disruptions; security threats, such as acts of sabotage, terrorism or war, natural disasters and weather events and patterns which could affect demand as well as availability of products for the agriculture industry; ability to protect and enforce the company's intellectual property rights; and successful integration of acquired businesses and separation of underperforming or non-strategic assets or businesses. The company undertakes no duty to publicly revise or update any forward-looking statements as a result of future developments, or new information or otherwise, should circumstances change, except as otherwise required by securities and other applicable laws.


News Article | February 22, 2017
Site: en.prnasia.com

Insect resistant corn seed trait targeted at an estimated $1 billion marketDES MOINES, Iowa, Feb. 22, 2017 /PRNewswire/ -- Origin (Origin Agritech, LLC, a subsidiary of Origin Agritech Ltd.) (NASDAQ: SEED), an agricultural biotechnology trait and seed provider, and Arcadia (Arcadia Biosciences, Inc., NASDAQ: RKDA), a California-based company that develops and commercializes agricultural productivity traits and nutritional products, today announced their collaboration to achieve the first-ever export of a key corn biotechnology product developed in China to the United States for completion of global regulatory trials. The successful movement of this corn seed, containing an insect resistance/herbicide tolerance trait discovered and developed in China, to the Arcadia greenhouse represents a key milestone in Origin's strategic business plan to achieve global regulatory approvals for cultivation and international grain movement. "This first-of-its-kind export validates Origin's leading position in China biotech and its close alignment with Chinese ministries leading the transformation of the domestic seed industry. Combining Origin's robust pipeline of value-added Chinese traits and elite corn germplasm with Arcadia's research and development infrastructure demonstrates our plan to capture a sizeable piece of China's estimated billion-dollar corn seed trait market," said Bill Niebur, Origin chief executive officer. "As a leader in agtech focused on modernizing the traditional corn seed market, our international team remains focused on accelerating research and development to improve the lives of Chinese farmers." Arcadia and Origin signed an agreement under which Arcadia will assist Origin in developing information for submission to regulatory authorities in the U.S., China and other countries for the approval of their traits in corn. This project involves production of inbred and hybrid seed lines under quarantine conditions in Arcadia greenhouses. "Arcadia has the proven expertise to bring traits through the regulatory process successfully and efficiently," said Raj Ketkar, Arcadia's president and CEO. "We have conducted hundreds of studies in the laboratory, greenhouse and field to gain regulatory approvals for various traits in major crops, and we have a strong regulatory team that has developed complete regulatory dossiers in multiple countries. This collaboration with Origin is an example of how our partners can leverage these capabilities to accelerate the commercialization of novel ag biotech traits." "Ultimately, this milestone achievement will create more choices and opportunities for farmers," said Jihong Liang, Origin chief technology officer. "This is an important achievement, showcasing Origin's competitive advantage in science and global reach through collaborations inside China and beyond its borders. Origin is leading the way in gaining regulatory approvals for this critical advanced technology globally to drive future business growth." Origin's investment and focus aligns tightly with China's 13th Five Year Plan, which calls for the modernization of agriculture as the foundation for building a prosperous society. The Chinese government, including the Ministry of Agriculture (MOA) and Chinese Academy of Agricultural Sciences (CAAS), has advanced a policy vision to facilitate seed industry innovation, improve the competitiveness of the Chinese ag tech industry and cultivate new seed varieties for farmers around the world. Through these actions, China has shown strong commitment to advancing its ag industry through new advances in biotechnology. Origin anticipates China commercialization of corn biotechnology at the end of this decade. Origin Agritech Limited, founded in 1997 and headquartered in Zhong-Guan-Cun (ZGC) Life Science Park in Beijing, is China's leading agricultural biotechnology company, specializing in crop seed breeding and genetic improvement, seed production, processing, distribution, and related technical services. Leading the development of crop seed biotechnologies, Origin Agritech's phytase corn was the first transgenic corn to receive the Bio-Safety Certificate from China's Ministry of Agriculture. Over the years, Origin has established a robust biotechnology seed pipeline including products with glyphosate tolerance and pest resistance (Bt) traits. Origin operates production centers, processing centers and breeding stations nationwide with sales centers located in key crop-planting regions. Product lines are vertically integrated for corn, rice and canola seeds. For further information, please visit the Company's website at: http://www.originseed.com.cn or http://www.originseed.com.cn/en/. Based in Davis, Calif., Arcadia Biosciences (Nasdaq: RKDA) develops agricultural products that create added value for farmers while benefitting the environment and enhancing human health. Arcadia's agronomic performance traits, including Nitrogen Use Efficiency, Water Use Efficiency, Salinity Tolerance, Heat Tolerance and Herbicide Tolerance, are all aimed at making agricultural production more economically efficient and environmentally sound. Arcadia's nutrition traits and products are aimed at creating healthier ingredients and whole foods with lower production costs. For more information, visit www.arcadiabio.com. This communication contains "forward-looking statements" within the meaning of the federal securities laws, including Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. In this context, forward-looking statements often address expected future business and financial performance and financial condition, and often contain words such as "expect," "anticipate," "intend," "plan," "believe," "seek," "see," "will," "would," "target," similar expressions, and variations or negatives of these words. Forward-looking statements by their nature address matters that are, to different degrees, uncertain, such as statements about the consummation of the proposed transaction and the anticipated benefits thereof. Forward-looking statements are not guarantees of future performance and are based on certain assumptions and expectations of future events which may not be realized. Forward-looking statements also involve risks and uncertainties, many of which are beyond the company's control. Some of the important factors that could cause the company's actual results to differ materially from those projected in any such forward-looking statements are: fluctuations in energy and raw material prices; failure to develop and market new products and optimally manage product life cycles; ability to respond to market acceptance, rules, regulations and policies affecting products based on biotechnology and, in general, for products for the agriculture industry; outcome of significant litigation and environmental matters, including realization of associated indemnification assets, if any; failure to appropriately manage process safety and product stewardship issues; changes in laws and regulations or political conditions; global economic and capital markets conditions, such as inflation, interest and currency exchange rates; business or supply disruptions; security threats, such as acts of sabotage, terrorism or war, natural disasters and weather events and patterns which could affect demand as well as availability of products for the agriculture industry; ability to protect and enforce the company's intellectual property rights; and successful integration of acquired businesses and separation of underperforming or non-strategic assets or businesses. The company undertakes no duty to publicly revise or update any forward-looking statements as a result of future developments, or new information or otherwise, should circumstances change, except as otherwise required by securities and other applicable laws. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/origin-arcadia-announce-china-biotechnology-collaboration-in-corn-300411337.html


Lin W.,Chinese Academy of Agricultural Sciences | Liu Y.,China Institute of Veterinary Drug Control | Cui S.,Chinese Academy of Agricultural Sciences | Liu H.,Anhui Agricultural University
Infection, Genetics and Evolution | Year: 2012

Encephalomyocarditis virus (EMCV) can cause myocarditis, respiratory failure, reproductive failure, and mortality in pregnant sows, fetuses, and ablactating piglets. Diseases caused by EMCV currently affect the swine industry worldwide. A virus was isolated from organs of dead piglets that presented with acute myocarditis in northern China. The production of a specific cytopathic effect on susceptible cells and the results of hemagglutination inhibition (HI) assay, PCR, electron microscopy (EM), and sequencing indicated that the pathogen was EMCV; the strain was named HB10. Other pathogenic agents causing myocarditis and death were excluded as possible pathogenic agents. Phylogenetic analyses of the capsid coding region and the VP3/VP1 genes using the neighbour-joining method revealed that EMCV isolates cluster into two groups (groups 1 and 2) with two sub-clusters within group 1 (group 1a and b). HB10 belongs to group 1a, along with strains CBNU, GX0601, BJC3, NJ08, and BEL-2887A/91. Five strains isolated from . Sus scrofa belong to group 2. The results of this and previous studies indicate that HB10 and other EMCV strains cause myocarditis of pigs in China. © 2012 Elsevier B.V..


Long Y.,Chinese Academy of Agricultural Sciences | Zhang J.,Chinese Academy of Agricultural Sciences | Tian X.,Chinese Academy of Agricultural Sciences | Wu S.,Chinese Academy of Agricultural Sciences | And 4 more authors.
BMC Genomics | Year: 2014

Background: Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants. Results: Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length=728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10-5. In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members. Conclusions: Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions. © Long et al.; licensee BioMed Central.


Gao Y.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | Gao Y.,Shanghai JiaoTong University | Yu G.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | Luo C.,Chinese Academy of Agricultural Sciences | Zhou P.,Shanghai JiaoTong University
PLoS ONE | Year: 2012

Protecting groundwater from nitrogen contamination is an important public-health concern and a major national environmental issue in China. In this study, we monitored water quality in 29 wells from 2009 to 2010 in a village in Shanghai city, whick belong to typical rural-urban continuum in China. The total N and NO 3-N exhibited seasonal changes, and there were large fluctuations in NH 4-N in residential areas, but without significant seasonal patterns. NO 2-N in the water was not stable, but was present at high levels. Total N and NO 3-N were significantly lower in residential areas than in agricultural areas. The groundwater quality in most wells belonged to Class III and IV in the Chinese water standard, which defines water that is unsuitable for human consumption. Our health risk assessments showed that NO 3-N posed the greatest carcinogenic risk, with risk values ranging from 19×10 -6 to 80×10 -6, which accounted for more than 90% of the total risk in the study area. © 2012 Gao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Hou J.C.,Northeast Agricultural University | Jiang C.G.,Chinese Academy of Agricultural Sciences | Long Z.C.,Husbandry and Veterinary Bureau of Yichun City
Food Control | Year: 2013

Nitrite is commonly present in pickled vegetables. Nitrite has been proven to have adverse effects on health, including changing the normal form of hemoglobin and the formation of carcinogenic nitrosamines. The aim of our study was to determine the levels of nitrite in pickled vegetable samples consumed in Harbin, China. In this study, 218 samples of pickled turnip (PT) (n = 42, packaged (PK) = 19; unpackaged (UPK) = 23), pickled tuber mustard (PTM) (n = 44, PK = 23; UPK = 21), pickled cucumber (PCC) (n = 48, PK = 25; UPK = 23), and pickled cabbage (PCB) (n = 84, PK = 39; UPK = 45) were analyzed between October 2011 and December 2011, using colorimetric nitrite assay based on the Griess reaction. A nitrite level of <5 mg/kg was normally predominant in 147 (67%) samples of the investigated pickled vegetables, ranging from 0.01 mg/kg to 42.03 mg/kg, while a nitrite level of >20 mg/kg was detected in 9 (4%) samples. The overall nitrite content was 4.02 ± 0.62 mg/kg for PT, 4.52 ± 1.07 mg/kg for PTM, 3.91 ± 0.69 mg/kg for PCC, and 4.86 ± 0.80 mg/kg for PCB. The content of nitrite in unpackaged pickled vegetables (PT, 5.47 ± 0.89; PTM, 6.84 ± 2.02; PCC, 5.32 ± 1.27; PCB, 6.41 ± 1.28; and total, 6.08 ± 0.71 mg/kg) was significantly higher than those in packaged products (PT, 2.68 ± 0.72; PTM, 2.30 ± 0.55; PCC, 2.62 ± 0.54; PCB, 3.08 ± 0.81; and total, 2.73 ± 0.36 mg/kg) (P < 0.05). The variance in the concentration of nitrite in the pickled vegetables probably resulted from differences in quality, processing technique, and storage condition of the pickled vegetables. Our results indicated that, in China, low level nitrite is widely present in pickled vegetables. It is therefore important to assess the content of nitrite in pickled vegetables in China. © 2012 Elsevier Ltd.


Peng S.,Cornell University | Derrien T.L.,Cornell University | Cui J.,Cornell University | Cui J.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Materials Today | Year: 2012

Materials need to be specially engineered to interface with cells; on the other hand, cells provide great inspiration for new material designs. Here, using examples mainly from our own research, we demonstrate that DNA can be used as both a genetic and generic material for various cell-related applications, including diagnostics, drug delivery, cell culture, protein production, and immuno-modulation. We envision that other cell-based materials such as RNA, proteins, polysaccharides, and lipids can be more pervasively employed in materials science and engineering. © 2012 Elsevier Ltd.


Xu M.,Chinese Academy of Agricultural Sciences | Lou Y.,Chinese Academy of Agricultural Sciences | Sun X.,CAS Nanjing Institute of Soil Science | Wang W.,Michigan State University | And 2 more authors.
Biology and Fertility of Soils | Year: 2011

Changes in total organic C (CT), water-soluble organic C (CWS), microbial biomass C (CMB), C mineralization, particulate organic C (CP), labile organic C (CL), C management index (CMI), and C storage in surface Hapli-Ustic Cambisol (0-20 cm) under straw incorporation after both 2- and 10-year durations were investigated in a maize (Zea mays L.) field experiment in northeast China, in order to examine the effectiveness of these active C fractions and CMI as early indicators for total C change. The treatments included straw removal (0%S), 50% of straw incorporation (50%S), and 100% of straw incorporation (100%S). Under the straw incorporation, CT concentration and C storage did not significantly change under 2-year duration, while were significantly increased under 10-year duration. However, CMB, total C mineralization (CTM), CP, and CL, and CMI were significantly increased under the straw incorporation even after only 2-year duration, and the responses were more significant after 10-year duration. There were positive correlations between all these C indicators with each other. Our findings demonstrate that the measured active C fractions (except for CWS) and CMI can provide an early indication of change in total soil organic C induced by straw incorporation. © 2011 Springer-Verlag.


Jiang Q.,Chinese Academy of Agricultural Sciences | Hou J.,Chinese Academy of Agricultural Sciences | Hao C.,Chinese Academy of Agricultural Sciences | Wang L.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Functional and Integrative Genomics | Year: 2011

Sucrose synthase catalyzes the reaction sucrose + UDP → UDP-glucose + fructose, the first step in the conversion of sucrose to starch in endosperm. Previous studies identified two tissue-specific, yet functionally redundant, sucrose synthase (SUS) genes, Sus1 and Sus2. In the present study, the wheat Sus2 orthologous gene (TaSus2) series was isolated and mapped on chromosomes 2A, 2B, and 2D. Based on sequencing in 61 wheat accessions, three single-nucleotide polymorphisms (SNPs) were detected in TaSus2-2B. These formed two haplotypes (Hap-H and Hap-L), but no diversity was found in either TaSus2-2A or TaSus2-2D. Based on the sequences of the two haplotypes, we developed a co-dominant marker, TaSus2-2B tgw, which amplified 423 or 381-bp fragments in different wheat accessions. TaSus2-2B tgw was located between markers Xbarc102.2 and Xbarc91 on chromosome 2BS in a RIL population from Xiaoyan 54 × Jing 411. Association analysis suggested that the two haplotypes were significantly associated with 1,000 grain weight (TGW) in 89 modern wheat varieties in the Chinese mini-core collection. Mean TGW difference between the two haplotypes over three cropping seasons was 4.26 g (varying from 3.71 to 4.94 g). Comparative genomics analysis detected major kernel weight QTLs not only in the chromosome region containing TaSus2-2B tgw, but also in the collinear regions of TaSus2 on rice chromosome 7 and maize chromosome 9. The preferred Hap-H haplotype for high TGW underwent very strong positive selection in Chinese wheat breeding, but not in Europe. The geographic distribution of Hap-H was perhaps determined by both latitude and the intensity of selection in wheat breeding. © 2010 Springer-Verlag.


Ye L.,CAS Institute of Zoology | Ye L.,Chinese Academy of Agricultural Sciences | Fu X.,CAS Institute of Zoology | Fu X.,Heilongjiang University | Ge F.,CAS Institute of Zoology
Journal of Experimental Botany | Year: 2012

Investigations of the effects of elevated ozone (O3) on the virus-plant system were conducted to inform virus pathogen management strategies better. One susceptible cultivar of tobacco (Nicotiana tabacum L. cv. Yongding) and a resistant cultivar (Nicotiana tabacum L. cv. Vam) to Potato virus Y petiole necrosis strain (PVY N) infection were grown in open-top chambers under ambient and elevated O3 concentrations. Above-ground biomass, foliage chlorophyll, nitrogen and total non-structural carbohydrate (TNCs), soluble protein, total amino acid (TAA) and nicotine content, and peroxidase (POD) activity were measured to estimate the effects of elevated O3 on the impact of PVY N in the two cultivars. Results showed that under ambient O3, the resistant cultivar possessed greater biomass and a lower C/N ratio after infection than the susceptible cultivar; however, under elevated O3, the resistant cultivar lost its biomass advantage but maintained a lower C/N ratio. Variation of foliar POD activity could be explained as a resistance cost which was significantly correlated with biomass and C/N ratio of the tobacco cultivar. Chlorophyll content remained steady in the resistant cultivar but decreased significantly in the susceptible cultivar when stressors were applied. Foliar soluble protein and free amino acid content, which were related to resistance cost changes, are also discussed. This study indicated that a virus-resistant tobacco cultivar showed increased sensitivity to elevated O3 compared to a virus-sensitive cultivar. © 2012 The Author.


Cao Y.,Chinese Academy of Agricultural Sciences | Cao Y.,Heilongjiang University | He S.,Chinese Academy of Agricultural Sciences | Zhou Z.,Chinese Academy of Agricultural Sciences | And 4 more authors.
Applied and Environmental Microbiology | Year: 2012

N-Acylated homoserine lactone (AHL) lactonases are capable of degrading signal molecules involved in bacterial quorum sensing and therefore represent a new approach to control bacterial infection. Here a gene responsible for the AHL lactonase activity of Bacillus sp. strain AI96, 753 bp in length, was cloned and then expressed in Escherichia coli. The deduced amino acid sequence of Bacillus sp. AI96 AiiA (AiiA AI96) is most similar to those of other Bacillus sp. AHL lactonases (~80% sequence identity) and was consequently categorized as a member of the metallo-β-lactamase superfamily. AiiA AI96 maintains~100% of its activity at 10°C to 40°C at pH 8.0, and it is very stable at 70°C at pH 8.0 for at least 1 h; no other Bacillus AHL lactonase has been found to be stable under these conditions. AiiAAI96 resists digestion by proteases and carp intestinal juice, and it has broad-spectrum substrate specificity. The supplementation of AiiAAI96 into fish feed by oral administration significantly attenuated Aeromonas hydrophila infection in zebrafish. This is the first report of the oral administration of an AHL lactonase for the efficient control of A. hydrophila. © 2012, American Society for Microbiology.


Wu K.,Chinese Academy of Agricultural Sciences | Yang M.,Chinese Academy of Agricultural Sciences | Liu H.,Chinese Academy of Agricultural Sciences | Tao Y.,Shanghai Major Biological Medicine Technology Co. | And 2 more authors.
BMC Genetics | Year: 2014

Background: Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design.Results: Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines.Conclusions: This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame. © 2014 Wu et al.; licensee BioMed Central Ltd.


Pan H.,Chinese Academy of Agricultural Sciences | Lu Y.,Chinese Academy of Agricultural Sciences | Wyckhuys K.A.G.,International Center for Tropical Agriculture Asia
PLoS ONE | Year: 2013

The mirid bugs Adelphocoris suturalis (Jakovlev), Adelphocoris lineolatus (Goeze) and Adelphocoris fasciaticollis (Reuter) (Hemiptera: Miridae) are common pests of several agricultural crops. These three species have vastly different geographical distributions, phenologies and abundances, all of which are linked to their reliance on local plants. Previous work has shown notable differences in Adelphocoris spp. host use for overwintering. In this study, we assessed the extent to which each of the Adelphocoris spp. relies on some of its major overwinter hosts for spring development. Over the course of four consecutive years (2009-2012), we conducted population surveys on 77 different plant species from 39 families. During the spring, A. fasciaticollis used the broadest range of hosts, as it was found on 35 plant species, followed by A. suturalis (15 species) and A. lineolatus (7 species). Abundances of the species greatly differed between host plants, with A. fasciaticollis reaching the highest abundance on Chinese date (Ziziphus jujuba Mill.), whereas both A. suturalis and A. lineolatus preferred alfalfa (Medicago sativa L.). The host breadths of the three Adelphocoris spp. differed greatly between subsequent spring and winter seasons. The generalist species exhibited the least host fidelity, with A. suturalis and A. lineolatus using 8 of 22 and 4 of 12 overwinter host species for spring development, respectively. By contrast, the comparative specialist A. fasciaticollis relied on 9 of its 11 overwinter plants as early-season hosts. We highlight important seasonal changes in host breadth and interspecific differences in the extent of host switching behavior between the winter and spring seasons. These findings benefit our understanding of the evolutionary interactions between mirid bugs and their host plants and can be used to guide early-season population management. © 2013 Pan et al.


Pan H.,Chinese Academy of Agricultural Sciences | Lu Y.,Chinese Academy of Agricultural Sciences | Wyckhuys K.A.G.,International Center for Tropical Agriculture Asia | Wu K.,Chinese Academy of Agricultural Sciences
PLoS ONE | Year: 2013

Apolygus lucorum (Meyer-Dür) (Hemiptera: Miridae) is one of the most important herbivores in a broad range of cultivated plants, including cotton, cereals, vegetables, and fruit crops in China. In this manuscript, we report on a 6-year long study in which (adult) A. lucorum abundance was recorded on 174 plant species from 39 families from early July to mid-September. Through the study period per year, the proportion of flowering plants exploited by adult A. lucorum was significantly greater than that of non-flowering plants. For a given plant species, A. lucorum adults reached peak abundance at the flowering stage, when the plant had the greatest attraction to the adults. More specifically, mean adult abundance on 26 species of major host plants and their relative standard attraction were 10.3-28.9 times and 9.3-19.5 times higher at flowering stage than during non-flowering periods, respectively. Among all the tested species, A. lucorum adults switched food plants according to the succession of flowering plant species. In early July, A. lucorum adults preferred some plant species in bloom, such as Vigna radiata, Gossypium hirsutum, Helianthus annuus and Chrysanthemum coronarium; since late July, adults dispersed into other flowering hosts (e.g. Ricinus communis, Impatiens balsamina, Humulus scandens, Ocimum basilicum, Agastache rugosus and Coriandrum sativum); in early September, they largely migrated to flowering Artemisia spp. (e.g. A. argyi, A. lavandulaefolia, A. annua and A. scoparia). Our findings underscore the important role of flowering plays in the population dynamics and inter-plant migration of this mirid bug. Also, our work helps understand evolutionary aspects of host plant use in polyphagous insects such as A. lucorum, and provides baseline information for the development of sustainable management strategies of this key agricultural pest. © 2013 Pan et al.


Zhang H.,Chinese Academy of Agricultural Sciences | Zhang J.,Chinese Academy of Agricultural Sciences | Quan R.,Chinese Academy of Agricultural Sciences | Pan X.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Planta | Year: 2013

OsERF3 is a transcriptional repressor with an ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motif (F/LDLNxxP), which transcriptionally represses the ethylene emission and drought tolerance in rice. However, its molecular mechanism to explore repression function remains unknown. Here, we first revealed that the expression of OsERF3 was induced by drought, salt, ACC and ABA treatment. In addition, it showed a higher expression level in the root and sheath than that in the leaf. Then, we generated transgenic rice overexpressing full-length OsERF3 (OE) and its mutation of EAR motif with the A 680/C substitution (mEAR), respectively. The physiological analyses showed that mEAR lines showed better drought tolerance and more ethylene emission compared with those of OE lines and wild type plants. Consistent with our previous research, the expression of ethylene synthesis genes, including ACO2, ACS2, and ACS6 was down-regulated in OE lines. However, the repression of OsERF3 was eliminated in mEAR lines. Specifically, ACS2 was up-regulated in mEAR lines compared with that in OE lines and WT plants, suggesting that the Leu/Ala substitution within the EAR motif resulted in loss of repression of OsERF3. Thus, our data reveal that the EAR motif is required for OsERF3 to transcriptionally regulate the ethylene synthesis and drought tolerance in rice, providing new insight to the roles of ethylene-response factor proteins in regulating ethylene biosynthesis and stress response. © 2013 Springer-Verlag Berlin Heidelberg.


Liu G.-H.,Chinese Academy of Agricultural Sciences | Liu G.-H.,Hunan Agricultural University | Gasser R.B.,University of Melbourne | Young N.D.,University of Melbourne | And 4 more authors.
Parasites and Vectors | Year: 2014

Background: Fascioliasis is an important and neglected disease of humans and other mammals, caused by trematodes of the genus Fasciola. Fasciola hepatica and F. gigantica are valid species that infect humans and animals, but the specific status of Fasciola sp. ('intermediate form') is unclear. Methods. Single specimens inferred to represent Fasciola sp. ('intermediate form'; Heilongjiang) and F. gigantica (Guangxi) from China were genetically identified and characterized using PCR-based sequencing of the first and second internal transcribed spacer regions of nuclear ribosomal DNA. The complete mitochondrial (mt) genomes of these representative specimens were then sequenced. The relationships of these specimens with selected members of the Trematoda were assessed by phylogenetic analysis of concatenated amino acid sequence datasets by Bayesian inference (BI). Results: The complete mt genomes of representatives of Fasciola sp. and F. gigantica were 14,453 bp and 14,478 bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lack an atp8 gene. All protein-coding genes are transcribed in the same direction, and the gene order in both mt genomes is the same as that published for F. hepatica. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 protein-coding genes showed that the specimen of Fasciola sp. was more closely related to F. gigantica than to F. hepatica. Conclusions: The mt genomes characterized here provide a rich source of markers, which can be used in combination with nuclear markers and imaging techniques, for future comparative studies of the biology of Fasciola sp. from China and other countries. © 2014 Liu et al.; licensee BioMed Central Ltd.


Lam H.-M.,Chinese University of Hong Kong | Xu X.,BGI Shenzhen | Xu X.,Key Laboratory of Genomics | Liu X.,BGI Shenzhen | And 16 more authors.
Nature Genetics | Year: 2010

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis. © 2010 Nature America, Inc. All rights reserved.


Qiao G.,Chinese Academy of Agricultural Sciences | Guo T.,Inner Mongolia Agricultural University | Klein K.K.,University of Lethbridge
Appetite | Year: 2010

Chinese consumers were shocked to learn in September 2008 that melamine, a chemical used in plastics, had been found in domestic dairy products and many people, especially young children, were experiencing adverse health impacts including death. A survey of consumers in four districts of Hohhot, Inner Mongolia, near where the two largest dairy companies in China are located, was conducted in November 2008. Findings reveal that consumption of fluid milk, yogurt, milk powder and ice cream, and perceptions of the safety of these products, which had plummeted in the days following the contamination announcement, had recovered strongly by the time of the survey. High proportions of respondents expressed high or moderate levels of confidence in the domestic dairy industry and generally were satisfied with corrective and remedial actions taken by the two large Hohhot-based companies, though there was less satisfaction for actions taken by companies located in other parts of the country. © 2010 Elsevier Ltd.


Huang Y.,Shanghai JiaoTong University | Wang J.,Chinese Academy of Agricultural Sciences | Zhang L.,Shanghai JiaoTong University | Zuo K.,Shanghai JiaoTong University
PLoS ONE | Year: 2013

Annexins are assumed to be involved in regulating cotton fiber elongation, but direct evidence remains to be presented. Here we cloned six Annexin genes (AnxGb) abundantly expressed in fiber from sea-island cotton (G. barbadense). qRT-PCR results indicated that all six G. barbadense annexin genes were expressed in elongating cotton fibers, while only the expression of AnxGb6 was cotton fiber-specific. Yeast two hybridization and BiFC analysis revealed that AnxGb6 homodimer interacted with a cotton fiber specific actin GbAct1. Ectopic-expressed AnxGb6 in Arabidopsis enhanced its root elongation without increasing the root cell number. Ectopic AnxGb6 expression resulted in more F-actin accumulation in the basal part of the root cell elongation zone. Analysis of AnxGb6 expression in three cotton genotypes with different fiber length confirmed that AnxGb6 expression was correlated to cotton fiber length, especially fiber elongation rate. Our results demonstrated that AnxGb6 was important for fiber elongation by potentially providing a domain for F-actin organization. © 2013 Huang et al.


Xu L.-N.,Anhui Academy of Agricultural Sciences | Xu L.-N.,Chinese Academy of Agricultural Sciences | Wang Y.-Q.,Chinese Academy of Agricultural Sciences | Wang Z.-Y.,Chinese Academy of Agricultural Sciences | And 3 more authors.
BMC Genomics | Year: 2015

Background: Asian corn borer (ACB), Ostrinia furnacalis (Guenée), is the major insect pest of maize in China and countries of East and Southeast Asia, the Pacific and Australasia. ACB can develop strong resistance to the transgenic Bt maize expressing Cry1Ab, the most widely commercialized Bt maize worldwide. However, the molecular basis for the resistance mechanisms of ACB to Cry1Ab remained unclear. Two biological replicates of the transcriptome of Bt susceptible (ACB-BtS) and Cry1Ab resistant (ACB-AbR) strains of ACB were sequenced using Solexa/Illumina RNA-Seq technology to identify Cry1Ab resistance-relevant genes. Results: The numbers of unigenes for two biological replications were 63,032 and 53,710 for ACB-BtS and 57,770 and 54,468 for ACB-AbR. There were 35,723 annotated unigenes from ACB reads found by BLAST searching NCBI non-redundant, NCBI non-redundant nucleotide, Swiss-prot protein, Kyoto Encyclopedia of Genes and Genomes, Cluster of Orthologous Groups of proteins, and Gene Ontology databases. Based on the NOISeq method, 3,793 unigenes were judged to be differentially expressed between ACB-BtS and ACB-AbR. Cry1Ab resistance appeared to be associated with change in the transcription level of enzymes involved in growth regulation, detoxification and metabolic/catabolic process. Among previously described Bt toxin receptors, the differentially expressed unigenes associated with aminopeptidase N and chymotrypsin/trypsin were up-regulated in ACB-AbR. Whereas, other putative Cry receptors, cadherin-like protein, alkaline phosphatase, glycolipid, actin, V-type proton ATPase vatalytic, heat shock protein, were under-transcripted. Finally, GPI-anchor biosynthesis was found to be involved in the significantly enriched pathway, and all genes mapped to the pathway were substantially down-regulated in ACB-AbR. Conclusion: To our knowledge, this is the first comparative transcriptome study to discover candidate genes involved in ACB Bt resistance. This study identified differentially expressed unigenes related to general Bt resistance in ACB. The assembled, annotated transcriptomes provides a valuable genomic resource for further understanding of the molecular basis of ACB Bt resistance mechanisms. © 2014 Xu et al.; licensee BioMed Central.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2012.3.1-03 | Award Amount: 1.24M | Year: 2012

The FIBRA network has as main target to link the research and development activities for fibre crop innovations carried out by universities and institutions in both EU and China. This proposal is set up to promote the communication between experts about the key issues of fibre crop production, processing and application, while attention towards quality and efficiency improvement, and product diversification will result in improved markets and enhanced economic scope for sustainable fibre crop production in EU and China. The creation of opportunities for networking and cooperation between experts from different disciplines from China and EU will result in a better exchange of know-how and is expected to bring the state of the art of fibre crop utilization to a higher level on both sides. The FIBRA network is set up to optimize the information exchange on specialized topics for fibre crop productivity, and innovation. The FIBRA network is to provide the basis for common R&D activities between Chinese and European partners. The FIBRA network will provide a long term vision on future common research activities on fibre crops that will contribute to the international policies of the EU and will improve researchers training opportunities.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2013.1.3-04 | Award Amount: 1.19M | Year: 2013

The continuous growth of the world population translates into a demand of animal protein that can only be achieved through technological advances in farming, intensification, and expansion of farmed land. These pressures, combined with the increasing international trade of animals and their products, will lead to the rapid spread of animal diseases across borders and the emergence of new pathogens. This can have a huge impact on trade, livelihoods and public health. China is no exception and is in fact the worlds largest livestock producer and consumer, with pig and poultry meat being the most consumed meats. Research has many of the answers to prevent and control animal diseases, either through the understanding of their spread (epidemiology) or through better diagnostics for disease detection and surveillance. Both the European Union (EU) and China are two major worldwide players in animal health research. With dozens of institutions working on livestock health, the cross-border coordination and networking of research becomes a top priority to avoid duplication, while maximizing efforts by bringing together new ideas, expertise, technologies and funds. LinkTADs brings together world-class research institutes and experts in cross-border cooperation with the aim to coordinate research between the EU and China, thus improving scientific excellence in animal health (epidemiology and laboratory). Main objectives: identify the priority areas, where joint actions are needed link the research activities carried out on by European and Chinese research programmes ensure a wide-range networking of scientific communities and stakeholders provide a long term vision and achieve coordinated planning on future common research contribute to the international policies of the EU improve the research capacity of organizations by supporting young researchers through exchange programmes and training share the results and methodologies within and outside the consortium.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-TP | Phase: KBBE.2012.3.1-02 | Award Amount: 7.96M | Year: 2012

Hemp is a sustainable high yielding crop well adapted to most European conditions, with advantageous environmental and agronomical characteristics. Traditionally cultivated for the fibres, seeds and psychoactive substances, it is now considered an ideal crop to produce innovative biomaterials. Once a key industrial crop for fibre, hemp production declined in the last century and was displaced by cotton and synthetic fibres. This explains why hemp has not been subject to the intensive breeding that has driven great improvements in major food crops in the last 50 years. However, cotton has one of the worst environmental footprints of any crop and there is renewed interest in hemp because it requires less water and agrochemicals and provides fibre and oil of superior quality. In the frame of multi-hemp, we will use cutting-edge genomic approaches to achieve rapid targeted improvements in hemp productivity and raw material quality for end-user requirements, whilst also advancing scientific understanding of gene-to-trait relationships in this crop. This work will be combined with innovations in agronomy, harvesting and processing methods to generate sustainable products from improved varieties. The project will include demonstration activities such as field trial and process scale up. The economic and environmental implications of each innovation will be assessed so as to maximise economic return and increase sustainability. This project brings together leading research groups with a vibrant group of industrial participants working from the level of molecular genetics through to end product demonstration. Our ambition is to develop an integrated hemp-based biorefinery in which improved feedstock is subject to efficient and modular processing steps to provide fibre, oil, construction materials, fine chemicals and biofuels using all components of the harvested biomass, and generating new opportunities within the developing knowledge based bioeconomy.


News Article | December 6, 2015
Site: www.reuters.com

The logo of Origin Agritech is seen at the company's headquarters in Beijing, November 27, 2015. Picture taken November 27, 2015. The logo of Origin Agritech is seen at the company's headquarters in Beijing, November 27, 2015. Picture taken November 27, 2015. The name of Origin Agritech is seen through the windows of the company's headquarters in Beijing, November 27, 2015. The plan by Beijing-based Origin Agritech to test its technology in the United States, which has dominated the sector with GMO giants such as Monsanto, is the latest effort by a Chinese firm to enter the global industry. Earlier this year, China National Chemical Corp sought to skirt obstacles at home and acquire a tried-and-tested GMO pipeline by bidding for the world's top agrichemicals firm Swiss-based Syngenta. Beijing's GMO policy has at times appeared inconsistent - billions of dollars have been spent on developing technology it hopes will ensure supplies for its 1.4 billion people, while no major food crops have been approved for cultivation given deep-seated anti-GMO sentiment in the country. Bumper harvests in the past decade have also reduced the urgency for new technologies. "Consumer attitude is one thing, but the government attitude is even more important," said Huang Dafang, professor at the Biotechnology Research Institute under the Chinese Academy of Agricultural Sciences. That leaves firms like Origin with few options to earn revenues from GMO products in China, he added. U.S.-listed Origin has invested more than 300 million yuan ($46.90 million) in biotech since 2005 and, without an opportunity to market its product at home, it now plans to enter the United States in 2016, according to a presentation on the Securities and Exchange Commission website. Entering the U.S. market could take several paths from licensing its technology to setting up a unit there, Origin's chief financial officer, James Chen, told Reuters. But getting a foothold in such a highly competitive market will not be easy, experts warn. Origin's most advanced product is a corn with two special characteristics, or "traits", that resist pests while top seed firm Monsanto already markets a GMO corn that combines or "stacks" as many as eight traits to combat pests. "The only way they might be able to break into the market is if their technology fees are going to be cheaper than Monsanto," said Carl Pray, professor at Rutgers University's agricultural, food and resource economics department. Referring to seed firm Beijing Dabeinong Technology Group's agreement to test its technology in Argentina, Pray said competition was tougher in the United States. "It's one thing to do this in Argentina, and another to go into the U.S." But Origin's Chen sees a market for its products there. "We think the technology has a fundamental value. Farmers are looking for alternatives to current products on offer," Chen said, adding that Origin would likely seek partners interested in licensing its traits to stack alongside others. The company will meet with potential partners at December's American Seed Trade Association conference in Chicago. But even with a local partner, the Chinese product would need U.S. regulatory approval, which could take years. A successful U.S. test could, however, boost confidence in Chinese technology and pave the way for Beijing to roll out its products. For Origin, it could mean a better valuation than the current $33.9 million. The company, which is looking to sell a majority stake in its conventional seed business, says it is undervalued due to the lack of a viable biotech market. "Our valuation on Nasdaq is much lower than the valuation of seed production companies in China. If we attract investment, our valuation will shoot up," said CFO Chen.


Teng C.,China Agricultural University | Yan Q.,China Agricultural University | Jiang Z.,China Agricultural University | Fan G.,China Agricultural University | Shi B.,Chinese Academy of Agricultural Sciences
Bioresource Technology | Year: 2010

The production of xylooligosaccharides (XOs) from corncobs was studied using a two-stage process based on a steam explosion pretreatment followed by enzymatic hydrolysis. Corncobs with different chip sizes were subjected to steam explosion under different experimental conditions of temperature and time, namely 188-204 °C for 2.5-7.5 min. The results indicate that corncobs were optimally steam exploded at 196 °C for 5 min, resulting in hemicellulose recovery of 22.8%. Especially, corncobs with large chip sizes (~100 mm) during steam explosion pretreatment were suitable to produce XOs. Furthermore, a thermostable xylanase from Paecilomyces themophila J18 was used to hydrolyze steam explosion liquor of corncobs (SELC) for the production of XOs. A maximum XOs yield of 28.6 g XOs/100 g xylan in corncobs was achieved and XOs syrup contained more than 90% of xylobiose and xylotriose when the hydrolysis was carried out under the optimized conditions (pH 7.0, 70 °C, 7.5 U mL -1 and 2.5 h). These results suggest that the process might be effective in production of XOs for industrial applications. © 2010 Elsevier Ltd. All rights reserved.


Zhang G.Q.,Chinese Academy of Agricultural Sciences | Dong X.F.,Chinese Academy of Agricultural Sciences | Wang Z.H.,Chinese Academy of Agricultural Sciences | Zhang Q.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Bioresource Technology | Year: 2010

A novel phytase was isolated from Aspergillus ficuum NTG-23 with a procedure involving ion-exchange chromatography on DEAE-cellulose, CM-cellulose and FPLC-gel filtration on Superdex 75. The protein exhibited a molecular mass of 65.5 kDa in gel filtration and SDS-PAGE. It possessed an optimal pH of 1.3 and an optimal temperature of 67 °C, and manifested a Km of 0.295 mM and a Vmax of 55.9 nmol (phosphate)/min. Phytase activity was not significantly affected by metal ions such as Ca2+, Mg2+, Mn2+, Zn2+, but was slightly stimulated in the presence of EDTA. The phytase was stable at 60 °C with no obvious loss of activity upon its incubation at 70 °C for 20 min. The enzyme exhibited a broad substrate selectivity and showed strong resistance toward pepsin and trypsin. The unique properties suggest that the phytase has the potential to be useful as an animal feed supplement. © 2010 Elsevier Ltd. All rights reserved.


You X.,Chinese Academy of Agricultural Sciences | You X.,China Agricultural University | Xing Z.,China Agricultural University | Liu F.,China Agricultural University | Zhang X.,China Agricultural University
Analytica Chimica Acta | Year: 2015

A novel air assisted liquid-liquid microextraction using the solidification of a floating organic droplet method (AALLME-SFO) was developed for the rapid and simple determination of seven fungicide residues in juice samples, using the gas chromatography with electron capture detector (GC-ECD). This method combines the advantages of AALLME and dispersive liquid-liquid microextraction based on the solidification of floating organic droplets (DLLME-SFO) for the first time. In this method, a low-density solvent with a melting point near room temperature was used as the extraction solvent, and the emulsion was rapidly formed by pulling in and pushing out the mixture of aqueous sample solution and extraction solvent for ten times repeatedly using a 10-mL glass syringe. After centrifugation, the extractant droplet could be easily collected from the top of the aqueous samples by solidifying it at a temperature lower than the melting point. Under the optimized conditions, good linearities with the correlation coefficients (γ) higher than 0.9959 were obtained and the limits of detection (LOD) varied between 0.02 and 0.25μgL-1. The proposed method was applied to determine the target fungicides in juice samples and acceptable recoveries ranged from 72.6% to 114.0% with the relative standard deviations (RSDs) of 2.3-13.0% were achieved. Compared with the conventional DLLME method, the newly proposed method will neither require a highly toxic chlorinated solvent for extraction nor an organic dispersive solvent in the application process; hence, it is more environmentally friendly. © 2015 Elsevier B.V.


Ye G.,International Rice Research Institute | Liang S.,International Rice Research Institute | Wan J.,Chinese Academy of Agricultural Sciences
Theoretical and Applied Genetics | Year: 2010

Protein content (PC) is an important component of rice nutritional quality. In order to better understand the genetic basis of this trait and increase related breeding efficiency, 21 single chromosome segment substitution (SCSS) lines grown in four sites over two growing seasons (regarded as eight environments) were used to associate PC with particular chromosome segments. Segments from 15 chromosomes were found to contain quantitative trait loci (QTLs) for PC in at least one environment. These included segments from chromosome 3 and 8, in which QTLs for PC had not previously been identified. The segment of chromosome 8 in CSSL-48 had the largest positive effect across all environments. The interaction between substitution and environment was highly significant. Some substitutions had large effects in one environment, but no effect in another (i.e. CSSL-08 and CSSL-17), while some substitutions significantly increased PC in one environment but decreased it in another (i.e. CSSL-41 and CSSL-43). By biplot and clustering analysis, the eight environments were grouped into two contrasting environment types, that is, Hainan and Jiangsu. The segment of chromosome 8 in CSSL-48 had PC-enhancing QTLs in both of the environment types. The segments in CSSL-34 had QTLs which increase PC in the Jiangsu environment but have no effect in the Hainan environment. For enhancing PC, CSSL-48 could be explored in breeding for wide adaptation across all environments, while CSSL-12, CSSL-14, CSSL-17, CSSL-41 and CSSL-43, and that in CSSL-34 could be explored in breeding for specific adaptation to the Hainan and Jiangsu environments, respectively. Near isogenic lines are under development to validate the QTLs with large effects in a range of genetic backgrounds relevant to Jiangsu and Hainan breeding programs. Secondary mapping populations are also being developed for further localising the responsible QTLs in CSSL-14, CSSL-34 and CSSL-48. © 2010 Springer-Verlag.


Wei J.,China Agricultural University | Hu X.,Chinese Academy of Agricultural Sciences | Yang J.,China Agricultural University | Yang W.,China Agricultural University
PLoS ONE | Year: 2012

The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. © 2012 Wei et al.


Zhang C.,China Agricultural University | Jia L.,Shandong Agricultural University | Wang S.,Chinese Academy of Agricultural Sciences | Qu J.,Chinese Academy of Agricultural Sciences | And 4 more authors.
Bioresource Technology | Year: 2010

Serratia spp. strain JC1 and JCN13, isolated from activated sludge, could degrade and utilize beta-cypermethrin (beta-CP) as the sole carbon and energy sources for growth in the minimal salt media (MSM). The two strains could effectively degrade beta-CP with total inocula biomass 0.1-0.3 g dry wt L-1, at 20-38 °C, pH 6-9, initial beta-CP 25-1000 mg L-1 and metabolize it by cleavage of ester and diphenyl ether to yield 3-phenoxybenzoic acid (3-PBA) and phenol, then completely mineralize it. Response surface methodology (RSM) was used to optimize degradation conditions. Under their own optimal degradation conditions, strain JC1 could degrade 92% beta-CP within 10 days and the degradation rate of strain JCN13 reached 89% within 4 days. Cell surface hydrophobicity (CSH) and biodegradation assays indicated that JCN13 has higher hydrophobicity and degradation ability than JC1, and it means the high hydrophobicity of strains could enhance the degradation of beta-CP. © 2010 Elsevier Ltd. All rights reserved.


Wan P.,Chinese Academy of Agricultural Sciences | Wan P.,Hubei Academy of Agricultural science | Huang Y.,Hubei University | Wu H.,Hubei Academy of Agricultural science | And 4 more authors.
PLoS ONE | Year: 2012

Transgenic crops producing insecticidal proteins from Bacillus thuringiensis (Bt) kill some key insect pests, but evolution of resistance by pests can reduce their efficacy. The main approach for delaying pest adaptation to Bt crops uses non-Bt host plants as "refuges" to increase survival of susceptible pests. To delay evolution of pest resistance to transgenic cotton producing Bt toxin Cry1Ac, the United States and some other countries have required refuges of non-Bt cotton, while farmers in China have relied on "natural" refuges of non-Bt host plants other than cotton. The "natural" refuge strategy focuses on cotton bollworm (Helicoverpa armigera), the primary target of Bt cotton in China that attacks many crops, but it does not apply to another major pest, pink bollworm (Pectinophora gossypiella), which feeds almost entirely on cotton in China. Here we report data showing field-evolved resistance to Cry1Ac by pink bollworm in the Yangtze River Valley of China. Laboratory bioassay data from 51 field-derived strains show that the susceptibility to Cry1Ac was significantly lower during 2008 to 2010 than 2005 to 2007. The percentage of field populations yielding one or more survivors at a diagnostic concentration of Cry1Ac increased from 0% in 2005-2007 to 56% in 2008-2010. However, the median survival at the diagnostic concentration was only 1.6% from 2008 to 2010 and failure of Bt cotton to control pink bollworm has not been reported in China. The early detection of resistance reported here may promote proactive countermeasures, such as a switch to transgenic cotton producing toxins distinct from Cry1A toxins, increased planting of non-Bt cotton, and integration of other management tactics together with Bt cotton. © 2012 Wan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Yuan Z.,Peking Union Medical College | Yuan Z.,Chinese Academy of Agricultural Sciences | Li J.,Chinese Academy of Agricultural Sciences | Zhang L.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Gene | Year: 2012

The main objective of this study was to investigate whether the bovine breast cancer 1 (BRCA1) gene was associated with mastitis resistance in Chinese commercial cattle. A total of 51 SNPs were screened from public data resources and DNA sequencing. Three SNPs (c.5682. G>C,c.26198. C>T and c.46126. G>T) were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and created restriction site PCR (CRS-PCR) methods and 21 combinations of these SNPs were observed. The single SNP and their genetic effects on somatic cell score (SCS) were evaluated and a significant association with SCS was found in c.46126. G>T. The mean SCS of individuals with genotype KK was significantly lower than those of genotypes KL and LL. The results of combined genotypes analysis of three SNPs showed that HHLLNN genotype with the highest SCS was easily for the mastitis susceptibility, whereas GGKKMM genotype with the lowest SCS was favorable for the mastitis resistance. The information provided in the present study will be very useful for improving mastitis resistance in dairy cattle by marker-assisted selection (MAS). © 2012.


Duan J.,Chinese Academy of Agricultural Sciences | Duan J.,China Agricultural University | Xia C.,Chinese Academy of Agricultural Sciences | Zhao G.,Chinese Academy of Agricultural Sciences | And 2 more authors.
BMC Genomics | Year: 2012

Background: Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq). The unprecedented sequencing depth provided by RNA-Seq makes it a powerful and cost-efficient method for transcriptome study, and it has been widely used in model organisms and non-model organisms to identify and quantify RNA. For non-model organisms lacking well-defined genomes, de novo assembly is typically required for downstream RNA-Seq analyses, including SNP discovery and identification of genes differentially expressed by phenotypes. Although RNA-Seq has been successfully used to sequence many non-model organisms, the results of de novo assembly from short reads can still be improved by using recent bioinformatic developments.Results: In this study, we used 212.6 million pair-end reads, which accounted for 16.2 Gb, to assemble the hexaploid wheat transcriptome. Two state-of-the-art assemblers, Trinity and Trans-ABySS, which use the single and multiple k-mer methods, respectively, were used, and the whole de novo assembly process was divided into the following four steps: pre-assembly, merging different samples, removal of redundancy and scaffolding. We documented every detail of these steps and how these steps influenced assembly performance to gain insight into transcriptome assembly from short reads. After optimization, the assembled transcripts were comparable to Sanger-derived ESTs in terms of both continuity and accuracy. We also provided considerable new wheat transcript data to the community.Conclusions: It is feasible to assemble the hexaploid wheat transcriptome from short reads. Special attention should be paid to dealing with multiple samples to balance the spectrum of expression levels and redundancy. To obtain an accurate overview of RNA profiling, removal of redundancy may be crucial in de novo assembly. © 2012 Duan et al.; licensee BioMed Central Ltd.


Fan F.,China Agricultural University | Fan F.,Chinese Academy of Agricultural Sciences | Zhang F.,China Agricultural University | Lu Y.,China Agricultural University
Soil Biology and Biochemistry | Year: 2011

Both plants and microbes influence soil nutrient cycling. However, the links between plants, microbes and nutrient cycling are poorly understood. In this study, we investigated how plant identity and interspecific competition influence soil nitrogen cycling and attempted to link plant identity and interspecific competition to community structures of bacterial and archaeal ammonia oxidizers based on terminal restriction fragment length polymorphism analysis (T-RFLP) of bacterial and archaeal ammonia monooxygenase (amoA) genes. Faba bean and maize monocultures and a faba bean/maize mixture were planted with two nitrogen levels (0 and 100mg Nkg -1 soil as urea). Soil mineral nitrogen, ammonia oxidizer function (potential nitrification activity, PNA) and community structures were measured 28 and 54 days after plant emergence. Faba bean and maize substantially differed in their influences on mineral nitrogen concentrations and PNA in rhizosphere soils. Soil mineral nitrogen and PNA in the rhizosphere soils of the faba bean/maize mixture were closer to those of the maize monoculture than to those of the faba bean monoculture. T-RFLP with restriction enzymes BsaJI and Hpy8I distinguished variations in bacterial and archaeal ammonia oxidizers community structure, respectively, and detected both between-cluster and within-cluster variations in bacterial ammonia oxidizers. T-RFLP data showed that nitrogen addition favored part of a Nitrosospira cluster 3b sequence type and suppressed part of a cluster Nitrosospira 3a sequence type of bacterial ammonia oxidizers, while it had no influence on the archaeal ammonia oxidizer community structure. Although multivariate analysis showed that the function and community structure of bacterial ammonia oxidizers were significantly correlated, plant species and interspecific competition did not significantly change the community structure of bacterial and archaeal ammonia oxidizers. These results indicate that plant species and interspecific competition regulate soil nitrogen cycling via a mechanism of other than alteration in the community structure of ammonia oxidizers as investigated by DNA based methods. © 2010 Elsevier Ltd.


Song A.,Chinese Academy of Agricultural Sciences | Li P.,Chinese Academy of Agricultural Sciences | Li Z.,Chinese Academy of Agricultural Sciences | Fan F.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Plant and Soil | Year: 2011

The objective of this study is to elucidate the roles of silicon (Si) in enhancing tolerance to excess zinc (Zn) in two contrasting rice (Oryza sativa L.) cultivars: i. e. cv. TY-167 (Zn-resistant) and cv. FYY-326 (Zn-sensitive). Root morphology, antioxidant defense reactions and lipid peroxidation, and histochemical staining were examined in rice plants grown in the nutrient solutions with normal (0.15 μM) and high (2 mM) Zn supply, without or with 1.5 mM Si. Significant inhibitory effects of high Zn treatment on plant growth were observed. Total root length (TRL), total root surface area (TRSA) and total root tip amount (TRTA) of both cultivars were decreased significantly in plants treated with high Zn, whereas these root parameters were significantly increased when Zn-stressed plants were supplied with 1. 5 mM Si. Supply of Si also significantly decreased Zn concentration in shoots of both cultivars, indicating lower root-to-shoot translocation of Zn. Moreover, superoxide dismutase (SOD), catalase (CAT), and asorbate peroxidase (APX) activities were increased, whereas malondialdehyde (MDA) and hydrogen peroxide (H2O2) concentrations were decreased in Si-supplied plants of both Zn-sensitive and Zn-resistant rice cultivars exposed to Zn stress. These alleviative effects of Si, further confirmed by the histochemical staining methods, were more prominent in the Zn-resistant cultivar than in the Zn-sensitive one. Taken together, all these results suggest that Si-mediated alleviation of Zn toxicity is mainly attributed to Si-mediated antioxidant defense capacity and membrane integrity. The possible role of Si in reduction of root-to-shoot translocation of Zn can also be considered. © 2011 Springer Science+Business Media B.V.


Yang A.,CAS Institute of Botany | Li Y.,Chinese Academy of Agricultural Sciences | Xu Y.,CAS Institute of Botany | Zhang W.-H.,CAS Institute of Botany | Zhang W.-H.,Chinese Academy of Sciences
Journal of Experimental Botany | Year: 2013

Iron (Fe) is one of the essential mineral elements for plant growth and development. Acquisition of Fe by plants is mediated by a complex network involving Fe mobilization, uptake by root cells, and transport within plants. Here, we evaluated the role of a previously clarified gene encoding a receptor-like protein from rice, OsRMC, in the regulation of Fe acquisition by comparing Fe concentration, biomass, and expression patterns of genes associated with Fe mobilization and transport in wild-type (WT) rice with those in OsRMC overexpression and RNA interference (RNAi) knockdown transgenic rice plants. Expression of OsRMC was upregulated in both shoots and roots upon exposure of WT to Fe-deficient medium. Expression levels of OsRMC were positively correlated with Fe concentration in rice plants under both Fe-sufficient and Fe-deficient conditions such that overexpression and RNAi lines had higher and lower Fe concentration in both roots and shoots than WT plants, respectively. Moreover, overexpression of OsRMC conferred greater accumulation of Fe in mature seeds under Fe-sufficient conditions. OsRMC may also play a role in regulation of Fe deficiency-induced changes in root growth, as evidenced by greater and smaller root systems of OsRMC overexpression lines and RNAi lines than WT under Fe-deficient conditions, respectively. Several Fe deficiency-responsive genes including OsDMAS1, OsNAS1, OsNAS2, OsNAAT1, OsIRT1, OsYSL15, and OsIRO2 were up- and downregulated in OsRMC-overexpressing and RNAi plants compared with WT rice plants. These novel findings highlight an important role of OsRMC played in mediation of Fe acquisition and root growth in rice, particularly under Fe-deficient conditions. © The Author 2013. Published by Oxford University Press on behalf of the Society for Experimental Biology.


Zhang N.,Northeast Normal University | Guo R.,Chinese Academy of Agricultural Sciences | Song P.,Northeast Normal University | Song P.,CAS Institute of Botany | And 2 more authors.
Soil Biology and Biochemistry | Year: 2013

Songnen Meadow Steppe, which is in northeast China, is increasingly affected by global warming and incremental increases in atmospheric nitrogen deposition. However, the responses of nitrogen (N) and phosphorus (P) in steppe soil, and of the coupling mechanism between them, to the dual effects of global warming and N deposition are still unknown. In this study, the effects of simulated atmospheric warming and N deposition on N and P in Songnen steppe soil, as well as on the coupling between N and P, were examined under in situ conditions. Infrared heaters were used to elevate soil temperature by approximately 1.7°C since 2006. N additions were treated once a year with aqueous ammonium nitrate at a rate of 10gm-2a-1. During the four-year study, addition of N increased the amount of total N, and available N, as well as the rate of N mineralization in the soil. Moreover, the amounts of total P and available P in the soil were considerably reduced. Thus, the N:P ratio increased, and the coupling between N and P decreased. Similar values for the N:P ratio were obtained for the addition of N by itself and for the combination of warming and addition of N, which indicates that a small amount of soil warming in Songnen Meadow Steppe would not have a substantial effect on the ratio. With the growth of China's industrialization, N deposition continues to increase. The study area of Songnen Meadow Steppe, and northeast China in general, are characterized by widespread distribution of saline alkali soil. Therefore, the finding of increased P limitation in the soil of Songnen Meadow Steppe has major implications for ecosystems in northeast China. Reasonable regulation and management of meadow soil nutrients will be of great importance in increasing soil productivity and promoting sustainable use of grassland ecosystems. © 2013 Elsevier Ltd.


Li J.,China Agricultural University | Li B.,Chinese Academy of Agricultural Sciences | Wendlandt S.,Institute of Farm Animal Genetics | Schwarz S.,Institute of Farm Animal Genetics | And 4 more authors.
Journal of Antimicrobial Chemotherapy | Year: 2014

Objectives: To investigate the genetic basis of pleuromutilin resistance in coagulase-negative staphylococci of porcine origin that do not carry known pleuromutilin resistance genes and to determine the localization and genetic environment of the identified resistance gene. Methods: Plasmid DNA of two pleuromutilin-resistant Staphylococcus cohnii and Staphylococcus simulans isolates was transformed into Staphylococcus aureus RN4220. The identified resistance plasmids were sequenced completely. The candidate gene for pleuromutilin resistance was cloned into shuttle vector pAM401. S. aureus RN4220 transformants carrying this recombinant shuttle vector were tested for their MICs. Results: S. cohnii isolate SA-7 and S. simulans isolate SSI1 carried the same plasmid of 5584 bp, designated pSA-7. A variant of the vga(E) gene was detected, which encodes a 524 amino acid ATP-binding cassette protein. The variant gene shared 85.7% nucleotide sequence identity and the variant protein 85.3% amino acid sequence identity with the original vga(E) gene and Vga(E) protein, respectively. The Vga(E) variant conferred cross-resistance to pleuromutilins, lincosamides and streptogramin A antibiotics. Plasmid pSA-7 showed an organization similar to that of the apmA-carrying plasmid pKKS49 from methicillin-resistant S. aureus and the dfrK-carrying plasmid pKKS966 from Staphylococcus hyicus. Sequence comparisons suggested that recombination events may have played a role in the acquisition of this vga(E) variant. Conclusions: A novel vga(E) gene variant was identified, which was located on a small plasmid and was not associated with the transposon Tn6133 [in contrast to the original vga(E) gene]. The plasmid location may enable its further dissemination to other staphylococci and possibly also to other bacteria. © The Author 2013. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved.


Wang Y.,China Agricultural University | Li D.,China Agricultural University | Wang L.-J.,China Agricultural University | Li S.-J.,Chinese Academy of Agricultural Sciences | Adhikari B.,University of Ballarat
Carbohydrate Polymers | Year: 2010

The effects of different drying methods (spray drying, freeze drying, vacuum drying, oven drying at 80 and 105 °C, and ethanol precipitation) on the color and functional properties such as zeta potential, foaming, gelling, and emulsion properties of flaxseed gum were studied. Spray dried powders had the lightest color among all the powders. The powder obtained from ethanol precipitation had the lowest zeta potential and the resultant emulsion was in the most stable state. The ethanol precipitated powders had the best emulsion capacity and stability, better than even the untreated samples. The oven dried (105 °C) powders had the best foaming capacity and the foam stability, while the 80 °C oven dried powder had highest gel strength among all the dried samples. These results will be helpful in selecting suitable drying method depending on the functional properties of the flaxseed gum powders. © 2010 Elsevier Ltd. All rights reserved.


Zhou S.,Chinese Academy of Agricultural Sciences | Liu X.,Anhui University of Traditional Chinese Medicine | Guo Y.,Peking Union Medical College | Wang Q.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Carbohydrate Polymers | Year: 2010

Differences in immunoregulatory activities of arabinoxylans (AXs) from wheat bran extracted by alkaline- and enzyme-based methods are unknown. We extracted AX from wheat bran by the 2 procedures. Chemical analysis revealed that alkaline-extracted AX (AXA) contained a lower amount of protein (4.10%) than enzyme-extracted AX (AXE, 9.85%) and no ferulic acid (as compared with 43.5 mg/100 g in AXE). AXA consisted of a highly substituted population with a ratio of arabinose to xylose of 0.83 (AXE: 0.56), meanwhile the weight-average molecular weight of AXA (3.517 × 105 Da) was about 10 times that of AXE (3.252 × 104 Da). Both AXA and AXE had potent stimulating effects on innate and acquired immune responses on oral administration in female BALB/c mice. AXE showed higher macrophage phagocytosis and delayed hypersensitivity reaction than did AXA, with no significant differences in enhancing lymphocyte proliferation. Whether extracted by alkaline- or enzyme-aided methods, the obtained AXs could be explored as potent natural immunomodulators. © 2010 Elsevier Ltd. All rights reserved.


Wang S.,Chinese Academy of Agricultural Sciences | Wang S.,Tsinghua University | Zhang C.,China Agricultural University | Yan Y.,Chinese Academy of Agricultural Sciences
Biodegradation | Year: 2012

Strain Yw12, isolated from activated sludge, could completely degrade and utilize methyl parathion as the sole carbon, phosphorus and energy sources for growth in the basic salt media. It could also completely degrade and utilize p-nitrophenol as the sole carbon and energy sources for growth in the minimal salt media. Phenotypic features, physiological and biochemical characteristics, and phylogenetic analysis of 16S rRNA sequence showed that this strain belongs to the genus of Agrobacterium sp. Response surface methodology was used to optimize degradation conditions. Under its optimal degradation conditions, 50 mg l -1 MP was completely degraded within 2 h by strain Yw12 and the degradation product PNP was also completely degraded within 6 h. Furthermore, strain Yw12 could also degrade phoxim, methamidophos, chlorpyrifos, carbofuran, deltamethrin and atrazine when provided as the sole carbon and energy sources. Enzymatic analysis revealed that the MP degrading enzyme of strain Yw12 is an intracellular enzyme and is expressed constitutively. These results indicated that strain Yw12 might be used as a potential and effective organophosphate pesticides degrader for bioremediation of contaminated sites. © 2011 Springer Science+Business Media B.V.


Fang F.,China Agricultural University | Fang F.,Chinese Academy of Agricultural Sciences | Huang W.-D.,China Agricultural University
European Food Research and Technology | Year: 2013

Salicylic acid (SA) is a key signaling molecule involved in plant defense responses, former work indicated its regulating effects on some defense genes in plant materials, while the relationship between SA and flavonol biosynthesis during grape berry development remains obscure. By using the techniques of in vivo incubation of the grape berry (Vitis vinifera L. cv. Cabernet Sauvignon) tissues in SA-contained medium, the effects of exogenous SA on flavonol biosynthesis in three key phases (the rapid growth phase, the lag phase of growth and the veraison) of grape berry development were investigated in this work. The results showed that exogenous SA could modulate flavonol biosynthesis, but the modulation effects differed greatly in different phases of grape berry development. During the lag phase of growth and veraison, exogenous SA activated flavonol synthase (FLS) activities and induced the synthesis of new FLS protein. The activation of FLS activity could be blocked by protein synthesis inhibitor cycloheximide and mRNA transcription inhibitor actinomycin D during the lag phase of growth, but only actinomycin D inhibited exogenous SA at veraison. In accordance with the changes of FLS activities and amounts, total flavonol content was found to be modulated accordingly. But the contents of free flavonols had no correlations with SA in the rapid growth phase and veraison. The results suggested that exogenous SA could modulate flavonol biosynthesis of grape berries by activating FLS activity at specific developing phases, while the accumulation of flavonol compounds might be involved in the development of acquired resistance mediated by SA. © 2013 Springer-Verlag Berlin Heidelberg.


Fan S.,Peking Union Medical College | Fan S.,Military Veterinary Research Institute of Academy of Military Medical science | Zhou L.,East China Normal University | Wu D.,Shanghai Municipal Agency of Wildlife Conservation | And 5 more authors.
Influenza and other Respiratory Viruses | Year: 2014

Migrating wild birds are considered natural reservoirs of influenza viruses and serve as a potential source of novel influenza strains in humans and livestock. During routine avian influenza surveillance conducted in eastern China, a novel H5N8 (SH-9) reassortant influenza virus was isolated from a mallard duck in China. blast analysis revealed that the HA, NA, PB1, PA, NP, and M segments of SH-9 were most closely related to the corresponding segments of A/duck/Jiangsu/k1203/2010 (H5N8). The SH-9 virus preferentially recognized avian-like influenza virus receptors and was highly pathogenic in mice. Our results suggest that wild birds could acquire the H5N8 virus from breeding ducks and spread the virus via migratory bird flyways. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.


Sun C.,China Agricultural University | Sun C.,Chinese Academy of Agricultural Sciences | Ren L.,China Agricultural University
Hydrological Processes | Year: 2014

Haihe plain is an important food production area in China, facing an increasing water shortage. The water used for agriculture accounts for about 70% of total water resources. Thus, it is critical to optimize the irrigation scheduling for saving water and increasing crop water productivity (CWP). This study first simulated crop yield and CWP for winter wheat and summer maize in historical scenario during 1961-2005 for Haihe plain using previously well-established Soil and Water Assessment Tool model. Then, scenarios under historical irrigation (scenario 1) and sufficient irrigation (scenario 2) were, respectively, simulated both with sufficient fertilizer. The crop yield in scenario 2 was considered as the potential crop yield. The optimal irrigation scheduling with sufficient fertilizer (scenario 3) was explored by iteratively adjusting irrigation scheduling based on the scenario 1 and previous studies related to water stress on crop growth. Results showed that net irrigation amount was, respectively, reduced 23.1% and 18.8% in scenario 3 for winter wheat and summer maize when compared with scenario 1. The CWP was 12.1% and 8.2% higher with very slight change of crop yield. Using optimal irrigation scheduling could save 8.8×108 m3 irrigation water and reduce about 16.3% groundwater over-exploitation in winter wheat growth period. The corresponding yield was 18.5% and 12.9% less than potential yield for winter wheat and summer maize but using less irrigation water. Therefore, it could be considered that the optimal irrigation was reasonable, which provided beneficial suggestions for increasing efficiency of agricultural water use with sustainable crop yield in Haihe plain. © 2013 John Wiley & Sons, Ltd.


Li Z.,Beijing Museum of Natural History | Wang N.,Chinese Academy of Agricultural Sciences | Yang D.,China Agricultural University
Zootaxa | Year: 2014

The species of the genus Hybos Meigen from Northwest China are reviewed. The following five species are described as new to science: Hybos elongatus sp. nov., H. flavitibialis sp. nov., H. projectus sp. nov., H. qinlingensis sp. nov., and H. xii sp. nov. A key to the 17 species of the genus Hybos from Northwest China is provided. Copyright © 2014 Magnolia Press.


Sun Y.-P.,China Agricultural University | Zhao L.-J.,China Agricultural University | Sun L.,Chinese Academy of Agricultural Sciences | Zhang S.-G.,CAS Institute of Zoology | Ban L.-P.,China Agricultural University
Chemical Senses | Year: 2013

The antennal sensilla of Myzus persicae were mapped using scanning and transmission electron microscopy. Placoid sensilla and coeloconic sensilla were found on the 6th segments, whereas 2 types of trichoid sensilla were present all through the length of the antenna. A single sensillum placoideum was located on the 5th segment, whereas alate aphids also presented placoid sensilla on the 3rd antennal segment. Immunocytochemical localization of odorant-binding proteins (OBPs) was performed on ultrathin sections of antennal chemosensilla. The antiserum against OBP7 intensively labeled all placoid sensilla from both primary and secondary rhinaria, with gold granules concentrated in the lymph surrounding the dendrite. OBP6 and OBP3 could also be detected in placoid sensilla, but less strongly than OBP7. Barely significant reaction or no reaction was observed with antibodies against OBP8. © The Author 2012. Published by Oxford University Press. All rights reserved.


Li D.,Liaocheng University | Chen L.,Liaocheng University | Zhang X.,Chinese Academy of Fishery Sciences | Ye N.,Chinese Academy of Fishery Sciences | Xing F.,Chinese Academy of Agricultural Sciences
Biomass and Bioenergy | Year: 2011

Marine algae have great potential as a third generation biofuel feedstock. The pyrolytic and kinetic characteristics of three kinds of red algae (Pophyra yezoensis, Plocamium telfairiae Harv and Corallina pilulifera) were studied at heating rates of 10, 30 and 50°Cmin-1 under an inert atmosphere. The most probable mechanism function and activation energy pre-exponential factors were calculated by the Popescu, FWO and KAS methods. Three stages appeared during pyrolysis: moisture evaporation, primary devolatilization and residual decomposition. Significant differences in the average activation energy, thermal stability, final residuals and reaction rates of the algae samples were observed. Stage II of the samples could be described by the Avramic-Erofeev equation. The average activation energy of all samples was similar when calculated by different methods. Kinetic compensation effects of the pre-exponential factors and activation energy were also observed. © 2011 Elsevier Ltd.


Zhang B.,CAS Institute of Botany | Zhang B.,Chinese Academy of Agricultural Sciences
Plant Gene | Year: 2015

Glycolysis is an indispensable biochemical pathway in both animals and plants and is required for almost all physiological processes. Previous studies have shown that glycolysis plays an important role in cotton fiber development process. However, the detailed mechanism by which glycolysis is regulated is still unclear. In this study, a total of 163 genes encoding different isoforms of 20 enzymes involved in the catalysis of glycolysis and fermentation were identified in diploid Asian cotton (Gossypium arboreum). These enzymes have unique subcellular localizations and phylogenies. Among these 163 genes, 125 were expressed in Asian cotton plants, but only 51 were highly expressed in elongating Asian cotton fibers. Cis-regulatory elements involved in phytohormone responses were identified in these 51 genes, suggesting that glycolysis might be regulated by phytohormones. Furthermore, the expression of fermentation-related genes and the wide distribution of cis-regulatory elements that promote anaerobic induction strongly suggested the involvement of anaerobic glycolysis in cotton fiber development, especially during the elongation process. © 2015 The Author. Published by Elsevier Inc.


Zhou L.,Tsinghua University | Xu L.,Chinese Academy of Agricultural Sciences | Ye J.,PLA Fourth Military Medical University | Li D.,Tsinghua University | And 6 more authors.
Hepatology | Year: 2012

High levels of dietary saturated fat have been closely associated with the development of hepatic steatosis, but the factors that mediate this process remain elusive. Here, we observed that the level of cell death-inducing DNA fragmentation factor-alpha-like effector a (Cidea) expression was highly correlated with the severity of hepatic steatosis in humans. Overexpression of Cidea in mouse liver resulted in increased hepatic lipid accumulation and the formation of large lipid droplets (LDs). In contrast, mice with a Cidea deficiency had decreased lipid accumulation and alleviated hepatic steatosis when they received a high-fat-diet feeding or in ob/ob mice. Furthermore, the knockdown of Cidea in livers of ob/ob mice resulted in significantly reduced hepatic lipid accumulation and smaller LDs. Importantly, we observed that Cidea expression in hepatocytes was specifically induced by saturated fatty acids (FAs), and such induction was reduced when sterol response element-binding protein (SREBP)1c was knocked down. In contrast, the overexpression of SREBP1c restored the saturated FA-induced expression of Cidea. In addition, we observed that the stability of Cidea protein in hepatocytes increased significantly in response to treatment with FAs. Conclusion: Cidea plays critical roles in promoting hepatic lipid accumulation and in the development of hepatic steatosis by acting as a sensor that responds to diets that contain FAs. © 2012 American Association for the Study of Liver Diseases.


Liu Y.,Chinese Academy of Agricultural Sciences | Shen D.,China Agricultural University | Zhou F.,China Agricultural University | Wang G.,Chinese Academy of Agricultural Sciences | An C.,China Agricultural University
PLoS ONE | Year: 2014

Background: Timmunity-related genes inhe Aentomopathogenic funginia furnseq analysisée)) is one of the most serious corn pests in Asia. Control of this pest with entomopathogenic fungus Beauveria bassiana has been proposed. However, the molecular mechanisms involved in the interactions between O. furnacalis and B. bassiana are unclear, especially under the conditions that the genomic information of O. furnacalis is currently unavailable. So we sequenced and characterized the transcriptome of O. furnacalis larvae infected by B. bassiana with special emphasis on immunity-related genes. Methodology/Principal Findings: Illumina Hiseq2000 was used to sequence 4.64 and 4.72 Gb of the transcriptome from water-injected and B. bassiana-injected O. furnacalis larvae, respectively. De novo assembly generated 62,382 unigenes with mean length of 729 nt. All unigenes were searched against Nt, Nr, Swiss-Prot, COG, and KEGG databases for annotations using BLASTN or BLASTX algorithm with an E-value cut-off of 1025. A total of 35,700 (57.2%) unigenes were annotated to at least one database. Pairwise comparisons resulted in 13,890 differentially expressed genes, with 5,843 up-regulated and 8,047 down-regulated. Based on sequence similarity to homologs known to participate in immune responses, we totally identified 190 potential immunity-related unigenes. They encode 45 pattern recognition proteins, 33 modulation proteins involved in the prophenoloxidase activation cascade, 46 signal transduction molecules, and 66 immune responsive effectors, respectively. The obtained transcriptome contains putative orthologs for nearly all components of the Toll, Imd, and JAK/STAT pathways. We randomly selected 24 immunity-related unigenes and investigated their expression profiles using quantitative RT-PCR assay. The results revealed variant expression patterns in response to the infection of B. bassiana. Conclusions/Significance: This study provides the comprehensive sequence resource and expression profiles of the immunity-related genes of O. furnacalis. The obtained data gives an insight into better understanding the molecular mechanisms of innate immune processes in O. furnacalis larvae against B. bassiana. © 2014 Liu et al.


Wang P.,Huazhong Agricultural University | Xing Y.,Huazhong Agricultural University | Li Z.,Chinese Academy of Agricultural Sciences | Li Z.,International Rice Research Institute | Yu S.,Huazhong Agricultural University
Molecular Breeding | Year: 2012

To facilitate marker-assisted transfer of desirable genes for improvement of yield traits, we used a set of backcross recombinant inbred lines (BRIL) derived from two elite parental lines, 'Zhenshan97' and '93-11', to resolve a quantitative trait loci (QTL) cluster for heading date and yield-related traits in rice. Four main-effect QTL (qHD6. 1, qHD6. 2, qHD7, and qHD8) and four epistatic QTL affecting heading date in the BRIL were detected in two experimental trials. The major QTL (qHD8) was confirmed in three heterogeneous inbred families (HIF) that segregated for this target region, and narrowed down to a 20-kb segment in a large HIF-derived population. qHD8 was found to interact with qHD7 and had a pleiotropic effect responsible for heading date and yield components. To test usability of the identified QTL in rice improvement, we further developed near-isogenic lines (NIL) containing one or more target genes by marker-assisted transfer of '93-11' alleles at qHD8, qHD7, and qHD6. 1, and the GS3 gene for grain size into 'Zhenshan97'. The pyramid line NIL(qHD8 + GS3) had higher yield potential, longer grains, and a more suitable heading date than 'Zhenshan97'. Comparison of the NIL showed existence of epistasis between alleles at different loci and background effect on qHD8, which are very important for pyramiding of desirable alleles at the target QTL. These results will be particularly useful not only to understand the genetic basis of yield-related traits but also to improve the efficiency of marker-assisted selection for favorable loci in rice breeding programs. © 2011 Springer Science+Business Media B.V.


Han Y.,China Agricultural University | Han Y.,CAS Institute of Genetics and Developmental Biology | Zhang Z.,Chinese Academy of Agricultural Sciences | Huang S.,Chinese Academy of Agricultural Sciences | Jin W.,China Agricultural University
BMC Genetics | Year: 2011

Background: Integration of molecular, genetic and cytological maps is still a challenge for most plant species. Recent progress in molecular and cytogenetic studies created a basis for developing integrated maps in cucumber (Cucumis sativus L.).Results: In this study, eleven fosmid clones and three plasmids containing 45S rDNA, the centromeric satellite repeat Type III and the pericentriomeric repeat CsRP1 sequences respectively were hybridized to cucumber metaphase chromosomes to assign their cytological location on chromosome 2. Moreover, an integrated molecular cytogenetic map of cucumber chromosomes 2 was constructed by fluorescence in situ hybridization (FISH) mapping of 11 fosmid clones together with the cucumber centromere-specific Type III sequence on meiotic pachytene chromosomes. The cytogenetic map was fully integrated with genetic linkage map since each fosmid clone was anchored by a genetically mapped simple sequence repeat marker (SSR). The relationship between the genetic and physical distances along chromosome was analyzed.Conclusions: Recombination was not evenly distributed along the physical length of chromosome 2. Suppression of recombination was found in centromeric and pericentromeric regions. Our results also indicated that the molecular markers composing the linkage map for chromosome 2 provided excellent coverage of the chromosome. © 2011 Han et al; licensee BioMed Central Ltd.


Xu C.,Cold Spring Harbor Laboratory | Liberatore K.L.,Cold Spring Harbor Laboratory | Liberatore K.L.,U.S. Department of Agriculture | Macalister C.A.,Cold Spring Harbor Laboratory | And 15 more authors.
Nature Genetics | Year: 2015

Shoot meristems of plants are composed of stem cells that are continuously replenished through a classical feedback circuit involving the homeobox WUSCHEL (WUS) gene and the CLAVATA (CLV) gene signaling pathway. In CLV signaling, the CLV1 receptor complex is bound by CLV3, a secreted peptide modified with sugars. However, the pathway responsible for modifying CLV3 and its relevance for CLV signaling are unknown. Here we show that tomato inflorescence branching mutants with extra flower and fruit organs due to enlarged meristems are defective in arabinosyltransferase genes. The most extreme mutant is disrupted in a hydroxyproline O-arabinosyltransferase and can be rescued with arabinosylated CLV3. Weaker mutants are defective in arabinosyltransferases that extend arabinose chains, indicating that CLV3 must be fully arabinosylated to maintain meristem size. Finally, we show that a mutation in CLV3 increased fruit size during domestication. Our findings uncover a new layer of complexity in the control of plant stem cell proliferation. © 2015 Nature America, Inc. All rights reserved.


Wu T.,China Agricultural University | Zhang H.-T.,Chinese Academy of Agricultural Sciences | Wang Y.,China Agricultural University | Jia W.-S.,China Agricultural University | And 3 more authors.
Journal of Experimental Botany | Year: 2012

Iron is a critical cofactor for a number of metalloenzymes involved in respiration and photosynthesis, but plants often suffer from iron deficiency due to limited supplies of soluble iron in the soil. Iron deficiency induces a series of adaptive responses in various plant species, but the mechanisms by which they are triggered remain largely unknown. Using pH imaging and hormone localization techniques, it has been demonstrated here that root Fe(III) reductase activity and proton extrusion upon iron deficiency are up-regulated by systemic auxin signalling in a Fe-efficient woody plant, Malus xiaojinensis. Split-root experiments demonstrated that Fe-deprivation in a portion of the root system induced a dramatic increase in Fe(III) reductase activity and proton extrusion in the Fe-supplied portion, suggesting that the iron deficiency responses were mediated by a systemic signalling. Reciprocal grafting experiments of M. xiaojinensis with Malus baccata, a plant with no capability to produce the corresponding responses, indicate that the initiation of the systemic signalling is likely to be determined by roots rather than shoots. Iron deficiency induced a substantial increase in the IAA content in the shoot apex and supplying exogenous IAA analogues (NAA) to the shoot apex could mimic the iron deficiency to trigger the corresponding responses. Conversely, preventing IAA transport from shoot to roots blocked the iron deficiency responses. These results strongly indicate that the iron deficiency-induced physiological responses are mediated by systemic auxin signalling. © 2011 The Author.


Ringo E.,University of Tromsø | Zhou Z.,Chinese Academy of Agricultural Sciences | Olsen R.E.,Norwegian Institute of Marine Research | Song S.K.,Handong Global University
Aquaculture Nutrition | Year: 2012

Chitin consists of β-1,4-linked N-acetylglucosamine residues and is estimated as the second most abundant biomass in the world after cellulose. However, relatively little chitin is utilized as a material for industrial, agricultural and medical applications and aquacultural purposes. Chitin may be useful as a constitutive material in formulated fish feed, and the interesting effects in fish merit further evaluation. There is evidence that fish and aquatic animals harbour a gut bacterial community that is distinctly different from that reported in the surrounding habitat or in the diet. Thus, the gut environment provides a specific niche, and bacterial activity in the gut is not merely a continuum of that observed in the environment. Today, it is well accepted that the gut microbiota in fish are modulated by dietary manipulations. But to what extent can dietary chitin and krill (chitin-rich) modulate the intestinal microbiota of fish and how do these dietary components affect the immune system? These questions will be discussed in the present review. © 2012 Blackwell Publishing Ltd.


Zheng J.,China Agricultural University | Lang Y.,China Agricultural University | Zhang Q.,China Agricultural University | Cui D.,China Agricultural University | And 8 more authors.
Genes and Development | Year: 2015

The central region of MDM2 is critical for p53 activation and tumor suppression. Upon ribosomal stress, this region is bound by ribosomal proteins, particularly ribosomal protein L11 (RPL11), leading to MDM2 inactivation and subsequent p53 activation. Here, we solved the complex structure of human MDM2-RPL11 at 2.4 Å. MDM2 extensively interacts with RPL11 through an acidic domain and two zinc fingers. Formation of the MDM2-RPL11 complex induces substantial conformational changes in both proteins. RPL11, unable to bind MDM2 mutants, fails to induce the activation of p53 in cells. MDM2 mimics 28S rRNA binding to RPL11. The C4 zinc finger determines RPL11 binding to MDM2 but not its homolog, MDMX. Our results highlight the essential role of the RPL11-MDM2 interaction in p53 activation and tumor suppression and provide a structural basis for potential new anti-tumor drug development. © 2015 Zheng et al.


Chen L.,China Agricultural University | Xing L.,Chinese Academy of Agricultural Sciences | Han L.,China Agricultural University
Waste Management | Year: 2010

Agro-residue is one of the important biomass resources in China and its efficient utilization is crucial for providing bio-energy, releasing risk of environmental pollution, and enhancing rural incomes. Densification is one of the important utilization routes of agro-residues. The objective of this paper is to explore the development of agro-residue densified fuel in China based on energetics analysis. The energetical property and energy potential of main agro-residues in China were firstly analyzed and then the development of agro-residue densified fuel in every region was evaluated based on energetics analysis. The results show that the main agro-residues in China are good feedstocks as densified fuel and they constitute enormous energy potential for developing densified fuel. However, the situation of every region should be considered for the development of agro-residue densified fuel. The primary energy embodied per unit of useful energy indicates that most of the regions in China are suitable for developing agro-residue densified fuel as it is energetically advantageous compared with coal, whereas only about 25% of regions near coal production locations are not suitable as they are less energetically advantageous. © 2009 Elsevier Ltd.


Xu X.,Chinese Academy of Agricultural Sciences | Xu X.,University of Aarhus | Enkegaard A.,University of Aarhus
Journal of Insect Science | Year: 2010

The prey preference of polyphagous predators plays an important role in suppressing different species of pest insects. In this study the prey preference of the predatory mite, Amblyseius swirskii (Athias-Henriot) (Acari: Phytoseiidae) was examined between nymphs of the twospotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae) and first instar larvae of the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), as well as between active and chrysalis spider mite protonymphs and active and chrysalis spider mite deutonymphs. The study was done in the laboratory on bean leaf discs at 25 ± 1° C and 70 ± 5% RH. Amblyseius swirskii had a clear preference for thrips compared to both spider mite protonymphs and deutonymphs. About twice as many thrips as spider mites were consumed. Amblyseius swirskii did not show a preference between active and chrysalis stages of spider mites.


Xu X.,China Agricultural University | Xu X.,Chinese Academy of Agricultural Sciences | Gao Y.,China Agricultural University | Sun L.,Chinese Academy of Agricultural Sciences
Food Research International | Year: 2012

Bee pollen is an abundant source of high-quality triterpene alcohols and has been used as a phytomedicine treating benign prostatic hyperplasia. Free and esterified triterpene alcohols were extracted by n-hexane and separated by column chromatography. Comprehensive analysis of triterpene alcohols in bee pollen from six botanical origins in China was carried out by gas chromatography-mass spectrometry/flame ionization detector (GC-MS/FID). Six 4-desmethylsterols, one 4-monomethylsterol, four 4, 4-dimethylsterols and another three triterpene alcohols were reported for the first time in the bee pollen. Significant difference (P<0.05) was found in the contents of free and esterified triterpene alcohols between bee-collected pollens from the selected plant origins. The total triterpene alcohol levels in bee pollen oil fractions have been found to vary between 2.6. g/100. g and 20.4. g/100. g oil. Triterpene alcohols in the bee pollen oils were dominated by steryl esters (>67%). Concurrently, esterified triterpene alcohols in lotus bee pollen oil fraction predominantly consisted of large amount of cycloartenol (11.2. g/100. g oil). © 2012 Elsevier Ltd.


Huang G.,China Agricultural University | Wang X.,Chinese Academy of Agricultural Sciences | Han L.,China Agricultural University
Bioresource Technology | Year: 2011

Regression equations which relate livestock and poultry manure nutrient content to its several physicochemical properties have been reported by previous researchers. This study explores the feasibility and efficiency to determine the nutrients (TN; TP; TK; Cu and Zn) in chicken manure during composting using physicochemical properties (pH, EC and DM), and compares the performances of regression equations in this study with those in the literature. The results show that DM is the best predictor to construct the single linear regressions for all the nutrients (R2≥0.84, p<0.001). In addition, the multiple linear regression equations based on DM and pH are all notable. These findings show the potential of physicochemical models for TN, TP, TK, Cu and Zn with more convenience and rapidness, but further research is needed to develop better models with higher accuracy for the above and other more nutrients. © 2010 Elsevier Ltd.


Zhang C.,China Agricultural University | Wang S.,Tsinghua University | Yan Y.,Chinese Academy of Agricultural Sciences
Bioresource Technology | Year: 2011

Pseudomonas aeruginosa CH7, isolated from activated sludge, was able not only to isomerize and degrade beta-cypermethrin but also to utilize it as the sole source of carbon and energy for growth and produce biosurfactant. The strain effectively degraded beta-cypermethrin with inocula biomass of 0.1-0.2gL-1 at 25-35°C, pH 6-9, and a final concentration of beta-cypermethrin 25-900mgL-1. Via response surface methodology analysis, we found the optimal condition was 29.4°C, pH 7.0, and inocula biomass of 0.15gL-1; under these conditions, about 90% of the beta-cypermethrin could be degraded within 12days. Noticeably, biosurfactant was detected in the MSM culture of strain CH7, suggesting that the biosurfactant (rhamnolipid) could potentially enhance the degradation of beta-cypermethrin by promoting the dissolution, adsorption, and absorption of the hydrophobic compounds. Therefore, CH7 may serve as a promising strain in the bioremediation of wastewater and soil polluted by beta-cypermethrin. © 2011 Elsevier Ltd.


Han Y.,Beijing Forestry University | Fan Y.,Chinese Academy of Agricultural Sciences | Yang P.,China Agricultural University | Wang X.,CAS Research Center for Eco Environmental Sciences | And 4 more authors.
Geoderma | Year: 2014

This study provides a new understanding to sources of nitrogen (N), and may serve as a foundation for further exploration of anthropogenic effects on N inputs. Estimation of net anthropogenic nitrogen inputs (NANI) was based on an inventory of atmospheric N deposition, N fertilizer use, N in human food and animal feed, seeding N and N fixation. This study took a step forward to calculate NANI in detail on a regional scale, and analyzed its temporal variations and geographic differences. Over the past 28years, NANI increased significantly in Mainland China, from 2360kgNkm-2yr-1 to 5013kgNkm-2yr-1. On a geographical basis, NANI was higher in southeast where China's eight major watersheds are located than in northwest, and the largest NANI, 26160kgNkm-2yr-1, appeared in Shanghai. The administrative regions corresponding to Haihe watershed, Huaihe watershed and Tai lake watershed have the largest NANI. N input of fertilizer is the largest source of NANI, followed by atmospheric N deposition and N fixation. The primary factor in relation to the change in NANI is total population density, followed by cultivated land area and total grain yield. In those densely populated large cities and watersheds, reasonably allocating the social resources to reduce the existing population density is the most effective way to address the problem of high N inputs, while in those agriculture-dominated regions and watersheds, the most effective way for reducing NANI is to improve fertilizer utilization efficiency in agriculture. © 2013 Elsevier B.V.


Li K.,China Agricultural University | Yang X.,China Agricultural University | Liu Z.,China Agricultural University | Zhang T.,CAS Institute of Atmospheric Physics | And 2 more authors.
European Journal of Agronomy | Year: 2014

The yield gap (YG) between the potential yields (Yp) and the average on-farm yields (Ya) is an indicator of the potential improvement for crop production. Understanding how large the current gap is and how this gap has changed over the past few decades is essential for increasing wheat production to meet increased food demand in China. This paper describes a study conducted using an APSIM-Wheat model and farm-level crop yield to analyze the spatio-temporal distribution of the yield gap of winter wheat from 1981 to 2010 in the North China Plain. Nine varieties were calibrated and evaluated based on the data from 16 agro-meteorological experimental sites and then potential yields were estimated considering cultivar replacement. In addition, a trend pattern analysis of on-farm yields for the period 1981-2010 was conducted. Results revealed an estimated yield gap across the entire North China Plain region of 1140-6810kgha-1, with a weight average of 3630kgha-1 in 1981-2010. Expressed as a relative yield (yield gap % of potential yields), the range was 15-80%, and the weight average was 45%. Despite the negative effects of increasing temperature and decreasing radiation, the potential yields significantly increased by 45kgha-1 per year due to cultivar improvement. On-farm yields increased even more notably because of new cultivar selection, increased fertilizer application and other management improvements, but were stagnating in 32.3% of wheat areas, located mainly in Hebei province, Shandong province, Beijing and Tianjin. The improvement of on-farm yields have substantially contributed to yield gap spatio-temporal variation. As a result, the yield gap decreased from 4200kgha-1 (56%) in 1981-1990 to 3000kgha-1 (35%) in 2001-2010 at a rate of -69kgha-1 per year. However, yields stagnation will expand to the northern Henan province without cultivar potential productivity improving, where yield gap was close to or less than 20% of the potential yields and proved difficult to reduce. To further improve the total production of winter wheat in the coming decades, efforts should be paid to break the potential ceiling and reduce the yield gap by breeding higher yield variety and introduction of new agricultural technology. © 2014 Elsevier B.V.


Alexandrov N.,International Rice Research Institute | Tai S.,BGI | Wang W.,Chinese Academy of Agricultural Sciences | Mansueto L.,International Rice Research Institute | And 9 more authors.
Nucleic Acids Research | Year: 2015

We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees ormultidimensional scaling plots. © The Author(s) 2014.


Yang N.-W.,Chinese Academy of Agricultural Sciences | Ji L.-L.,Chinese Academy of Agricultural Sciences | Lovei G.L.,Chinese Academy of Agricultural Sciences | Lovei G.L.,University of Aarhus | Wan F.-H.,Chinese Academy of Agricultural Sciences
PLoS ONE | Year: 2012

Destructive host-feeding is common in hymenopteran parasitoids. Such feeding may be restricted to host stages not preferred for oviposition. However, whether this is a fixed strategy or can vary according to resource levels or parasitoid needs is less clear. We tested the trade-off between host feeding and oviposition on two whitefly parasitoids under varying host densities. Females of two aphelinid parasitoids, Eretmocerus hayati and Encarsia sophia were exposed to nine different densities of their whitefly host, Bemisia tabaci, in single-instar tests to identify their functional response. Mixed-instar host choice tests were also conducted by exposing whiteflies at four densities to the parasitoids. We hypothesized that the parasitoid females can detect different host densities, and decide on oviposition vs. host-feeding accordingly. The results showed that both Er. hayati and En. sophia females tended to increase both oviposition and host-feeding with increased host density within a certain range. Oviposition reached a plateau at lower host density than host-feeding in Er. hayati, while En. sophia reached its oviposition plateau at higher densities. At low densities, Er. hayati parasitized most on first and second (the optimal ones), and fed most on third nymphal instars (the suboptimal one) of the whitefly host as theory predicts, while at high densities, both parasitism and host-feeding occurred on first and second instars which are preferred for oviposition. En. sophia parasitized most on third and fourth (the optimal ones), while fed on first instars (the suboptimal one) at low densities, and utilized third and fourth instars for both at high densities. In conclusion, oviposition vs. host-feeding strategy of parasitoid females was found to vary at different host densities. The balance between reserving optimal hosts for oviposition or using them for host-feeding depended on parasitoid life history and the availability of host resources. © 2012 Yang et al.


Sun Z.-M.,Chinese Academy of Agricultural Sciences | Sun Z.-M.,China Agricultural University | Zhou M.-L.,Chinese Academy of Agricultural Sciences | Xiao X.-G.,China Agricultural University | And 2 more authors.
Functional and Integrative Genomics | Year: 2014

Lotus corniculatus is used in agriculture as a main forage plant. Members of the Apetala2/ethylene response factor (AP2/ERF) family play important roles in regulating gene expression in response to many forms of stress, including drought and salt. Here, starting from database of the L. corniculatus var. japonicus genome, we identified 127 AP2/ERF genes by insilico cloning method. The phylogeny, gene structures, and putative conserved motifs in L. corniculatus var. japonicus ERF proteins were analyzed. Based on the number of AP2/ERF domains and the function of the genes, 127 AP2/ERF genes from L. corniculatus var. japonicus were classified into five subfamilies named the AP2, dehydration-responsive element binding factor (DREB), ERF, RAV, and a soloist. Outside the AP2/ERF domain, many L. corniculatus var. japonicus-specific conserved motifs were detected. Expression profile analysis of AP2/ERF genes by quantitative real-time PCR revealed that 19 LcERF genes, including LcERF054 (KJ004728), were significantly induced by salt stress. The results showed that the LcERF054 gene encodes a nuclear transcription activator. Overexpression of LcERF054 in Arabidopsis enhanced the tolerances to salt stress, showed higher germination ratio of seeds, and had elevated levels of relative moisture contents, soluble sugars, proline, and lower levels of malondialdehyde under stress conditions compared to wild-type plants. The expression of hyperosmotic salinity response genes COR15A, LEA4-5, P5CS1, and RD29A was found to be elevated in the LcERF054-overexpressing Arabidopsis plants compared to wild type. These results revealed that the LcERF genes play important roles in L. corniculatus cv Leo under salt stress and that LcERFs are attractive engineering targets in applied efforts to improve abiotic stress tolerances in L. corniculatus cv Leo or other crops. © 2014 Springer-Verlag.


Xu Y.,Chinese Academy of Agricultural Sciences | Xu Y.,University of Arizona | Zhou T.,Utah State University | Espinosa-Artiles P.,University of Arizona | And 4 more authors.
ACS Chemical Biology | Year: 2014

The phytotoxic fungal polyketides lasiodiplodin and resorcylide inhibit human blood coagulation factor XIIIa, mineralocorticoid receptors, and prostaglandin biosynthesis. These secondary metabolites belong to the 12-membered resorcylic acid lactone (RAL12) subclass of the benzenediol lactone (BDL) family. Identification of genomic loci for the biosynthesis of lasiodiplodin from Lasiodiplodia theobromae and resorcylide from Acremonium zeae revealed collaborating iterative polyketide synthase (iPKS) pairs whose efficient heterologous expression in Saccharomyces cerevisiae provided a convenient access to the RAL12 scaffolds desmethyl-lasiodiplodin and trans-resorcylide, respectively. Lasiodiplodin production was reconstituted in the heterologous host by co-expressing an O-methyltransferase also encoded in the lasiodiplodin cluster, while a glutathione-S-transferase was found not to be necessary for heterologous production. Clarification of the biogenesis of known resorcylide congeners in the heterologous host helped to disentangle the roles that biosynthetic irregularities and chemical interconversions play in generating chemical diversity. Observation of 14-membered RAL homologues during in vivo heterologous biosynthesis of RAL12 metabolites revealed stuttering by fungal iPKSs. The close global and domain-level sequence similarities of the orthologous BDL synthases across different structural subclasses implicate repeated horizontal gene transfers and/or cluster losses in different fungal lineages. The absence of straightforward correlations between enzyme sequences and product structural features (the size of the macrocycle, the conformation of the exocyclic methyl group, or the extent of reduction by the hrPKS) suggest that BDL structural variety is the result of a select few mutations in key active site cavity positions. © 2014 American Chemical Society.


Hu X.,Chinese Academy of Agricultural Sciences | Wang H.,China Agricultural University | Chen J.,China Agricultural University | Yang A.W.,China Agricultural University
Pakistan Journal of Botany | Year: 2012

Twenty-six morphological traits as well as 47 single nucleotide polymorphism and simple sequence repeat markers were used to investigate genetic variation in 67 tomato (Solanum lycopersicum L.) varieties collected from Argentina between 1932 and 1974. Approximately 65.0% of the morphological traits and 55.3% of the molecular markers showed polymorphisms in the 67 varieties. Average taxonomic distance between any two varieties ranged from 0.6643 to 1.1776, while Nei's genetic distance varied from 0 to 0.2022. Cluster analysis indicated that 67 varieties could be grouped into three clusters at both morphological and molecular levels. The varieties collected before 1960 had larger genetic variation than those collected after 1960.


Xing L.,Chinese Academy of Agricultural Sciences | Chen L.,China Agricultural University
Spectroscopy Letters | Year: 2013

Data preprocessing and multivariate regression methods are two key factors influencing the model prediction ability of near-infrared (NIR) spectroscopy. The present paper evaluated the application of the combined stationary wavelet transform-support vector machine method for developing juice NIR models. The performance of this method has been compared with other methods, such as stand normal variate-partial least squares, stationary wavelet transform-partial least squares, and stand normal variate-stationary wavelet transform methods. The result showed that compared with other methods, the stationary wavelet transform-support vector machine method can provide good quantitative analysis on saccharose concentration in juice. © 2013 Copyright Taylor and Francis Group, LLC.


Wendlandt S.,Institute of Farm Animal Genetics | Shen J.,China Agricultural University | Kadlec K.,Institute of Farm Animal Genetics | Wang Y.,China Agricultural University | And 5 more authors.
Trends in Microbiology | Year: 2015

Most antimicrobial resistance genes known so far to occur in staphylococci of animal origin confer resistance to a specific class of antimicrobial agents or to selected members within such a class. However, there are also a few examples of multidrug resistance (MDR) genes that confer resistance to antimicrobial agents of different classes by either target site methylation or active efflux via ATP-binding cassette (ABC) transporters. The present review provides an overview of these MDR genes with particular reference to those genes involved in resistance to critically or highly important antimicrobial agents used in human and veterinary medicine. Moreover, their location on mobile genetic elements and colocated resistance genes, which may play a role in coselection and persistence of the MDR genes, are addressed. © 2014 Elsevier Ltd.


Dong X.,China Agricultural University | Zhang Y.-J.,Chinese Academy of Agricultural Sciences | Zhang Z.,China Agricultural University
PLoS ONE | Year: 2013

Background: As one of the most important virulence factor types in gram-negative pathogenic bacteria, type-III effectors (TTEs) play a crucial role in pathogen-host interactions by directly influencing immune signaling pathways within host cells. Based on the hypothesis that type-III secretion signals may be comprised of some weakly conserved sequence motifs, here we used profile-based amino acid pair information to develop an accurate TTE predictor. Results: For a TTE or non-TTE, we first used a hidden Markov model-based sequence searching method (i.e., HHblits) to detect its weakly homologous sequences and extracted the profile-based k-spaced amino acid pair composition (HH-CKSAAP) from the N-terminal sequences. In the next step, the feature vector HH-CKSAAP was used to train a linear support vector machine model, which we designate as BEAN (Bacterial Effector ANalyzer). We compared our method with four existing TTE predictors through an independent test set, and our method revealed improved performance. Furthermore, we listed the most predictive amino acid pairs according to their weights in the established classification model. Evolutionary analysis shows that predictive amino acid pairs tend to be more conserved. Some predictive amino acid pairs also show significantly different position distributions between TTEs and non-TTEs. These analyses confirmed that some weakly conserved sequence motifs may play important roles in type-III secretion signals. Finally, we also used BEAN to scan one plant pathogen genome and showed that BEAN can be used for genome-wide TTE identification. The webserver and stand-alone version of BEAN are available at http://protein.cau.edu.cn:8080/bean/. © 2013 Dong et al.


Chen L.,Chinese Academy of Agricultural Sciences | Wang J.,China Agricultural University | Ye Z.,Chinese Academy of Agricultural Sciences | Zhao J.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Food Chemistry | Year: 2012

The feasibility of near infrared (NIR) spectroscopy and multivariate analysis as tools to classify Chinese honey samples according to their different floral origins was explored. Five kinds of honey, namely, acacia, linden, rape, vitex and jujube, were analysed using a NIR spectrophotometer with a fibre optic probe. Classification models based on the NIR spectra were developed using Mahalanobis-distance discriminant analysis (MD-DA) and a back propagation artificial neural network (BP-ANN). By the MD-DA model, total correct classification rates of 87.4% and 85.3% were observed for the calibration and validation samples, respectively, while the ANN model resulted in total correct classification rates of 90.9% and 89.3% for the calibration and validation sets, respectively. By ANN, the respective correct classification rates of linden, acacia, vitex, rape and jujube were 97.1%, 94.3%, 80.0%, 97.1%, and 85.7% in calibration, and 100%, 93.3%, 80.0%, 100%, and 73.3% in validation. The results indicated that NIR combined with a classification technique could be a suitable technology for the classification of Chinese honeys from different botanical origins. © 2012 Elsevier Ltd. All rights reserved.


Jiang Y.,China Agricultural University | Han Y.Z.,China Agricultural University | Zhang X.M.,Chinese Academy of Agricultural Sciences
Russian Journal of Plant Physiology | Year: 2011

Soybean (Glycine max L.) is a typical short-day crop, and its flowering is strictly restricted by specific photoperiod conditions. CONSTANS (CO) plays a pivotal role in the photoperiod pathway of flowering regulation. CO-like genes are present in many plant species. Here we describe the isolation of the CO homologue GmCOL11 (Glycine max CO-like 11) from the soybean cv. Kennong 18. Sequence comparisons show that GmCOL11 is a group II CO-like gene with some similarity to AtCOL6 and AtCOL16. Its sequence includes a conserved B box and a CCT domain. The study of GmCOL11 expression using quantitative real time RT-PCR demonstrated that this gene was regulated in a diurnal rather than in a circadian manner. The gene was expressed throughout the plant, but mainly in adult leaves and maturing seeds; its expression was enhanced following flowering. Apparently GmCOL11 is involved in several aspects of soybean development. © 2011 Pleiades Publishing, Ltd.


Wang N.,Chinese Academy of Agricultural Sciences | Yang D.,China Agricultural University
Transactions of the American Entomological Society | Year: 2014

The species of the genus Hybos Meigen from Tibet are reviewed. The following seven species are described as new to science: Hybos beibenganus sp. nov., Hybos brevifurcatus sp. nov., Hybos curvus sp. nov., Hybos hanmianus sp. nov., Hybos lihuae sp. nov., Hybos nigripes sp. nov., and Hybos beibenganus sp. nov. A key to the species of the genus Hybos from Tibet is presented for the first time.


Li J.,Chinese Academy of Agricultural Sciences | Chen W.,China Agricultural University | Wu J.,Chinese Academy of Agricultural Sciences | Peng W.,Chinese Academy of Agricultural Sciences | And 3 more authors.
International Journal for Parasitology | Year: 2012

Bumblebees (Bombus spp.) are important pollinators of many economically important crops and microsporidia are among the most important infections of these hosts. Using molecular markers, we screened a large sample (n= 1,009 bees) of workers of 27 different Bombus spp. from China (Sichuan, Qinghai, Inner Mongolia, and Gansu provinces). The results showed that 62 individuals representing 12 Bombus spp. were infected by microsporidia with an overall prevalence of 6.1%. Based on the haplotypes (ssrRNA sequences), we confirmed the presence of Nosema bombi, Nosema ceranae and (likely) Nosema thomsoni. In addition, four new putatively novel taxa were identified by phylogenetic reconstruction: Nosema A, Nosema B-complex, Nosema C-complex and Nosema D-complex. In many cases, hosts were infected by more than one Nosema taxon. Possible caveats of sequence analyses are discussed. © 2011 Australian Society for Parasitology Inc.


Chen P.,China Agricultural University | Li J.,China Agricultural University | Li Q.X.,University of Hawaii at Manoa | Wang Y.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Bioresource Technology | Year: 2012

Rhodococcus sp. CPZ24 was isolated from swine wastewater and identified. Batch (0.25L flask) experiments of nitrogen removal under aerobic growth conditions showed complete removal of 50mgL -1 ammonium nitrogen within 20h, while nitrate nitrogen removal reached 67%. A bioreactor (50L) was used to further assess the heterotrophic nitrification and aerobic denitrification abilities of Rhodococcus sp. CPZ24. The results showed that 85% of the ammonium nitrogen (100mgL -1) was transformed to nitrification products (NO3--N and NO2--N) (13%), intracellular nitrogen (24%), and gaseous denitrification products (48%) within 25h. The ammonium nitrogen removal rate was 3.4mg L -1h -1. The results indicate that the strain CPZ24 carries out simultaneous nitrification and denitrification, demonstrating a potential use of the strain for wastewater treatment. © 2012 Elsevier Ltd.


Zhang N.-Z.,Chinese Academy of Agricultural Sciences | Chen J.,Chinese Academy of Agricultural Sciences | Wang M.,Chinese Academy of Agricultural Sciences | Petersen E.,University of Aarhus | And 2 more authors.
Expert Review of Vaccines | Year: 2013

Toxoplasmosis caused by the protozoan Toxoplasma gondii is a major public health problem, infecting one-third of the world human beings, and leads to abortion in domestic animals. A vaccine strategy would be an ideal tool for improving disease control. Many efforts have been made to develop vaccines against T. gondii to reduce oocyst shedding in cats and tissue cyst formation in mammals over the last 20 years, but only a live-attenuated vaccine based on the S48 strain has been licensed for veterinary use. Here, the authors review the recent development of T. gondii vaccines in cats, food-producing animals and mice, and present its future perspectives. However, a single or only a few antigen candidates revealed by various experimental studies are limited by only eliciting partial protective immunity against T. gondii. Future studies of T. gondii vaccines should include as many CTL epitopes as the live attenuated vaccines. © 2013 Informa UK Ltd.


Wang R.,Chinese Academy of Agricultural Sciences | Wang R.,CAS Institute of Botany | Wang J.-F.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | Qiu Z.-J.,CAS Institute of Botany | And 3 more authors.
New Phytologist | Year: 2011

With growing concerns over serious ecological problems, a particular challenge is to reveal the complex mechanisms underlying rapid expansion of invasive species. Ageratina adenophora is of particular interest in addressing this question. We used geographic information systems and logistic regression to identify the geographic and environmental factors contributing to the presence of A. adenophora. Join-count spatial statistics with reproduction mode examination were employed to elucidate the spatiotemporal dispersal mechanisms. Multiple factors have significantly contributed to the rapid expansion of A. adenophora. Its biological traits, favoring dispersal by water and wind coupled with local spatiotemporally heterogeneous geography and ecology, promote invasion downstream and upstream along river valleys, while other factors associated with human activities facilitate its invasion over high mountains and across river valleys, providing new scope for progressive invasions. We further identified an unusual invasion event of A. adenophora subsequent to a great flood that amplified its dispersal ability from vegetative propagules and seeds. These findings suggest that dynamic interactions of multiple factors in heterogeneous ecogeographical environments - a 'combinatorial' invasion mechanism - would generate an unexpected invasion rate of an alien species or a seemingly stochastic invasion event. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.


Zhao M.,Key Laboratory of Plant and Soil Interactions | Zhao M.,China Agricultural University | Tai H.,Key Laboratory of Plant and Soil Interactions | Sun S.,Key Laboratory of Plant and Soil Interactions | And 5 more authors.
PLoS ONE | Year: 2012

Although recent studies indicated that miRNAs regulate plant adaptive responses to nutrient deprivation, the functional significance of miRNAs in adaptive responses to nitrogen (N) limitation remains to be explored. To elucidate the molecular biology underlying N sensing/signaling in maize, we constructed four small RNA libraries and one degradome from maize seedlings exposed to N deficiency. We discovered a total of 99 absolutely new loci belonging to 47 miRNA families by small RNA deep sequencing and degradome sequencing, as well as 9 new loci were the paralogs of previously reported miR169, miR171, and miR398, significantly expanding the reported 150 high confidence genes within 26 miRNA families in maize. Bioinformatic and subsequent small RNA northern blot analysis identified eight miRNA families (five conserved and three newly identified) differentially expressed under the N-deficient condition. Predicted and degradome-validated targets of the newly identified miRNAs suggest their involvement in a broad range of cellular responses and metabolic processes. Because maize is not only an important crop but is also a genetic model for basic biological research, our research contributes to the understanding of the regulatory roles of miRNAs in plant adaption to N-deficiency stress. © 2012 Zhao et al.


Xu Z.,Shandong Agricultural University | Xu Z.,CAS Institute of Botany | Yu Z.,Shandong Agricultural University | Zhao J.,Chinese Academy of Agricultural Sciences
Journal of the Science of Food and Agriculture | Year: 2013

Food security is becoming a crucial concern worldwide. In this study, we focus on wheat - a staple crop in China - as a model to review its history, status quo and future scenarios, with regard to key production technologies and management practices for wheat production and associated food security issues since the new era in China: the post-1949 era. First, the dominant technologies and management practices over the past 60years are reviewed. Secondly, we outline several key innovative technologies and their theoretical bases over the last decade, including (i) prohibiting excessively early senescence at a later growth stage to maintain viable leaves with higher photosynthetic capacity, (ii) postponing top dressing nitrogen application to balance carbon and nitrogen nutrition, and (iii) achieving both high yield and better grain quality mainly by increasing soil productivity and balancing the ratio of nutrient elements. Finally, concerns such as water shortages and excessive application of chemical fertilizers are presented. Nevertheless, under high negative conditions, including global warming, rapid population growth, decreasing amounts of arable land, increasing competition with cash crops and severe environmental pollution, we conclude that domestic food production will be able to meet Chinese demand in the mid to long term, because increasingly innovative technologies and improved management practices have been and may continue to be applied appropriately. © 2013 Society of Chemical Industry.


Wang W.-S.,Chinese Academy of Agricultural Sciences | Wang W.-S.,International Rice Research Institute | Pan Y.-J.,Chinese Academy of Agricultural Sciences | Zhao X.-Q.,Chinese Academy of Agricultural Sciences | And 7 more authors.
Journal of Experimental Botany | Year: 2011

An indica pyramiding line, DK151, and its recurrent parent, IR64, were evaluated under drought stress and non-stress conditions for three consecutive seasons. DK151 showed significantly improved tolerance to drought. The DNA methylation changes in DK151 and IR64 under drought stress and subsequent recovery were assessed using methylation-sensitive amplified polymorphism analysis. Our results indicate that drought-induced genome-wide DNA methylation changes accounted for ∼12.1% of the total site-specific methylation differences in the rice genome. This drought-induced DNA methylation pattern showed three interesting properties. The most important one was its genotypic specificity reflected by large differences in the detected DNA methylation/demethylation sites between DK151 and IR64, which result from introgressed genomic fragments in DK151. Second, most drought-induced methylation/demethylation sites were of two major types distinguished by their reversibility, including 70% of the sites at which drought-induced epigenetic changes were reversed to their original status after recovery, and 29% of sites at which the drought-induced DNA demethylation/methylation changes remain even after recovery. Third, the drought-induced DNA methylation alteration showed a significant level of developmental and tissue specificity. Together, these properties are expected to have contributed greatly to rice response and adaptation to drought stress. Thus, induced epigenetic changes in rice genome can be considered as a very important regulatory mechanism for rice plants to adapt to drought and possibly other environmental stresses. © 2010 The Author(s).


Qiao F.,Qinghai Normal University | Qiao F.,Chinese Academy of Agricultural Sciences | Zhao K.-J.,Chinese Academy of Agricultural Sciences
Plant Molecular Biology Reporter | Year: 2011

The rice height has been proposed to involve gibberellin biosynthesis. In order to regulate rice height, we suppressed expression of OsGA20ox2 by the double-stranded RNA interference (RNAi) method. For this purpose, we constructed two different RNAi vectors, pCH1CK and pCH12CK, then performed Agrobacterium-mediated transformation of rice varieties QX1 and Zhongzuo0201. The RNAi transgenic lines derived from pCH1CK and pCH12CK demonstrated a clear reduction in height compared with the control plants (P < 0.01). The height of dwarf lines from pCH1CK and pCH12CK were about 75-84% and 54-74% of that of the control plants, respectively. Transcripts for semi-dwarf lines from pCH1CK and pCH12CK were also reduced in comparison with the control plants. Analyses of seeds per panicle, 1,000-grain weight, and seed yield per plant suggested that the RNAi semi-dwarf lines showed stable grain yield compared with the wild-type plants. We further showed that the RNAi semi-dwarf lines could be restored to normal plant height by applying exogenous GA3. The results also indicate that different fragment of the same RNAi target can be practically applied to produce different extent semi-dwarf of rice plants. © 2011 Springer-Verlag.


Ma G.,China Agricultural University | Huang J.,China Agricultural University | Wu W.,Chinese Academy of Agricultural Sciences | Fan J.,National Satellite Meteorological Center | And 2 more authors.
Mathematical and Computer Modelling | Year: 2013

Crop growth models have been applied successfully in forecasting crop yield at a local scale, while satellite remote sensing has the advantage of retrieving regional crop parameters. The new assimilation method of integrating the crop growth model with remote sensing has presented great potential in regional crop yield assessment. In this study, the Moderate Resolution Imaging Spectrometer (MODIS) leaf area index (LAI) data product was assimilated into the World Food Studies (WOFOST) crop growth model. Using the Extended Fourier Amplitude Sensitivity Test (EFAST) global sensitivity analysis approach, several local and regional crop parameters were identified to be recalibrated. The Shuffled Complex Evolution (SCE) optimization algorithm was used to estimate the emergence date, initial biomass and initial available soil water by minimizing the differences between the corrected MODIS-LAI and simulated LAI. Results indicated that the accuracy of water-limited crop yield was improved significantly after the assimilation. The root mean square error (RMSE) reduced from 983kg/ha to 474kg/ha and 667kg/ha respectively in two different optimization schemes. © 2011 Elsevier Ltd.


Liang L.,China Agricultural University | Liang L.,Ohio State University | Lal R.,Ohio State University | Du Z.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Agriculture, Ecosystems and Environment | Year: 2013

Livestock farming systems are major sources of heat trapping greenhouse gases (GHG) and the attendant global warming. From 2007 to 2009, the total quantity of GHG emissions from livestock sector in Beijing was 1.67 Tg CO2eyr-1, of which N2ON and CH4 emissions were 1.04Ggyr-1 (489 Gg CO2eyr-1) and 47.25Ggyr-1 (1181.25 Gg CO2eyr-1), respectively. The emission intensity per 10,000 RMB was 1.2Mg CO2e, which accounted for 63% of the averaged value of 1.9Mg CO2e in Beijing. Consequently, Beijing's modern urban agriculture has made progress to some extent. To reduce GHG emissions from the livestock sector, relevant strategies such as improving rearing technologies, breeding, strengthening management and developing large-scale biogas industry should be considered. Theoretical, biogas industry could offset about 80% of GHG emissions from livestock sector, yet there are some barriers, which need to be overcome to enhance cooperation among government agencies, market organizations and livestock enterprises. Furthermore, it is both essential and feasible to adopt a healthy lifestyle, clean cooking, and low-C food systems to mitigate and reduce GHG emissions. © 2013 Elsevier B.V.


Yuan Z.,Peking Union Medical College | Yuan Z.,Chinese Academy of Agricultural Sciences | Li J.,Chinese Academy of Agricultural Sciences | Gao X.,Chinese Academy of Agricultural Sciences | Xu S.,Chinese Academy of Agricultural Sciences
Molecular Biology Reports | Year: 2013

The objective of this study was to investigate the single nucleotide polymorphisms (SNPs) within bovine binding lectin-liver (A) gene (MBL1) and to explore its correlation analysis with milk somatic cell score (SCS) which reflects mastitis resistance in cattle. Through polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), created restriction site-PCR (CRS-PCR) and DNA sequencing methods, three allelic variant corresponding to the G→A mutation at c.1252G>A in intron1, G→A mutation at c.2534G>A and T→C mutation at c.2569T>C in exon2 of bovine MBL1 gene, could be detected, respectively. The c.2534G>A was a nonsynonymous mutation, resulting in Valine (Val) to Isoleucine (Ile) amino acid replacement (p.Val24Ile). The correlation analysis between the MBL1 SNPs gene and milk SCS were analyzed and a significant correlation with milk SCS was detected in c.2534G>A. The value of milk SCS for individuals with genotype GG was significantly lower than those of genotype GA and AA. Results showed that genotype GG with the lowest milk SCS was favorable for mastitis resistance, whereas genotype AA with the highest milk SCS was easily for mastitis susceptibility. Although more investigations are needed to better clarify the role of these SNPs on mastitis resistance, MBL1 polymorphism appears to be a promising indirect marker to improve dairy mastitis resistance traits in cattle. © 2012 Springer Science+Business Media Dordrecht.


Li H.,China Agricultural University | Peng Z.,CAS Beijing Institute of Genomics | Yang X.,China Agricultural University | Wang W.,China Agricultural University | And 16 more authors.
Nature Genetics | Year: 2013

Maize kernel oil is a valuable source of nutrition. Here we extensively examine the genetic architecture of maize oil biosynthesis in a genome-wide association study using 1.03 million SNPs characterized in 368 maize inbred lines, including 'high-oil' lines. We identified 74 loci significantly associated with kernel oil concentration and fatty acid composition (P < 1.8 × 10 -6), which we subsequently examined using expression quantitative trait loci (QTL) mapping, linkage mapping and coexpression analysis. More than half of the identified loci localized in mapped QTL intervals, and one-third of the candidate genes were annotated as enzymes in the oil metabolic pathway. The 26 loci associated with oil concentration could explain up to 83% of the phenotypic variation using a simple additive model. Our results provide insights into the genetic basis of oil biosynthesis in maize kernels and may facilitate marker-based breeding for oil quantity and quality. © 2013 Nature America, Inc. All rights reserved.


Yuan Z.,Peking Union Medical College | Yuan Z.,Chinese Academy of Agricultural Sciences | Li J.,Chinese Academy of Agricultural Sciences | Gao X.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Molecular Biology Reports | Year: 2013

This study was designed to investigate the candidate single nucleotide polymorphisms (SNPs) in the exon's region of bovine diacylglycerol O-acyltransferase (DGAT1) gene using bioinformatics and experimental methods. A total of 17 SNPs were screened from public data resources and DNA sequencing. Three SNPs (c.572A>G, c.1241C>T and c.1416T>G) of these candidate SNPs were genotyped by created restriction site-polymerase chain reaction (CRS-PCR) methods. The gene-specific SNP markers and their effects on meat and carcass fatness quality traits were evaluated in Chinese commercial cattle. The c.572A>G and c.1416T>G significantly effected on backfat thickness, longissimus muscle area, marbling score, fat color and Warner-Bratzler shear force. No significant association was detected between the c.1241C>T and measured traits. Results from this study suggested that the SNP markers may be effective for the marker-assisted selection of meat and carcass fatness quality traits, and added new evidence that DGAT1 gene is an important candidate gene for the improvement of meat and carcass fatness quality in beef cattle industry. © 2012 Springer Science+Business Media Dordrecht.


Suramaythangkoor T.,King Mongkut's University of Technology Thonburi | Li Z.,Key Laboratory of Resources Remote Sensing and Digital Agriculture | Li Z.,Chinese Academy of Agricultural Sciences
Renewable and Sustainable Energy Reviews | Year: 2012

Cane trash could viably substitute fossil fuels in heat and power generation projects to avoid air pollution from open burning and reduce greenhouse gas (GHG) emission. It is competitive with bituminous and other agro-industrial biomass. Using cane trash for heat generation project could provide a higher reliability and return on investment than power generation project. The heat generation project could be viable (Financial Internal Rate of Return, FIRR = 36-81%) without feedstock subsidy. With current investment and support conditions, the capacity of 5 MW option of power generation project is the most viable (FIRR = 13.6-15.3%); but 30 MW, 1 MW and 10 MW options require feedstock subsidy 450-1100 Baht/t-cane trash to strengthen financial viability. Furthermore, the revenue from carbon credit sales could compensate the revenue from current energy price adder and increases 0.5-1.0% FIRR of power generation project. Using cane trash for 1 MW power generation could reduce GHG emission 637-861 t CO 2eq and avoid air pollutant emissions of 3.35 kg nitrogen oxides (NO x), 0.41 kg sulfur oxides (SO x) and 2.05 kg volatile organic compounds (VOC). Also, 1 t steam generation from cane trash could avoid pollutant emissions of 0.6 kg NO x, 0.07 kg SO x, and 0.37 kg VOC. The potential of cane trash to cause fouling/slagging as well as erosion are not significantly different from other biomass, but chlorinated organic compounds and NO x could be higher than bituminous and current biomass feedstock at sugar mill (bagasse and rice husk). © 2012 Elsevier Ltd. All right reserved.


He F.,China Agricultural University | He F.,Chinese Academy of Agricultural Sciences | Ma C.,China Agricultural University
Computers and Electronics in Agriculture | Year: 2010

A back propagation neural network (BPNN) based on principal component analysis (PCA) was proposed for modeling the internal greenhouse humidity in winter of North China. The environment factors influencing the inside humidity include outside air temperature and humidity, wind speed, solar radiation, inside air temperature, open angle of top vent and side vent, and open ration of sunshade curtain, which were all collected as data samples. Through PCA of these data samples, 4 main factors were extracted, and the relationship between the main factors and the original data was discussed. Taking the principal component values as the input of BPNN, the model showed a good performance. A comparison was made between the performances of the BPNN based on PCA and the stepwise regression method with 20 data samples which had not been used to establish the NN model, and the prediction of stepwise regression method was less accurate than the BPNN based on PCA. © 2009 Elsevier B.V. All rights reserved.


Chen X.,China Agricultural University | Cui Z.,China Agricultural University | Fan M.,Stanford University | Vitousek P.,Chinese Academy of Agricultural Sciences | And 28 more authors.
Nature | Year: 2014

Agriculture faces great challenges to ensure global food security by increasing yields while reducing environmental costs1,2. Here we address this challenge by conducting a total of 153 site-year field experiments covering the main agro-ecological areas for rice, wheat and maize production in China. As et of integrated soil-crop systemmanagement practices based ona modern understanding of crop ecophysiology and soil biogeochemistry increases average yields for rice, wheat and maize from 7.2 million grams per hectare (Mg ha-1), 7.2Mg ha-1 and 10.5Mgha-1 to 8.5Mgha-1, 8.9Mgha-1 and 14.2Mgha-1, respectively, without any increase in nitrogen fertilizer. Model simulation and life-cycle assessment3 show that reactive nitrogen losses and greenhouse gasemissions are reduced substantially by integrated soil-crop system management. If farmers in China could achieve average grain yields equivalent to 80%of this treatment by 2030, over the sameplanting area as in 2012, total production of rice, wheat and maize in China would be more than enough to meet the demand for direct human consumption and a substantially increased demand for animal feed, while decreasing the environmental costs of intensive agriculture. © 2014 Macmillan Publishers Limited. All rights reserved.


Chen L.,China Agricultural University | Xing L.,Chinese Academy of Agricultural Sciences | Han L.,China Agricultural University
Journal of Environmental Quality | Year: 2013

Animal manure contains a variety of chemical constituents that are highly valuable to agriculture, including nitrogen, phosphorus, potassium, and metal micronutrients. Although appropriately applied manure has numerous positive attributes, the excessive application of manure may lead to pollution of the atmosphere, water, or soil. To reconcile precision agriculture and the potential negative environmental influences of animal manure, it is necessary to develop rapid and robust methods to evaluate the chemical composition of animal manure. This paper summarizes recent advances in nearinfrared reflectance spectroscopy (NIRS) in predicting moisture, dry matter, organic matter, nitrogen, phosphorus, carbon, and metal content in animal manure. The results indicate the high potential of NIRS as an efficient tool for monitoring the chemical composition of animal manure. Future prospects and needs related to increasing the feasibility of the industrial application of NIRS and improving NIRS prediction precision in determining the chemical composition of animal manure are discussed. ©American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.


Shi J.,China Agricultural University | Zhang L.,China Agricultural University | Zhang L.,Chinese Academy of Agricultural Sciences | Gao X.,China Agricultural University
Pest Management Science | Year: 2011

BACKGROUND: Spinosad, a relatively new, effective and safe pesticide, has been widely used in pest control over the last 10 years. However, different levels of resistance to this insecticide have developed in some insects worldwide. RESULTS: After continuous selection for 27 generations, a strain (SpRR) of the housefly developed 247-fold resistance to spinosad compared with the laboratory susceptible strain (CSS). The estimated realised heritability (h 2) of spinosad resistance was 0.14. There was no significant difference in the LD 50 values and slopes between reciprocal progenies F 1 and F 1', and values of 0.33 (F 1) and 0.30 (F 1') were obtained for the degree of dominance. Chi-square analysis from responses of self-bred (F 2) and backcrosses (BC 1 and BC 2) were highly significant, suggesting that the resistance was probably controlled by more than one gene. Synergists piperonyl butoxide (PBO), diethyl maleate (DEM) and S,S,S-tributyl phosphorotrithioate (DEF) affected the toxicity of spinosad at a low level, and demonstrated that metabolic-mediated detoxification was not an important factor in conferring resistance to spinosad in the SpRR strain. CONCLUSION: It was concluded that spinosad resistance in the housefly was autosomal and incompletely dominant, and the resistance was probably controlled by more than one gene. These results provide the basic information for designing successful management programmes for the control of houseflies. © 2011 Society of Chemical Industry.


Yang C.,CAS Institute of Botany | Yang C.,CAS Wuhan Botanical Garden | Wang Y.,CAS Institute of Botany | Wu B.,CAS Institute of Botany | And 2 more authors.
Food Chemistry | Year: 2011

Volatile compounds of three different flavour table-grapes, 'Jingxiu', 'Bimeijia' and 'Jingya', were investigated during and after maturation using SPME/GC-MS. All the alcohols and carbonyls, along with most of the C6 compounds and terpenoids, were evident before veraison, while most of the esters were detected at or after veraison. C6 compounds increased in the early period of maturation, and then decreased. Most alcohols and carbonyls tended to continuously decrease during ripening. Except for geraniol, terpenoids increased until maturation, then decreased. Some esters continued to increase after maturation. Principal component analysis showed that terpenoids and esters were the characteristic volatiles of ripe 'Bimeijia' and 'Jingya' grapes, respectively. 'Bimeijia' had the highest terpenoid content at maturity, while 'Jingya' continued to accumulate some esters after maturation. To achieve berries of full-bodied aroma, 'Bimeijia' should be harvested at maturity and 'Jingya' should have a delayed harvest. For the neutral grape 'Jingxiu', delayed harvest is recommended to reduce the 'green' odour. © 2010 Elsevier Ltd. All rights reserved.


Zhu Y.Z.,Chinese Academy of Agricultural Sciences | Liu D.W.,Heilongjiang Province Hospital | Liu D.W.,Heilongjiang University of Chinese Medicine | Liu Z.Y.,Chinese Academy of Agricultural Sciences | Li Y.F.,Northeast Agricultural University
Environmental Toxicology and Pharmacology | Year: 2013

Aluminum (Al) is widely used in daily life and will lead to environmental release and exposure. The toxicity of Al had been documented, and which attracted a growing concern on human and animal health. The immune system appears to be sensitive to Al exposure. But few studies focused on the potential immunological responses induced by Al. It is imperative to study the effects of Al on the immune function and this review discusses the effects of Al on autoimmunity, oral tolerance, expression of the immune cells, hypersensitivity and erythrocyte immune function. It will provide evidence to study the association between Al and immune function. © 2012 Elsevier B.V.


Wang Y.,Tianjin Normal University | Wang Z.-L.,Tianjin Normal University | Wang H.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | Guo C.,Tianjin Normal University | Bao W.,Chinese Academy of Agricultural Sciences
Canadian Journal of Forest Research | Year: 2012

Although litterfall respiration (R L) is a key process of soil carbon dynamics in forests, factors that drive R L and its contribution to soil respiration (R S) have not been sufficiently studied. Using a litter removal method, we researched R L and the ratio of R L:R S in a 20-year-old exotic slash pine (Pinus elliottii Englem.) plantation in subtropical China. Soil temperature explained 67%, 78%, and 25% of variation in R S, mineral soil respiration (R S-L), and R L, respectively, but had little impact on R L:R S. To study influences besides temperature, measured R S and R S-L were normalized using the Arrhenius equation. Even though this subtropical plantation was characterized by a humid climate with abundant precipitation, a rainfall pulse induced increase in soil moisture primarily drove R L and its contribution to R S but depressed R S-L. The response of R L to rainfall and soil moisture was significantly more sensitive than that of R S-L. Furthermore, the effects of rainfall and soil moisture on R S, R L, and R L:R S were higher during the dry season (July-December) than during the wet season (January- June). In the context of climate change, R L and its contribution to R S are expected to decrease because of the predicted decrease in rainfall amount and frequency in subtropical regions.


Li J.,China Agricultural University | Wang Q.,China Agricultural University | Zhang L.,Chinese Academy of Agricultural Sciences | Gao X.,China Agricultural University
Pesticide Biochemistry and Physiology | Year: 2012

In recent years, imidacloprid was introduced to control the housefly in China and it was documented that the housefly indeed showed signs of resistance to imidacloprid somewhere but not in China. Therefore, a housefly population collected from filed (IFS) was selected continuously with imidacloprid to establish the resistant strain (IRS) and the basic characteristics were investigated in this study. After continuous selection over 21 generations, the resistance ratio increased from 9.01 to 140, and different levels of cross-resistance were developed to beta-cypermethrin, chlorpyrifos, chlorfenapyr, acetamiprid and azamethiphos in the IRS strain. The realized heritability of resistance was 0.10. The synergistic ratios for IRS pretreated with DEF, DEM and PBO were 1.68, 1.52 and 2.53, and the corresponding ones for IFS were 3.17, 1.87 and 2.67, respectively. Synergistic and biochemical assays suggested that the cytochrome P450 may play an important role in the imidacloprid resistance comparing with GSTs- and carboxylesterases-mediated detoxification in the IRS strain, and there might be additional mechanisms (e.g. reduced target-site sensitivity) contributed to imidacloprid resistance in the IRS strain. © 2012.


Zhang B.,China Agricultural University | Dong C.,Chinese Academy of Agricultural Sciences | Shang Q.,Chinese Academy of Agricultural Sciences | Han Y.,China Agricultural University | Li P.,China Agricultural University
Biochimica et Biophysica Acta - Biomembranes | Year: 2013

Bacillomycin L, a natural iturinic lipopeptide produced by Bacillus amyloliquefaciens, is characterized by strong antifungal activities against a variety of agronomically important filamentous fungi including Rhizoctonia solani Kühn. Prior to this study, the role of membrane permeabilization in the antimicrobial activity of bacillomycin L against plant pathogenic fungi had not been investigated. To shed light on the mechanism of this antifungal activity, the permeabilization of R. solani hyphae by bacillomycin L was investigated and compared with that by amphotericin B, a polyene antibiotic which is thought to act primarily through membrane disruption. Our results derived from electron microscopy, various fluorescent techniques and gel retardation experiments revealed that the antifungal activity of bacillomycin L may be not solely a consequence of fungal membrane permeabilization, but related to the interaction of it with intracellular targets. Our findings provide more insights into the mode of action of bacillomycin L and other iturins, which could in turn help to develop new or improved antifungal formulations or result in novel strategies to prevent fungal spoilage. © 2013 Published by Elsevier B.V. All rights reserved.


Liu G.-H.,Chinese Academy of Agricultural Sciences | Liu G.-H.,Hunan Agricultural University | Shao R.,University of The Sunshine Coast | Li J.-Y.,Chinese Academy of Agricultural Sciences | And 4 more authors.
BMC Genomics | Year: 2013

Background: Analyses of mitochondrial (mt) genome sequences in recent years challenge the current working hypothesis of Nematoda phylogeny proposed from morphology, ecology and nuclear small subunit rRNA gene sequences, and raise the need to sequence additional mt genomes for a broad range of nematode lineages.Results: We sequenced the complete mt genomes of three Ascaridia species (family Ascaridiidae) that infest chickens, pigeons and parrots, respectively. These three Ascaridia species have an identical arrangement of mt genes to each other but differ substantially from other nematodes. Phylogenetic analyses of the mt genome sequences of the Ascaridia species, together with 62 other nematode species, support the monophylies of seven high-level taxa of the phylum Nematoda: 1) the subclass Dorylaimia; 2) the orders Rhabditida, Trichinellida and Mermithida; 3) the suborder Rhabditina; and 4) the infraorders Spiruromorpha and Oxyuridomorpha. Analyses of mt genome sequences, however, reject the monophylies of the suborders Spirurina and Tylenchina, and the infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. Monophyly of the infraorder Ascaridomorpha varies depending on the methods of phylogenetic analysis. The Ascaridomorpha was more closely related to the infraorders Rhabditomorpha and Diplogasteromorpha (suborder Rhabditina) than they were to the other two infraorders of the Spirurina: Oxyuridorpha and Spiruromorpha. The closer relationship among Ascaridomorpha, Rhabditomorpha and Diplogasteromorpha was also supported by a shared common pattern of mitochondrial gene arrangement.Conclusions: Analyses of mitochondrial genome sequences and gene arrangement has provided novel insights into the phylogenetic relationships among several major lineages of nematodes. Many lineages of nematodes, however, are underrepresented or not represented in these analyses. Expanding taxon sampling is necessary for future phylogenetic studies of nematodes with mt genome sequences. © 2013 Liu et al.; licensee BioMed Central Ltd.


Liao Y.,China Agricultural University | Liao Y.,Chinese Academy of Agricultural Sciences | Wu W.L.,China Agricultural University | Meng F.Q.,China Agricultural University | And 2 more authors.
Biogeosciences | Year: 2015

Agricultural intensification has contributed greatly to the sustained food supply of China's population of 1.3 billion over the 30-year period from 1982 to 2011. Intensification has several and widely recognized negative environmental impacts including depletion of water resources, pollution of water bodies, greenhouse gas emissions and soil acidification. However, there have been few studies over this period on the impacts of intensification on soil organic carbon (SOC) at the regional level. The present study was conducted in Huantai County, a typical intensive farming region in northern China, to analyze the temporal dynamics of SOC influenced by climate and farming practices. The results indicate that from 1982 to 2011, SOC content and density in the 0-20 cm layer of the cropland increased from 7.8 ± 1.6 to 11.0 ± 2.3 g kg-1 (41%) and from 21.4 ± 4.3 to 33.0 ± 7.0 Mg ha-1 (54%), respectively. The SOC stock (0-20 cm) of the farmland for the entire county increased from 0.75 to 1.2 Tg (59%). Correlation analysis revealed that incorporation of crop residues significantly increased SOC, while an increase in the mean annual temperature decreased the SOC level. Therefore, agricultural intensification has increased crop productivity and contributed to SOC sequestration in northern China. In the near future, more appropriate technologies and practices must be developed and implemented for a maintenance or enhancement of SOC in this region and elsewhere in northern China, which also reduce non-CO2 greenhouse gas emissions, since the climate benefit from the additional SOC storage is estimated to be smaller than the negative climate impacts of N2O from N fertilizer additions © Author(s) 2015. CC Attribution 3.0 License.


Wang D.,Chinese Academy of Agricultural Sciences | Wang D.,Shenyang University | Pan Y.,Chinese Academy of Agricultural Sciences | Zhao X.,Chinese Academy of Agricultural Sciences | And 4 more authors.
BMC Genomics | Year: 2011

Background: Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements.Results: There were 5,284 genes detected to be differentially expressed under drought stress. Most of these genes were tissue- or stage-specific regulated by drought. The tissue-specific down-regulated genes showed distinct function categories as photosynthesis-related genes prevalent in leaf, and the genes involved in cell membrane biogenesis and cell wall modification over-presented in root and young panicle. In a drought environment, several genes, such as GA2ox, SAP15, and Chitinase III, were regulated in a reciprocal way in two tissues at the same development stage. A total of 261 transcription factor genes were detected to be differentially regulated by drought stress. Most of them were also regulated in a tissue- or stage-specific manner. A cis-element containing special CGCG box was identified to over-present in the upstream of 55 common induced genes, and it may be very important for rice plants responding to drought environment.Conclusions: Genome-wide gene expression profiling revealed that most of the drought differentially expressed genes (DEGs) were under temporal and spatial regulation, suggesting a crosstalk between various development cues and environmental stimuli. The identification of the differentially regulated DEGs, including TF genes and unique candidate cis-element for drought responsiveness, is a very useful resource for the functional dissection of the molecular mechanism in rice responding to environment stress. © 2011 Wang et al; licensee BioMed Central Ltd.


Sun W.,CAS Institute of Botany | Xu X.,Xuzhou Normal University | Zhu H.,CAS Institute of Botany | Liu A.,CAS Institute of Botany | And 3 more authors.
Plant and Cell Physiology | Year: 2010

Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Extensive research has been focused on physiological and quantitative trait locus (QTL) characterization of wild tomato species in comparison with cultivated tomato. However, the global gene expression modification of wild tomato in response to salt stress is not well known. A wild tomato genotype, Solanum pimpinellifolium 'PI365967' is significantly more salt tolerant than the cultivar, Solanum lycopersicum 'Moneymaker', as evidenced by its higher survival rate and lower growth inhibition at the vegetative stage. The Affymetrix Tomato Genome Array containing 9,200 probe sets was used to compare the transcriptome of PI365967 and Moneymaker. After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared with Moneymaker. The salt overly sensitive (SOS) pathway was found to be more active in PI365967 than in Moneymaker, coinciding with relatively less accumulation of Na+ in shoots of PI365967. A gene encoding salicylic acid-binding protein 2 (SABP2) was induced by salinity only in PI365967, suggesting a possible role for salicylic acid signaling in the salt response of PI365967. The fact that two genes encoding lactoylglutathione lyase were salt inducible only in PI365967, together with much higher basal expression of several glutathione S-transferase genes, suggested a more effective detoxification system in PI365967. The specific down-regulation in PI365967 of a putative high-affinity nitrate transporter, known as a repressor of lateral root initiation, may explain the better root growth of this genotype during salt stress. © 2010 The Author.


Wu X.-Y.,CAS Institute of Botany | Kuai B.-K.,Fudan University | Jia J.-Z.,Chinese Academy of Agricultural Sciences | Jing H.-C.,CAS Institute of Botany
Journal of Integrative Plant Biology | Year: 2012

Leaf senescence can impact crop production by either changing photosynthesis duration, or by modifying the nutrient remobilization efficiency and harvest index. The doubling of the grain yield in major cereals in the last 50 years was primarily achieved through the extension of photosynthesis duration and the increase in crop biomass partitioning, two things that are intrinsically coupled with leaf senescence. In this review, we consider the functionality of a leaf as a function of leaf age, and divide a leaf's life into three phases: the functionality increasing phase at the early growth stage, the full functionality phase, and the senescence and functionality decreasing phase. A genetic framework is proposed to describe gene actions at various checkpoints to regulate leaf development and senescence. Four categories of genes contribute to crop production: those which regulate (I) the speed and transition of early leaf growth, (II) photosynthesis rate, (III) the onset and (IV) the progression of leaf senescence. Current advances in isolating and characterizing senescence regulatory genes are discussed in the leaf aging and crop production context. We argue that the breeding of crops with leaf senescence ideotypes should be an essential part of further crop genetic improvement. © 2012 Institute of Botany, Chinese Academy of Sciences.


Zhang M.,Chinese Academy of Agricultural Sciences | Shen S.,CAS Institute of Botany
Journal of Separation Science | Year: 2013

Protein extraction is a crucial step for proteomics studies. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis (2DE) analysis in Jerusalem artichoke (Helianthus tuberosus L.), three different protein extraction methods - trichloroacetic acid/acetone, Mg/NP-40, and phenol/ammonium acetate - were evaluated using Jerusalem artichoke leaves as source materials. Of the three methods, trichloroacetic acid/acetone yielded the best protein separation pattern and highest number of protein spots in 2DE analysis. Proteins highly abundant in leaves, such as Rubisco, are typically problematic during leaf 2DE analysis, however, and this disadvantage was evident using trichloroacetic acid/acetone. To reduce the influence of abundant proteins on the detection of low-abundance proteins, we optimized the trichloroacetic acid/acetone method by incorporating a PEG fractionation approach. After optimization, 363 additional (36.2%) protein spots were detected on the 2DE gel. Our results suggest that trichloroacetic acid/acetone method is a better protein extraction technique than Mg/NP-40 and phenol/ammonium acetate in Jerusalem artichoke leaf 2DE analysis, and that trichloroacetic acid/acetone method combined with PEG fractionation procedure is the most effective approach for leaf 2DE analysis of Jerusalem artichoke. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Xiao Z.,Chinese Academy of Agricultural Sciences | Yang Y.,Chinese Academy of Agricultural Sciences | Li Y.,Chinese Academy of Agricultural Sciences | Fan X.,Chinese Academy of Agricultural Sciences | Ding S.,China Agricultural University
Analytica Chimica Acta | Year: 2013

A rapid, sensitive, and environmental-friendly multi-residue method has been developed for the simultaneous determination of seven neonicotinoid insecticides (dinotefuran, nitenpyram, thiamethoxam, imidacloprid, clothianidin, acetamiprid, and thiacloprid) residues in eel samples. Subcritical water extraction was investigated as a novel and alternative technology for the extraction of neonicotinoids from eel matrices and the results were compared with the conventional ultrasonic and shaking extraction. The target compounds were identified and quantitatively determined by ultra-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry (UPLC-MS/MS) operated in multiple reaction monitoring mode. Under the current optimized chromatographic conditions, each LC run was completed in 5min. Average recoveries of the seven analytes from fortified samples ranged between 84.6% and 102.0%, with relative standard deviations (RSD) lower than 10.8%. The limits of detection (LODs) and quantification (LOQs) for neonicotinoids were in the ranges of 0.12-0.36μgkg-1 and 0.42-1.12μgkg-1, respectively. The proposed method is fast, sensitive, easy to perform, water-based thus more environmentally acceptable, making it applicable for high-throughput monitoring of insecticides residues in aquatic products. © 2013 Elsevier B.V.


Du T.,China Agricultural University | Kang S.,China Agricultural University | Sun J.,Chinese Academy of Agricultural Sciences | Zhang X.,CAS Institute of Genetics and Developmental Biology | Zhang J.,Hong Kong Baptist University
Agricultural Water Management | Year: 2010

Water shortage is the major bottleneck that limits sustainable development of agriculture in north China. Crop physiological water-saving irrigation methods such as temporal (regulated deficit irrigation) and spatial (partial root zone irrigation) deficit irrigation have been tested with much improved crop water use efficiency (WUE) without significant yield reduction. Field experiments were conducted to investigate the effect of (1) spatial deficit irrigation on spring maize in arid Inland River Basin of northwest China during 1997-2000; (2) temporal deficit irrigation on winter wheat in semi-arid Haihe River Basin during 2003-2007 and (3) temporal deficit irrigation on winter wheat and summer maize in Yellow River Basin during 2006-2007. Results showed that alternate furrow irrigation (AFI) maintained similar photosynthetic rate (Pn) but reduced transpiration rate (Tr), and thus increased leaf WUE of maize. It also showed that the improved WUE might only be gained for AFI under less water amount per irrigation. The feasible irrigation cycle is 7d in the extremely arid condition in Inner River Basin of northwest China and less water amount with more irrigation frequency is better for both grain yield and WUE in semi-arid Haihe River Basin of north China. Field experiment in Yellow River Basin of north China also suggests that mild water deficit at early seedling stage is beneficial for grain yield and WUE of summer maize, and the deficit timing and severity should be modulated according to the drought tolerance of different crop varieties. The economical evapotranspiration for winter wheat in Haihe River Basin, summer maize in Yellow River Basin of north China and spring maize in Inland River Basin of northwest China are 420.0 mm, 432.5 mm and 450.0 mm respectively. Our study in the three regions in recent decade also showed that AFI should be a useful water-saving irrigation method for wide-spaced cereals in arid region, but mild water deficit in earlier stage might be a practical irrigation strategy for close-planting cereals. Application of such temporal and spatial deficit irrigation in field-grown crops has greater potential in saving water, maintaining economic yield and improving WUE. © 2009 Elsevier B.V. All rights reserved.


Askarian F.,University of Tromsø | Zhou Z.,Chinese Academy of Agricultural Sciences | Olsen R.E.,Norwegian Institute of Marine Research | Sperstad S.,University of Tromsø | Ringo E.,University of Tromsø
Aquaculture | Year: 2012

The present investigation evaluated the effect of chitin (5% supplementation) on the adherent aerobic intestinal microbiota of Atlantic salmon (Salmo salar L.). One hundred and seventy three isolates were isolated but 34 isolates died prior to positive identification. Sixty four out of 139 autochthonous gut bacteria were further identified by 16S rRNA gene sequencing and further tested for protease, amylase, cellulase, phytase, lipase and chitinase activities. Moreover, the most promising enzyme-producing bacteria and intestinal lactic acid bacteria (LAB) were tested for in vitro growth inhibition of four important fish pathogens: Aeromonas salmonicida subsp. salmonicida, Vibrio (Listonella) anguillarum, Moritella viscosa and Carnobacterium maltaromaticum. Dietary chitin modulates the gut microbiota but not the portion of enzyme-producing gut bacteria. LAB were only isolated from fish fed the chitin supplemented diet and they were able to inhibit in vitro growth of 3 of the 4 pathogens. However, the most promising gut bacteria isolated in the present study with respect to enzyme production and in vitro growth inhibition showed high similarity to Bacillus thuringiensis by 16S rRNA gene sequencing. © 2011 Elsevier B.V.


Dong H.-Y.,China Agricultural University | Kong C.-H.,China Agricultural University | Wang P.,CAS Shenyang Institute of Applied Ecology | Huang Q.-L.,Chinese Academy of Agricultural Sciences
Soil Biology and Biochemistry | Year: 2014

Despite increasing knowledge of soil microbial community dynamics involved in various factors, relatively little is known about plant-derived allelochemicals and their impact on the development of soil microbial community either independently or synergistically with the other factors. Here we examined an allelochemical friedelin and its relation to microbial community in soils from a long-term agroecosystem under different land uses and seasons. Four land uses (paddy field, maize field, barren and fallow) in an eight-year old continuous establishment were selected to conduct the experiments. Soil samples were taken in spring, summer, autumn and winter at different depths. Friedelin was quantified by gas chromatography (GC) and microbial communities were characterized by phospholipid fatty acid (PLFA) analysis. Subsequently, friedelin was found in all soils but its concentration varied with land uses, seasons and soil depths. The largest observed concentrations always occurred in surface soils and winter samples of all four land uses. Compared with tillage fields, barren and fallow contained a greater amount of friedelin. Both soil microbial community and friedelin varied seasonally, and there were positive relationships between friedelin and microbial community. The signature lipid biomarkers of soil bacteria and fungi, and soil microbial community structure were affected under friedelin application. The results suggest that friedelin may be one of the factors involved in microbial community dynamics under different land-use scenarios and seasonal variations, and friedelin-specific influences in the corresponding microbial community composition result in changes in the microbial community structure in soils from a given agroecosystem. © 2013 Elsevier Ltd.


Wang Y.,China Agricultural University | He L.,China Agricultural University | He L.,China National Institute of Biological Sciences | Li H.-D.,China Agricultural University | And 4 more authors.
Cell Research | Year: 2010

Potassium transporters play crucial roles in K+ uptake and translocation in plants. However, so far little is known about the regulatory mechanism of potassium transporters. Here, we show that a Shaker-like potassium channel AtKC1, encoded by the AtLKT1 gene cloned from the Arabidopsis thaliana low-K+ (LK)-tolerant mutant Atlkt1, significantly regulates AKT1-mediated K+ uptake under LK conditions. Under LK conditions, the Atkc1 mutants maintained their root growth, whereas wild-type plants stopped their root growth. Lesion of AtKC1 significantly enhanced the tolerance of the Atkc1 mutants to LK stress and markedly increased K+ uptake and K+ accumulation in the Atkc1-mutant roots under LK conditions. Electrophysiological results showed that AtKC1 inhibited the AKT1-mediated inward K+ currents and negatively shifted the voltage dependence of AKT1 channels. These results demonstrate that the 'silent' K+ channel α-subunit AtKC1 negatively regulates the AKT1-mediated K+ uptake in Arabidopsis roots and consequently alters the ratio of root-to-shoot under LK stress conditions. © 2010 IBCB, SIBS, CAS. All rights reserved.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: SFS-13-2015 | Award Amount: 5.24M | Year: 2016

MyToolBox mobilises a multi-actor partnership (academia, farmers, technology SMEs, food industry and policy stakeholders) to develop novel interventions aimed at achieving a 20-90% reduction in crop losses due to fungal and mycotoxin contamination. MyToolBox will not only pursue a field-to-fork approach but will also consider safe use options of contaminated batches, such as the efficient production of biofuels. A major component of MyToolBox, which also distinguishes this proposal from previous efforts in the area mycotoxin reduction, is to provide the recommended measures to the end users along the food and feed chain in a web-based Toolbox. Cutting edge research will result in new interventions, which will be integrated together with existing measures in the Toolbox that will guide the end user as to the most effective measure(s) to be taken to reduce crop losses. We will focus on small grain cereals, maize, peanuts and dried figs, applicable to agricultural conditions in EU and China. Crop losses using existing practices will be compared with crop losses after novel pre-harvest interventions including investigation of genetic resistance to fungal infection, cultural control, the use of novel biopesticides (organic-farming compliant), competitive biocontrol treatment and development of forecasting models to predict mycotoxin contamination. Research into post-harvest measures including real-time monitoring during storage, innovative sorting of crops using vision-technology and novel milling technology will enable cereals with higher mycotoxin levels to be processed without breaching regulatory limits in finished products. Research into the effects of baking on mycotoxin levels will provide better understanding of process factors used in mycotoxin risk assessment. Involvement of leading institutions from China are aimed at establishing a sustainable cooperation in mycotoxin research between the EU and China.


Chen L.J.,China Agricultural University | Xing L.,Chinese Academy of Agricultural Sciences | Han L.J.,China Agricultural University
Journal of Environmental Quality | Year: 2010

With increasing concern over potential pollution from farm wastes, there is a need for rapid and robust methods that can analyze livestock manure nutrient content. The near infrared spectroscopy (NIRS) method was used to determine nutrient content in diverse poultry manure samples (n = 91). Various standard preprocessing methods (derivatives, multiplicative scatter correction, Savitsky-Golay smoothing, and standard normal variate) were applied to reduce data systemic noise. In addition, a new preprocessing method known as direct orthogonal signal correction (DOSC) was tested. Calibration models for ammonium nitrogen, total potassium, total nitrogen, and total phosphorus were developed with the partial least squares (PLS) method. The results showed that all the preprocessed data improved prediction results compared with the non-preprocessing method. Compared with the other preprocessing methods, the DOSC method gave the best results. The DOSC method achieved moderately successful prediction for ammonium nitrogen, total nitrogen, and total phosphorus. However, all preprocessing methods did not provide reliable prediction for total potassium. This indicates the DOSC method, especially combined with other preprocessing methods, needs further study to allow a more complete predictive analysis of manure nutrient content. Copyright © 2010 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.


Wang H.-f.,Chinese Academy of Agricultural Sciences | Zong X.-x.,Chinese Academy of Agricultural Sciences | Guan J.-p.,Chinese Academy of Agricultural Sciences | Yang T.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Theoretical and Applied Genetics | Year: 2012

Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit. © 2011 Springer-Verlag.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2010.1.4-05 | Award Amount: 575.53K | Year: 2011

OPTICHINA (Breeding to Optimise Chinese Agriculture) aims to link the crop breeding research activities carried out by European and Chinese researchers. This Co-ordination Action build on previous and ongoing collaborative research experience of European and Chinese partners collaborating in this consortium. To date there have not been specific actions devoted to coordination of breeding research activities for better crop adaptation to abiotic stresses. Despite this European and Chinese scientists have been collaborating in a number of EC-funded research projects from 5th and 6th FP, together with other projects from specific EU member States, aimed at breeding the major grain crops for improved adaptation to abiotic stresses. OPTICHINA will focus specifically on research requirements to breeding for improved adaptation to abiotic stresses and sustainability of major herbaceous crops in both China and Europe. This require an integrative approach linking diverse disciplines and scales.This Co-ordination Action will integrate Chinese and European scientists internationally recognized as experts in different areas around crop breeding and adaptation to major abiotic stresses and avenues to raise yield potential. Coordinators and partners of different International Cooperation European projects together with Chinese researchers with high ranking of bilateral collaboration between China and Europe will actively participate. The specific aims of the OPTICHINA initiative are: To support networks of European agricultural scientists working with China. To develop an inventory of experimental resources and datasets. To ensure adoption of existing knowledge and technology and the implementation of best practices. To fund short training visits of Chinese researchers in other laboratories To build links between research scientists working in molecular, genetic, bioinformatics and physiological, environmental research and the end users of their science. To build up fut


Ying H.,Zhejiang GongShang University | Jiang H.,Chinese Academy of Agricultural Sciences | Liu H.,Zhejiang GongShang University | Chen F.,Zhejiang GongShang University | Du Q.,Zhejiang GongShang University
Journal of Chromatography A | Year: 2014

High-speed countercurrent chromatographic separation (HSCCC) possesses the property of zero-loss of sample, which is very useful for the screening of bioactive components. In the present study, the ethyl acetate. n-butanol gradient HSCCC solvent system composed of n-hexane-ethyl acetate. n-butanol-water was investigated for the screening of bioactive substances. To screen the antiproliferative compounds in okra extract, we used the stationary phase ethyl acetate n-butanol-water (1:1:10) as the stationary phase, and eluted the antiproliferative components by 6-steps of gradient using mobile phases n-hexane-ethyl acetate (1:2), n-hexane-ethyl acetate (1:4), n-hexane-ethyl acetate (0:4), n-butanol-ethyl acetate (1:4) n-butanol-ethyl acetate (1:2), n-butanol-ethyl acetate (2:2), and n-butanol-ethyl acetate (2:1). The fractions collected from HSCCC separation with the gradient solvent system were assayed for antiproliferative activity against cancer cells. Bioactive components were identified: a major anti-cancer compound, 4'-hydroxy phenethyl trans-ferulate, with middle activity, and a minor anti-cancer compound, carolignan, with strong activity. The result shows that the gradient solvent system is potential for the screening of bioactive compounds from natural products. © 2014 Elsevier B.V.


Zuo Z.,Hunan University | Zuo Z.,University of California at Los Angeles | Liu H.,University of California at Los Angeles | Liu B.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Current Biology | Year: 2011

Cryptochromes are blue light receptors that mediate light regulation of gene expression in all major evolution lineages, but the molecular mechanism underlying cryptochrome signal transduction remains not fully understood [1, 2]. It has been reported that cryptochromes suppress activity of the multifunctional E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) to regulate gene expression in response to blue light [3, 4]. But how plant cryptochromes mediate light suppression of COP1 activity remains unclear. We report here that Arabidopsis CRY2 (cryptochrome 2) undergoes blue light-dependent interaction with the COP1-interacting protein SUPPRESSOR OF PHYTOCHROME A 1 (SPA1) [5, 6]. We demonstrate that SPA1 acts genetically downstream from CRY2 to mediate blue light suppression of the COP1-dependent proteolysis of the flowering-time regulator CONSTANS (CO) [7, 8]. We further show that blue light-dependent CRY2-SPA1 interaction stimulates CRY2-COP1 interaction. These results reveal for the first time a wavelength-specific mechanism by which a cryptochrome photoreceptor mediates light regulation of protein degradation to modulate developmental timing in Arabidopsis. © 2011 Elsevier Ltd.


Zhang L.,Chinese Academy of Agricultural Sciences | Zhang L.,Inner Mongolia Agricultural University | Li Z.,Chinese Academy of Agricultural Sciences | Quan R.,Chinese Academy of Agricultural Sciences | And 5 more authors.
Plant Physiology | Year: 2011

Accumulating investigations reveal that ethylene signaling is involved in the salt response in Arabidopsis (Arabidopsis thaliana), and it has been reported that overexpression of a number of ethylene response factor (ERF) genes enhances salt tolerance; however, transcriptional regulation of the ethylene signal component ETHYLENE INSENSITIVE3 (EIN3) in the salt response has not been clearly defined. Consulting microarray data and transcriptional confirmations showed that three of the ERF genes were ethylene and salt inducible, named ESE1 to ESE3. Additionally, the expression of one of the ESE genes (ESE1) was suppressed in ein2, ein3-1, eil1-3, and ein3 eil1 but enhanced in EIN3-overexpressing (EIN3ox) lines. Inhibitors of ethylene biosynthesis, aminoethoxyvinylglycine, and ethylene action, AgNO3, reduced the expression of ESE1, while ethylene overproduction eto mutants enhanced the expression of ESE1, indicating that ESE1 is an ethylene-modulated gene downstream of EIN3/EIL1. Further analyses with biochemical and molecular approaches revealed that EIN3 physically binds to the ESE1 promoter, demonstrating that ESE1 was one target of EIN3. ESE1 in turn binds to promoters of salt-related genes, such as RD29A and COR15A. Moreover, either EIN3ox or ESE1ox was sufficient to enhance transcript levels of salt-related genes and salt tolerance. In addition, ESE1ox in ein3 enhanced the salt response during seed germination and seedling development, demonstrating that ESE1 is genetically downstream of EIN3. Thus, the evidence in this report reveals that the transcriptional complex of EIN3-ESE1 is a crucial event in the salt response, thereby connecting the transcriptional regulation of EIN3 and the downstream ERF protein ESE1 in the salt response. © 2011 American Society of Plant Biologists. All rights reserved.


Zhang Z.,Chinese Academy of Agricultural Sciences | Ji R.,Chinese Academy of Agricultural Sciences | Li H.,Chinese Academy of Agricultural Sciences | Zhao T.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Molecular Plant | Year: 2015

Arabidopsis phytochrome B (phyB) is the major photoreceptor that senses the ratio of red to far-red light (R:FR) to regulate the shade-avoidance response (SAR). It has been hypothesized that altered homeostasis of phytohormones such as auxin and strigolactone is at least partially responsible for SAR, but the mechanism underlying phyB regulation of the hormonal change is not fully understood. Previously we reported that CONSTANS-LIKE 7 (COL7) enhances branching number under high R:FR but not under low R:FR, implying that COL7 may be involved in the phyB-mediated SAR. In this study, we provide evidence that COL7 reduces auxin levels in a high R:FR-dependent manner. We found that the phyB mutation suppresses the COL7-induced branching proliferation. Moreover, COL7 promotes mRNA expression of SUPERROOT 2 (SUR2), which encodes a suppressor of auxin biosynthesis, in high R:FR but not in low R:FR. Consistently with these results, deficiency of phyB suppresses the elevated transcription of SUR2 in COL7 overexpression plants grown in high R:FR. Taking these results together with data suggesting that photo-excited phyB is required for stabilization of the COL7 protein, we argue that COL7 is a critical factor linking light perception to changes in auxin level in Arabidopsis. © 2014 The Authors. All rights reserved.


Cheng Y.,Shanghai Key Laboratory of Veterinary Biotechnology | Sun Y.,Chinese Academy of Agricultural Sciences | Wang H.,Shanghai Key Laboratory of Veterinary Biotechnology | Yan Y.,Shanghai Key Laboratory of Veterinary Biotechnology | And 2 more authors.
Journal of Immunology | Year: 2015

Stimulator of IFN genes (STING) is an adaptor that functions downstream of retinoic acid-inducible gene I (RIG-I) in mammalian cells; however, RIG-I is absent in chickens. We identified chicken STING (chSTING) as a critical mediator of virus-triggered type I IFN signaling in RIG-I-null chicken cells. Overexpression of chSTING in DF-1 cells inhibited Newcastle disease virus and avian influenza virus (AIV) viral replication and activated IRF-7 and NF-κB to induce expression of type I IFNs. Knockdown of endogenous chSTING abolished virus-triggered activation of IRF-7 and IFN-β and increased viral yield. chSTING was a critical component in the virus-triggered IRF-7 activation pathway and the cellular antiviral response. chSTING predominantly localized to the outer membrane of the endoplasmic reticulum and was also found in the mitochondrial membrane. Furthermore, knockdown of chSTING blocked polyinosinic-polycytidylic acid-, poly(deoxyadenylic-deoxythymidylic) acid-, and melanoma differentiation-associated gene 5 (MDA5)-stimulated induction of IFN-β. Coimmunoprecipitation experiments indicated that chicken MDA5 could interact with chSTING, and this interaction was enhanced by ectopically expressed chicken mitochondrial antiviral-signaling protein. Together, these results indicated that chSTING is an important regulator of chicken innate immune signaling and might be involved in the MDA5 signaling pathway in chicken cells. These results help with understanding the biological role of STING in innate immunity during evolution. Copyright © 2015 by The American Association of Immunologists, Inc.


Chen H.,Chinese Academy of Agricultural Sciences | Wang L.,Chinese Academy of Agricultural Sciences | Wang S.,Chinese Academy of Agricultural Sciences | Liu C.,CSIRO | And 2 more authors.
PLoS ONE | Year: 2015

Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina pairedend sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value < 1.0E-5). A total of 6,585 (8.3%) were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species. Copyright: © 2015 Chen et al.


Liu B.,Chinese Academy of Agricultural Sciences | Liu B.,University of California at Los Angeles | Zuo Z.,University of California at Los Angeles | Zuo Z.,Hunan University | And 4 more authors.
Genes and Development | Year: 2011

Plant photoreceptors mediate light suppression of the E3 ubiquitin ligase COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) to affect gene expression and photomorphogenesis. However, how photoreceptors mediate light regulation of COP1 activity remains unknown. We report here that Arabidopsis blue-light receptor cryptochrome 1 (CRY1) undergoes blue-light-dependent interaction with the COP1-interacting protein SPA1 (SUPPRESSOR OF PHYTOCHROME A). We further show that the CRY1- SPA1 interaction suppresses the SPA1-COP1 interaction and COP1-dependent degradation of the transcription factor HY5. These results are consistent with a hypothesis that photoexcited CRY1 interacts with SPA1 to modulate COP1 activity and plant development. © 2011 by Cold Spring Harbor Laboratory Press.


Wang J.,Tsinghua University | Zhang Y.,Tsinghua University | Chen Y.,Nanjing University of Technology | Lin M.,Chinese Academy of Agricultural Sciences | Lin Z.,Tsinghua University
Biotechnology and Bioengineering | Year: 2012

Lignocellulosic biomass is regarded as the most viable source of feedstock for industrial biorefinery, but the harmful inhibitors generated from the indispensable pretreatments prior to fermentation remain a daunting technical hurdle. Using an exogenous regulator, irrE, from the radiation-resistant Deinococcus radiodurans, we previously showed that a novel global regulator engineering (GRE) approach significantly enhanced tolerances of Escherichia coli to alcohol and acetate stresses. In this work, an irrE library was subjected to selection under various stresses of furfural, a typical hydrolysate inhibitor. Three furfural tolerant irrE mutants including F1-37 and F2-1 were successfully obtained. The cells containing these mutants reached OD600 levels of 4- to 16-fold of that for the pMD18T cells in growth assay under 0.2% (v/v) furfural stress. The cells containing irrE F1-37 and F2-1 also showed considerably reduced intracellular oxygen species (ROS) levels under furfural stress. Moreover, these two irrE mutants were subsequently found to confer significant cross tolerances to two other most common inhibitors, 5-hydroxymethyl-2-furaldehyde (HMF), vanillin, as well as real lignocellulosic hydrolysates. When evaluated in Luria-Bertani (LB) medium supplemented with corn stover cellulosic hydrolysate (prepared with a solid loading of 30%), the cells containing the mutants exhibited lag phases markedly shortened by 24-44h in comparison with the control cells. This work thus presents a promising step forward to resolve the inhibitor problem for E. coli. From the view of synthetic biology, irrE can be considered as an evolvable "part" for various stresses. Furthermore, this GRE approach can be extended to exploit other exogenous global regulators from extremophiles, and the native counterparts in E. coli, for eliciting industrially useful phenotypes. © 2012 Wiley Periodicals, Inc.


Tang Y.,CAS Shanghai Institutes for Biological Sciences | Zhong G.,Chinese Academy of Agricultural Sciences | Zhu L.,CAS Shanghai Institutes for Biological Sciences | Liu X.,CAS Shanghai Institutes for Biological Sciences | And 6 more authors.
Journal of Immunology | Year: 2010

Ubiquitin-like protein ISG15, which is robustly induced by IFN or virus, is implicated to inhibit influenza Avirus (IAV) in vivo. But the underlying mechanism still remains largely unknown. In this study, we report that Herc5 could catalyze conjugation of ISG15 onto IAV-NS1 protein, the critical virulence factor of IAV. This modification produces two more species, respectively mapped to IAVNS1 at lysine 20, 41, 217, 219, and 108, 110, and 126. The ISGylated IAV-NS1 fails to form homodimers and inhibits relevant antiviral processes. Knockdown of Herc5 or ISG15 could partially alleviate IFN-β-induced antiviral activities against IAV, whereas ectopic expression of the Herc5-mediated ISGylation system could distinctly potentiate IFN-β-induced antiviral effects against IAV. Notably, IAV-NS1s of H5N1 avian IAVs display less ISGylation species than that of IAV-PR8/34 (human H1N1). Consistently, IAV-PR8/34 mutants deprived of IAV-NS1's ISGylation exhibit augmented viral propagation and virulence in both cultured cells and mice. Our study reports the first microbial target of ISGylation and uncovers the direct antiviral function and mechanism of this novel modification. Copyright © 2010 by The American Association of Immunologists, Inc.


Guo Y.,Chinese Academy of Agricultural Sciences | Gan S.-S.,Cornell University
Journal of Experimental Botany | Year: 2014

Leaf senescence is a very important trait that limits yield and biomass accumulation of agronomic crops and reduces post-harvest performance and the nutritional value of horticultural crops. Significant advance in physiological and molecular understanding of leaf senescence has made it possible to devise ways of manipulating leaf senescence for agricultural improvement. There are three major strategies in this regard: (i) plant hormone biology-based leaf senescence manipulation technology, the senescence-specific gene promoter-directed IPT system in particular; (ii) leaf senescence-specific transcription factor biology-based technology; and (iii) translation initiation factor biology-based technology. Among the first strategy, the P SAG12-IPT autoregulatory senescence inhibition system has been widely explored and successfully used in a variety of plant species for manipulating senescence. The vast majority of the related research articles (more than 2000) showed that crops harbouring the autoregulatory system displayed a significant delay in leaf senescence without any abnormalities in growth and development, a marked increase in grain yield and biomass, dramatic improvement in horticultural performance, and/or enhanced tolerance to drought stress. This technology is approaching commercialization. The transcription factor biology-based and translation initiation factor biology-based technologies have also been shown to be very promising and have great potentials for manipulating leaf senescence in crops. Finally, it is speculated that technologies based on the molecular understanding of nutrient recycling during leaf senescence are highly desirable and are expected to be developed in future translational leaf senescence research. © 2014 The Author.


Shao W.,CAS Shanghai Institutes for Biological Sciences | Zhao Q.-Y.,CAS Shanghai Institutes for Biological Sciences | Wang X.-Y.,CAS Shanghai Institutes for Biological Sciences | Xu X.-Y.,CAS Shanghai Institutes for Biological Sciences | And 4 more authors.
RNA | Year: 2012

Alternative splicing and trans-splicing events have not been systematically studied in the silkworm Bombyx mori. Here, the silkworm transcriptome was analyzed by RNA-seq. We identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans-splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is expressed sex-specifically in silkworm gonads. Trans-splicing of mod(mdg4) in silkworm was experimentally confirmed. We identified integrations from a common 5′-gene with 46 newly identified alternative 3′-exons that are located on both DNA strands over a 500-kb region. Other trans-splicing events in B. mori were predicted by bioinformatic analysis, in which 12 events were confirmed by RT-PCR, six events were further validated by chimeric SNPs, and two events were confirmed by allele-specific RT-PCR in F 1 hybrids from distinct silkworm lines of JS and L10, indicating that trans-splicing is more widespread in insects than previously thought. Analysis of the B. mori transcriptome by RNA-seq provides valuable information of regulatory alternative splicing events. The conservation of splicing events across species and newly identified trans-splicing events suggest that B. mori is a good model for future studies. Published by Cold Spring Harbor Laboratory Press. Copyright © 2012 RNA Society.


Zhang J.,Hebei Academy of Agriculture and Forestry science | Liang S.,Tsinghua University | Duan J.,Chinese Academy of Agricultural Sciences | Wang J.,Hebei Academy of Agriculture and Forestry science | And 5 more authors.
BMC Genomics | Year: 2012

Background: The peanut (Arachis hypogaea L.) is an important oilseed crop in tropical and subtropical regions of the world. However, little about the molecular biology of the peanut is currently known. Recently, next-generation sequencing technology, termed RNA-seq, has provided a powerful approach for analysing the transcriptome, and for shedding light on the molecular biology of peanut.Results: In this study, we employed RNA-seq to analyse the transcriptomes of the immature seeds of three different peanut varieties with different oil contents. A total of 26.1-27.2 million paired-end reads with lengths of 100 bp were generated from the three varieties and 59,077 unigenes were assembled with N50 of 823 bp. Based on sequence similarity search with known proteins, a total of 40,100 genes were identified. Among these unigenes, only 8,252 unigenes were annotated with 42 gene ontology (GO) functional categories. And 18,028 unigenes mapped to 125 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, 3,919 microsatellite markers were developed in the unigene library, and 160 PCR primers of SSR loci were used for validation of the amplification and the polymorphism.Conclusion: We completed a successful global analysis of the peanut transcriptome using RNA-seq, a large number of unigenes were assembled, and almost four thousand SSR primers were developed. These data will facilitate gene discovery and functional genomic studies of the peanut plant. In addition, this study provides insight into the complex transcriptome of the peanut and established a biotechnological platform for future research. © 2012 Zhang et al; licensee BioMed Central Ltd.


Shwab E.K.,University of Tennessee at Knoxville | Zhu X.-Q.,Chinese Academy of Agricultural Sciences | Majumdar D.,University of Tennessee at Knoxville | Pena H.F.J.,University of Sao Paulo | And 4 more authors.
Parasitology | Year: 2014

In recent years, an extensive collection of Toxoplasma gondii samples have been typed using a set of 10 PCR-RFLP genetic markers. Here we summarize the data reported until the end of 2012. A total of 1457 samples were typed into 189 genotypes. Overall, only a few genotypes dominate in the northern hemisphere, which is in stark contrast to the southern hemisphere where hundreds of genotypes coexist with none being notably dominant. PCR-RFLP genotype #1 (Type II clonal), #2 (Type III), #3 (Type II variant) and #10 (Type I) are identified globally. Genotypes #2 and #3 dominate in Africa, genotypes #9 (Chinese 1) and #10 are prevalent in Asia, genotypes #1, #2 and #3 are prevalent in Europe, genotypes #1, #2, #3, #4 and #5 dominate in North America (#4 and #5 are collectively known as Type 12). In Central and South America, there is no clear dominance of any genotype even though a few have relatively higher frequencies. Statistical analysis indicates significant differences among populations in Africa, Asia, Europe, North America, and Central and South America, with only Europe and North America exhibiting similar diversity. Collectively, the results revealed distinct population structures and geographical patterns of diversity in T. gondii. © Cambridge University Press 2013 This is a work of the U.S. Government and is not subject to copyright protection in the United States..


Sun Y.,Chinese Academy of Agricultural Sciences | Wang J.,Chinese Academy of Agricultural Sciences | Crouch J.H.,International Maize and Wheat Improvement Center | Xu Y.,International Maize and Wheat Improvement Center
Molecular Breeding | Year: 2010

Selective genotyping of individuals from the two tails of the phenotypic distribution of a population provides a cost efficient alternative to analysis of the entire population for genetic mapping. Past applications of this approach have been confounded by the small size of entire and tail populations, and insufficient marker density, which result in a high probability of false positives in the detection of quantitative trait loci (QTL). We studied the effect of these factors on the power of QTL detection by simulation of mapping experiments using population sizes of up to 3,000 individuals and tail population sizes of various proportions, and marker densities up to one marker per centiMorgan using complex genetic models including QTL linkage and epistasis. The results indicate that QTL mapping based on selective genotyping is more powerful than simple interval mapping but less powerful than inclusive composite interval mapping. Selective genotyping can be used, along with pooled DNA analysis, to replace genotyping the entire population, for mapping QTL with relatively small effects, as well as linked and interacting QTL. Using diverse germplasm including all available genetics and breeding materials, it is theoretically possible to develop an "all-in-one plate" approach where one 384-well plate could be designed to map almost all agronomic traits of importance in a crop species. Selective genotyping can also be used for genomewide association mapping where it can be integrated with selective phenotyping approaches. We also propose a breeding-to-genetics approach, which starts with identification of extreme phenotypes from segregating populations generated from multiple parental lines and is followed by rapid discovery of individual genes and combinations of gene effects together with simultaneous manipulation in breeding programs. © 2010 Springer Science+Business Media B.V.


Prasanna B.M.,Indian Agricultural Research Institute | Pixley K.,International Maize and Wheat Improvement Center | Pixley K.,University of Wisconsin - Madison | Warburton M.L.,U.S. Department of Agriculture | Xie C.-X.,Chinese Academy of Agricultural Sciences
Molecular Breeding | Year: 2010

Maize is one of the most important food and feed crops in Asia, and is a source of income for several million farmers. Despite impressive progress made in the last few decades through conventional breeding in the "Asia-7" (China, India, Indonesia, Nepal, Philippines, Thailand, and Vietnam), average maize yields remain low and the demand is expected to increasingly exceed the production in the coming years. Molecular marker-assisted breeding is accelerating yield gains in USA and elsewhere, and offers tremendous potential for enhancing the productivity and value of Asian maize germplasm. We discuss the importance of such efforts in meeting the growing demand for maize in Asia, and provide examples of the recent use of molecular markers with respect to (i) DNA fingerprinting and genetic diversity analysis of maize germplasm (inbreds and landraces/OPVs), (ii) QTL analysis of important biotic and abiotic stresses, and (iii) marker-assisted selection (MAS) for maize improvement. We also highlight the constraints faced by research institutions wishing to adopt the available and emerging molecular technologies, and conclude that innovative models for resource-pooling and intellectual-property-respecting partnerships will be required for enhancing the level and scope of molecular marker-assisted breeding for maize improvement in Asia. Scientists must ensure that the tools of molecular marker-assisted breeding are focused on developing commercially viable cultivars, improved to ameliorate the most important constraints to maize production in Asia. © 2010 Springer Science+Business Media B.V.


Wang L.,Chinese Academy of Agricultural Sciences | Li G.,Shandong Academy of Agricultural Sciences | Pena R.J.,International Maize and Wheat Improvement Center | Xia X.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Journal of Cereal Science | Year: 2010

Low-molecular-weight glutenin subunits (LMW-GS) play a key role in determining the processing quality of the end-use products of common wheat. The objectives of this study were to identify genes at Glu-A3 locus, develop the STS markers, and establish multiplex PCR with the STS markers for Glu-A3 alleles. Gene-specific PCR primers were designed to amplify six near-isogenic lines (NILs) and Glenlea with different Glu-A3 alleles (a, b, c, d, e, f and g) defined by the protein electrophoretic mobility. Three Glu-A3 genes with complete coding sequence were cloned, designated as GluA3-1, GluA3-2 and GluA3-3, respectively. Seven dominant allele-specific STS (sequence tagged sites) markers were designed based on the SNPs (single nucleotide polymorphisms) among different allelic variants for the discrimination of the Glu-A3 protein alleles a, b, c, d, e, f and g. Four multiplex PCRs were established including Glu-A3b + Glu-A3f, Glu-A3d + Glu-A3f, Glu-A3d + Glu-A3g, and Glu-A3b + Glu-A3e. These markers and multiplex-PCR systems were validated on 141 CIMMYT wheat varieties and advanced lines with different Glu-A3 alleles, confirming that they can be efficiently used in marker-assisted breeding. © 2010 Elsevier Ltd. All rights reserved.


Chen M.,Chinese Academy of Agricultural Sciences | Chen M.,Tsinghua University | Chen J.,Tsinghua University | Sun F.,Tsinghua University
Science of the Total Environment | Year: 2010

Agriculture related pollution has attracted the attention of policy makers as well as scientists in China as its contribution to water impairment has increased, and quantitative information at the national and regional levels is being sought to support decision making. However, traditional approaches are either time-consuming, expensive (e.g. national surveys) or oversimplified and crude (e.g. coefficient methods). Therefore, this study proposed an extended substance flow analysis (SFA) framework to estimate nutrient releases from agricultural and rural activities in China by depicting the nutrient flows in Chinese agro-ecosystems. The six-step process proposed herein includes: (a) system definition; (b) model development; (c) database development; (d) model validation; (e) results interpretation; and (f) uncertainty analysis. The developed Eubolism (Elementary Unit based nutrient Balance m. Ode. LIng in agro-eco. Syste. M) model combined a nutrient balance module with an emission inventory module to quantify the nutrient flows in the agro-ecosystem. The model was validated and then applied to estimate the total agricultural nutrient loads, identify the contribution of different agricultural and rural activities and different land use types to the total loads, and analyze the spatial pattern of agricultural nutrient emissions in China. These results could provide an entire picture of agricultural pollution at the national level and be used to support policy making. Furthermore, uncertainties associated with the structure of the elementary units, spatial resolution, and inputs/parameters were also analyzed to evaluate the robustness of the model results. © 2010 Elsevier B.V.


Liu Y.,Jilin University | Liu Y.,Academy of Military Medical Science | Zheng J.,Chinese Academy of Agricultural Sciences | Li J.,Jilin University | And 2 more authors.
Parasitology Research | Year: 2013

Rhomboid protein in Apicomplexa was associated with the process of host cell invasion. To evaluate the potential of the protein in eliciting protective immunity against challenge, a DNA vaccine pVAX1-Rho encoding Eimeria tenella rhomboid was constructed. Recombinant protein was expressed in Hela cells and verified by indirect immunofluorescence and western blotting analysis. In vivo experiments, 1-week-old chickens were randomly divided into three groups. Experimental group of chickens were immunized with DNA vaccines while control group of chickens were injected with pVAX1 plasmid alone or sterile water. Two weeks following the booster dose, all chickens were inoculated orally with 5 × 104 sporulated oocysts of E. tenella. The host immunity and protective efficacy of this vaccine against E. tenella challenge in broilers were evaluated. Results showed that specific antibody, the levels of interleukin-2 (IL-2), interferon-γ (IFN-γ), and the percentages of CD4+ and CD8+ T lymphocyte cells were significantly increased in the pVAX1-Rho group. Challenge experiments demonstrated that pVAX1-Rho vaccination could reduce oocyst excretion, decrease cecal lesion, increase bodyweight gains and provide chickens with oocysts decrease ratio around 75.8 %. These results suggest that the pVAX1-Rho was able to induce humoral and cellular responses and generate protective immunity against E. tenella infection. © 2012 Springer-Verlag Berlin Heidelberg.


Liu K.J.,Rice University | Dai J.,Rice University | Truong K.,Rice University | Song Y.,Chinese Academy of Agricultural Sciences | And 2 more authors.
PLoS Computational Biology | Year: 2014

One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM-a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism. © 2014 Liu et al.


Dong F.,Chinese Academy of Agricultural Sciences | Chen X.,Chinese Academy of Agricultural Sciences | Liu X.,Chinese Academy of Agricultural Sciences | Xu J.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Journal of Chromatography A | Year: 2012

The sensitive analytical method using quick, easy, cheap, effective, rugged, and safe (QuEChERS) procedure for simultaneous determination of five novel pyrazole fungicides residues in cereals (rice and wheat), vegetables (cucumber, tomato, and lettuce), and fruits (apple and grape) was developed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The five pyrazole fungicides (bixafen, fluxapyroxad, furametpyr, pyraclostrobin, and rabenzazole) were extracted from seven matrices using acetonitrile and subsequently cleaned up by octadecylsilane (C18) or graphitized carbon black (GCB) prior to LC-MS/MS analysis. The determination of the target compounds was achieved in less than 3.0min using an electrospray ionization source in positive mode (ESI+) for furametpyr, pyraclostrobin, and rabenzazole, while negative mode (ESI-) for bixafen and fluxapyroxad. The method showed excellent linearity (at least R2≥0.990) for all studied analytes. The limits of detection were below 3.0μgkg-1, and the limits of quantification did not exceed 9μgkg-1 in all matrices. The overall average recoveries in rice, wheat, cucumber, tomato, lettuce, apple, and grape at three levels (10, 100 and 1000μgkg-1) were ranged from 70.0% to 108% with all RSDs values less than 20.9% for all analytes. The method is demonstrated to be convenient and reliable for the routine monitoring of pyrazole fungicides in cereals, vegetables and fruits. © 2012 Elsevier B.V.


Liu G.-H.,Chinese Academy of Agricultural Sciences | Shao R.,University of The Sunshine Coast | Cai X.-Q.,Chinese Academy of Agricultural Sciences | Li W.-W.,Sun Yat Sen University | Zhu X.-Q.,Chinese Academy of Agricultural Sciences
Scientific Reports | Year: 2015

Human gnathostomiasis is an emerging food-borne parasitic disease caused by nematodes in the genus Gnathostoma. In spite of their significance as pathogens, these parasites remain poorly understood at the molecular level. In the present study, we sequenced the mitochondrial (mt) genome of G. spinigerum, which infects a range of definitive hosts including dogs, cats, tigers, leopards and humans. The mt genome of G. spinigerum is 14,079 bp in size and shows substantial changes in gene order compared to other nematodes studied to date. Phylogenetic analyses of mt genome sequences by Bayesian inference (BI) revealed that the infraorder Gnathostomatomorpha (represented by G. spinigerum) is closely related to the infraorder Ascaridomorpha. G. spinigerum is the first species from the infraorder Gnathostomatomorpha for which a complete mt genome has been sequenced. The new data will help understand the evolution, population genetics and systematics of this medically important group of parasites. © 2015 Macmillan Publishers Limited.


Ma B.,University of Jinan | Xie N.,Chinese Academy of Agricultural Sciences
ICCMS 2010 - 2010 International Conference on Computer Modeling and Simulation | Year: 2010

Automatically getting their Petri nets models is the precondition to compose semantic web services with Petri nets technology, based on OWL-S, this paper discusses the method to describe semantic web services with Petri nets markup language (PNML) and Web Ontology Language (OWL), which supports automatic sharing synthesis operates of Petri nets and could be used to implement automatic composition of semantic web services. Firstly, parsing the OWL-S atomic process models of semantic web services and getting their Petri nets incidence matrix, secondly, getting Petri nets description of semantic web services through Petri nets automatic sharing synthesis for composite processes based on ontology reasoning, which resolves the automatic modeling of semantic web services with Petri nets and proposes a technology approach of dynamic and automatic composition of semantic web services. © 2010 IEEE.


Zhu X.F.,Zhejiang University | Lei G.J.,Zhejiang University | Wang Z.W.,Zhejiang University | Shi Y.Z.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Plant Physiology | Year: 2013

Whether aluminum toxicity is an apoplastic or symplastic phenomenon is still a matter of debate. Here, we found that three auxin overproducing mutants, yucca, the recessive mutant superroot2, and superroot1 had increased aluminum sensitivity, while a transfer DNA insertion mutant, xyloglucan endotransglucosylase/hydrolases15 (xth15), showed enhanced aluminum resistance, accompanied by low endogenous indole-3-acetic acid levels, implying that auxin may be involved in plant responses to aluminum stress. We used yucca and xth15 mutants for further study. The two mutants accumulated similar total aluminum in roots and had significantly reduced cell wall aluminum and increased symplastic aluminum content relative to the wild-type ecotype Columbia, indicating that altered aluminum levels in the symplast or cell wall cannot fully explain the differential aluminum resistance of these two mutants. The expression of Al sensitive1 (ALS1), a gene that functions in aluminum redistribution between the cytoplasm and vacuole and contributes to symplastic aluminum detoxification, was less abundant in yucca and more abundant in xth15 than the wild type, consistent with possible ALS1 function conferring altered aluminum sensitivity in the two mutants. Consistent with the idea that xth15 can tolerate more symplastic aluminum because of possible ALS1 targeting to the vacuole, morin staining of yucca root tip sections showed more aluminum accumulation in the cytosol than in the wild type, and xth15 showed reduced morin staining of cytosolic aluminum, even though yucca and xth15 had similar overall symplastic aluminum content. Exogenous application of an active auxin analog, naphthylacetic acid, to the wild type mimicked the aluminum sensitivity and distribution phenotypes of yucca, verifying that auxin may regulate aluminum distribution in cells. Together, these data demonstrate that auxin negatively regulates aluminum tolerance through altering ALS1 expression and aluminum distribution within plant cells, and plants must coordinate exclusion and internal detoxification to reduce aluminum toxicity effectively. © 2013 American Society of Plant Biologists. All Rights Reserved.


Chen T.,Tsinghua University | Wang J.,Tsinghua University | Yang R.,Tsinghua University | Yang R.,Massachusetts Institute of Technology | And 3 more authors.
PLoS ONE | Year: 2011

Background: The tolerance of cells toward different stresses is very important for industrial strains of microbes, but difficult to improve by the manipulation of single genes. Traditional methods for enhancing cellular tolerances are inefficient and time-consuming. Recently, approaches employing global transcriptional or translational engineering methods have been increasingly explored. We found that an exogenous global regulator, irrE from an extremely radiation-resistant bacterium, Deinococcus radiodurans, has the potential to act as a global regulator in Escherichia coli, and that laboratory-evolution might be applied to alter this regulator to elicit different phenotypes for E. coli. Methodology/Principal Findings: To extend the methodology for strain improvement and to obtain higher tolerances toward different stresses, we here describe an approach of engineering irrE gene in E. coli. An irrE library was constructed by randomly mutating the gene, and this library was then selected for tolerance to ethanol, butanol and acetate stresses. Several mutants showing significant tolerances were obtained and characterized. The tolerances of E. coli cells containing these mutants were enhanced 2 to 50-fold, based on cell growth tests using different concentrations of alcohols or acetate, and enhanced 10 to 100-fold based on ethanol or butanol shock experiments. Intracellular reactive oxygen species (ROS) assays showed that intracellular ROS levels were sharply reduced for cells containing the irrE mutants. Sequence analysis of the mutants revealed that the mutations distribute cross all three domains of the protein. Conclusions: To our knowledge, this is the first time that an exogenous global regulator has been artificially evolved to suit its new host. The successes suggest the possibility of improving tolerances of industrial strains by introducing and engineering exogenous global regulators, such as those from extremophiles. This new approach can be applied alone or in combination with other global methods, such as global transcriptional machinery engineering (gTME) for strain improvements. Copyright: © 2011 Chen et al.


Li C.,State Key Laboratory for Molecular Biology of Special Economic Animals | Li C.,Chinese Academy of Agricultural Sciences | Zhao H.,State Key Laboratory for Molecular Biology of Special Economic Animals | Zhao H.,Chinese Academy of Agricultural Sciences | And 3 more authors.
International Journal of Biochemistry and Cell Biology | Year: 2014

Deer antler is the only mammalian organ that can fully grow back once lost from its pedicle - the base from which it grows. Therefore, antlers probably offer the most pertinent model for studying organ regeneration in mammals. This paper reviews our current understanding of the mechanisms underlying regeneration of antlers, and provides insights into the possible use for human regenerative medicine. Based on the definition, antler renewal belongs to a special type of regeneration termed epimorphic. However, histological examination failed to detect dedifferentiation of any cell type on the pedicle stump and the formation of a blastema, which are hallmark features of classic epimorphic regeneration. Instead, antler regeneration is achieved through the recruitment, proliferation and differentiation of the single cell type in the pedicle periosteum (PP). The PP cells are the direct derivatives of cells resident in the antlerogenic periosteum (AP), a tissue that exists in prepubertal deer calves and can induce ectopic antler formation when transplanted elsewhere on the deer body. Both the AP and PP cells express key embryonic stem cell markers and can be induced to differentiate into multiple cell lineages in vitro and, therefore, they are termed antler stem cells, and antler regeneration is a stem cell-based epimorphic regeneration. Comparisons between the healing process on the stumps from an amputated mouse limb and early regeneration of antlers suggest that the stump of a mouse limb cannot regenerate because of the limited potential of periosteal cells in long bones to proliferate. If we can impart a greater potential of these periosteal cells to proliferate, we might at least be able to partially regenerate limbs lost from humans. Taken together, a greater understanding of the mechanisms that regulate the regeneration of antlers may provide a valuable insight to aid the field of regenerative medicine. This article is part of a Directed Issue entitled: Regenerative Medicine: the challenge of translation. © 2014 Elsevier Ltd.


Hou X.-Y.,Chinese Academy of Agricultural Sciences | Han Y.,Chinese Academy of Agricultural Sciences | Li F.Y.,Agresearch Ltd.
Rangeland Journal | Year: 2012

The herdsmen in the desert steppe region in Northern China live primarily on the native rangelands. The semiarid climate has a profound impact on the economy and the livelihood of rural communities. Adaptation to the highly variable climate is the norm in pastoral management in the region but the increasing aridity and variability projected by climate change models provides new challenges for sustainable living in the harsh environment. The study surveyed the herdsmen's perception of climate change and variability in the desert steppe region of Inner Mongolia, and compared it with the observed climatic patterns and the recorded disastrous climatic events. The existing rangeland and livestock management strategies used by local herdsmen to cope with variable climate were also investigated in order to assist in the development of better management adaptation strategies. The herdsman perceived temperature changes over the past 30 years, which matched well with the meteorological observations, while their perceived change in precipitation (decrease) did not agree with the meteorological records (no change). The discrepancy between the observed and perceived precipitation changes may have arisen from the combination of large seasonal and inter-annual fluctuation of precipitation, more recent drought years and a herdsmen's desire to have a 'wet year', and more forage demand from increased livestock numbers. Herdsmen also had a reasonably good perception of strong wind/dust storms and snow storms, and their sensitivity to these extreme disastrous climatic events appeared to be related to the perception of drought. The herdsmen had better perceptions of recent short-term climate change and possibly to use it to assess the long-term changes. The major adaptive management strategies to cope with disastrous climatic events included selling livestock, buying feed, seeking other grazing resources, housing livestock and looking for other alternative jobs to compensate for the economic loss. Grazing other resources, either the reserved winter rangelands in the growing season in current household farm systems or the common winter rangelands in a traditional nomadic system, played a vital role in buffering the effects of extreme climatic events. Setting appropriate stocking rates and growing forage crops in suitable land areas may contribute to increasing the resilience of rangeland systems. Raising the herdsmen's awareness of long-term climate change and its effects on rangelands is needed to improve their preparedness to adapt to the future climate. © 2012 Australian Rangeland Society.


Baumann A.,Ohio State University | Barry J.,Ohio State University | Wang S.,Ohio State University | Wang S.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Genetics | Year: 2010

Juvenile hormone (JH) is critical for multiple aspects of insect development and physiology. Although roles for the hormone have received considerable study, an understanding of the molecules necessary for JH action in insects has been frustratingly slow to evolve. Methoprene-tolerant (Met) in Drosophila melanogaster fulfills many of the requirements for a hormone receptor gene. A paralogous gene, germ-cell expressed (gce), possesses homology and is a candidate as a Met partner in JH action. Expression of gce was found to occur at multiple times and in multiple tissues during development, similar to that previously found for Met. To probe roles of this gene in JH action, we carried out in vivo gce over- and underexpression studies. We show by overexpression studies that gce can substitute in vivo for Met, alleviating preadult but not adult phenotypic characters. We also demonstrate that RNA interference-driven knockdown of gce expression in transgenic flies results in preadult lethality in the absence of MET. These results show that (1) unlike Met, gce is a vital gene and shows functional flexibility and (2) both gene products appear to promote JH action in preadult but not adult development. Copyright © 2010 by the Genetics Society of America.


Fan F.,Chinese Academy of Agricultural Sciences | Yang Q.,Chinese Academy of Agricultural Sciences | Li Z.,Chinese Academy of Agricultural Sciences | Wei D.,Heilongjiang Academy of Agricultural science | And 2 more authors.
Microbial Ecology | Year: 2011

The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification. © 2011 Springer Science+Business Media, LLC.


Hu P.,Tsinghua University | Zhou W.,Tsinghua University | Cheng Z.,Tsinghua University | Cheng Z.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Molecular Cell | Year: 2013

Plants evolve effective mechanisms to protect themselves from environmental stresses and employ jasmonates as vital defense signals to defend against insect attack and pathogen infection. Jasmonates are also recognized as an essential growth regulator by which diverse developmental processes are mediated. Despite substantial research, there are no key signaling components reported yet to control jasmonate-regulated plant defense independent of developmental responses. We identify JAV1, a key gene in the jasmonate pathway, which functions as a negative regulator to control plant defense but does not play a detectable role in plant development. Our results suggest that when encountering insect attack and pathogen infection, plants accumulate jasmonates that trigger JAV1 degradation via the 26S proteasome to activate defensive gene expression and elevate resistances against both insects and pathogens. These findings have provided insight into the molecular mechanism by which plants integrate jasmonate signals to protect themselves from insect attack and pathogen infection. © 2013 Elsevier Inc.


Liu K.J.,Rice University | Liu K.J.,Michigan State University | Steinberg E.,Rice University | Yozzo A.,Rice University | And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

We report on a genome-wide scan for introgression between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus), using samples from the ranges of sympatry and allopatry in Africa and Europe. Our analysis reveals wide variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the autosomes in each genome harbor all detectable introgression, whereas the X chromosome has none. Further, European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we infer, first, that at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent (one presumably due to warfarin rodenticide selection). Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, functional analysis revealed introgressed genes that are essential to fitness, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies. © 2015, National Academy of Sciences. All rights reserved.


Bi L.,Hohai University | Yao S.,Chinese Academy of Agricultural Sciences | Zhang B.,Chinese Academy of Agricultural Sciences
Soil and Tillage Research | Year: 2015

Soil puddlability measures the susceptibility of a soil to puddling, and can influence transplantation and the growth of rice plants. The effects of chemical fertilizers and organic amendments on soil puddlability of paddy soils are poorly understood. This study used two 26-year field experiments (1) to compare the effects of chemical and organic fertilization on soil puddlability by measuring sinkage resistance and hard clod content after puddling, (2) to characterize physical properties of hard clods and (3) to explain the change in soil puddlability. Each of the two experiments consisted of nine treatments of chemical fertilizers alone or in combination with organic amendments. The sinkage resistance and the content of hard clods were higher in the treatments with chemical fertilization alone than in the treatments with organic amendments. The sinkage resistance was positively correlated with the content of hard clods and negatively correlated to content of soil organic C (SOC) and mean weight diameter (MWD). The bulk density, water sorptivity and apparent porosity were similar among individual hard clods from different treatments, suggesting that the hard clods were formed under the same processes. The formation of hard clods was likely attributed to the breakdown of the compacted topsoil by puddling tillage, which formed due to clogging pores by fine particles produced during previous puddling tillage and due to shrinkage upon drying during rice growth period. Compared with the organic amendment treatments, the chemical fertilization treatments contained more and larger hard clods, indicating that the compacted topsoil was thicker due to higher soil dispersibility due to N fertilization and lower SOC content in the chemical fertilization treatments than in the organic amendment treatments. The study also suggests that continuous input of organic C at an annual rate of >2.5Mgha-1 is needed to maintain SOC content and soil structure under chemical fertilization in the study region. © 2015 Elsevier B.V.


Wu L.,Chinese Academy of Agricultural Sciences | Wu L.,China National Institute of Biological Sciences | Mao L.,Chinese Academy of Agricultural Sciences | Qi Y.,China National Institute of Biological Sciences | Qi Y.,Tsinghua University
Plant Physiology | Year: 2012

Trans-acting small interfering RNAs (ta-siRNAs; TAS) emerge as a class of plant-specific small RNAs that are initiated from microRNA-mediated cleavage of TAS gene transcripts. It has been revealed that ta-siRNAs are generated by the sequential activities of SUPPRESSOR OF GENE SILENCING3 (SGS3), RNA-DEPENDENT RNA POLYMERASE6 (RDR6), and DICERLIKE4 (DCL4), and loaded into ARGONAUTE1 (AGO1) proteins to posttranscriptionally regulate several target genes by messenger RNA cleavage in trans. Here, we showed a high cytosine DNA methylation status at ta-siRNA-generating loci in Arabidopsis (Arabidopsis thaliana), which is dependent on RDR6, SGS3, and DNA-DIRECTED RNA POLYMERASE V (PolV). More important, we found that DCL1 is the only DCL protein that is required for TAS3 loci DNA methylation, and all four DCLs exert combinatory functions in the methylation of TAS1 loci, suggesting a previously unknown role for DCL1 in directly processing TAS gene transcripts. Furthermore, we demonstrated that AGO4/6 complexes rather than AGO1 are responsible for TAS siRNA-guided DNA methylation. Based upon these findings, we propose a novel ta-siRNA pathway that acts at both the messenger RNA and chromatin level. © 2012 American Society of Plant Biologists. All Rights Reserved.


Gou M.,Cornell University | Shi Z.,Cornell University | Shi Z.,CAS Institute of Plant Physiology and Ecology | Zhu Y.,Cornell University | And 4 more authors.
Plant Journal | Year: 2012

Disease resistance (R) proteins, as central regulators of plant immunity, are tightly regulated for effective defense responses and to prevent constitutive defense activation under non-pathogenic conditions. Here we report the identification of an F-box protein CPR1/CPR30 as a negative regulator of an R protein SNC1 likely through SCF (Skp1-cullin-F-box) mediated protein degradation. The cpr1-2 (cpr30-1) loss-of-function mutant has constitutive defense responses, and it interacts synergistically with a gain-of function mutant snc1-1 and a bon1-1 mutant where SNC1 is upregulated. The loss of SNC1 function suppresses the mutant phenotypes of cpr1-2 and cpr1-2 bon1-1, while overexpression of CPR1 rescues mutant phenotypes of both bon1-1 and snc1-1. Furthermore, the amount of SNC1 protein is upregulated in the cpr1-2 mutant and down-regulated when CPR1 is overexpressed. The regulation of SNC1 by CPR1 is dependent on the 26S proteosome as a protease inhibitor MG132 stabilizes SNC1 and reverses the effect of CPR1 on SNC1. Interestingly, CPR1 is induced after infection of both virulent and avirulent pathogens similarly to the other negative defense regulator BON1. Thus, this study reveals a new mechanism in R protein regulation likely through protein degradation and suggests negative regulation as a critical component in fine control of plant immunity. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.


Sun Y.,Chinese Academy of Agricultural Sciences | He Z.,Chinese Academy of Agricultural Sciences | He Z.,International Maize and Wheat Improvement Center | Ma W.,Murdoch University | Xia X.,Chinese Academy of Agricultural Sciences
Functional and Integrative Genomics | Year: 2011

Polyphenol oxidase (PPO) plays a crucial role in browning reactions in fresh and processed fruits and vegetables, as well as products made from cereal grains. Common wheat (Triticum aestivum L.) has a large genome, representing an interesting system to advance our understanding of plant PPO gene expression, regulation and function. In the present study, we characterized the expression of Ppo-A1, a major PPO gene located on wheat chromosome 2A, using DNA sequencing, semi-quantitative RT-PCR, PPO activity assays and whole-grain staining methods during grain development. The results indicated that the expression of the Ppo-A1b allele was regulated by alternative splicing of pre-mRNAs, resulting from a 191-bp insertion in intron 1 and one C/G SNP in exon 2. Eight mRNA isoforms were identified in developing grains based on alignments between cDNA and genomic DNA sequences. Only the constitutively spliced isoform b encodes a putative full-length PPO protein based on its coding sequence whereas the other seven spliced isoforms, a, c, d, e, f, g and h, have premature termination codons resulting in potential nonsense-mediated mRNA decay. The differences in expression of Ppo-A1a and Ppo-A1b were confirmed by PPO activity assays and whole grain staining, providing direct evidence for the influence of alternative splicing in the coding region of Ppo-A1 on polyphenol oxidase activity in common wheat grains. © 2010 Springer-Verlag.


Wang W.,Southwest University | Liu G.,Chinese Academy of Agricultural Sciences | Niu H.,Southwest University | Timko M.P.,University of Virginia | Zhang H.,Southwest University
Journal of Experimental Botany | Year: 2014

Jasmonate (JA) plays an important role in regulating plant male fertility and secondary metabolism, but its role in regulating primary metabolism remains unclear. The F-box protein CORONATINE INSENSITIVE 1 (COI1) is a critical component of the JA receptor, and mediates JA-signalling by targeting JASMONATE ZIM-domain (JAZ) proteins for proteasomal degradation in response to JA perception. Here, we found that RNA interference-mediated knockdown of NtCOI1 in tobacco (Nicotiana tabacum L. cv. TN90) recapitulated many previously observed phenotypes in coi1 mutants, including male sterility, JA insensitivity, and loss of floral anthocyanin production. It also affected starch metabolism in the pollen, anther wall, and floral nectary, leading to pollen abortion and loss of floral nectar. Transcript levels of genes encoding starch metabolism enzymes were significantly altered in the pollen, anther wall, and floral nectary of NtCOI1-silenced tobacco. Changes in leaf primary metabolism were also observed in the NtCOI1-silenced tobacco. The expression of NtMYB305, an orthologue of MYB305 previously identified as a flavonoid metabolic regulator in Antirrhinum majus flowers and as a floral-nectar regulator mediating starch synthesis in ornamental tobacco, was extremely downregulated in NtCOI1-silenced tobacco. These findings suggest that NtCOI1 functions upstream of NtMYB305 and plays a fundamental role in coordinating plant primary carbohydrate metabolism and correlative physiological processes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.


Xu L.,Tsinghua University | Xu L.,Chinese Academy of Agricultural Sciences | Zhou L.,Tsinghua University | Li P.,Tsinghua University
Arteriosclerosis, Thrombosis, and Vascular Biology | Year: 2012

Lipid homeostasis is maintained through the coordination of lipid metabolism in various tissues, including adipose tissue and the liver. The disruption of lipid homeostasis often results in the development of metabolic disorders such as obesity, diabetes mellitus, liver steatosis, and cardiovascular diseases. Cell death-inducing DNA fragmentation factor 45-like effector family proteins, including Cidea, Cideb, and Fsp27 (Cidec), are emerging as important regulators of various lipid metabolic pathways and play pivotal roles in the development of metabolic disorders. This review summarizes the latest cell death-inducing DNA fragmentation factor 45-like effector protein discoveries related to the control of lipid metabolism, with emphasis on the role of these proteins in lipid droplet growth in adipocytes and in the regulation of very low-density lipoprotein lipidation and maturation in hepatocytes. © 2012 American Heart Association, Inc.


Gao Y.,Shandong University of Technology | Yao Y.,Chinese Academy of Agricultural Sciences | Zhu Y.,University of Liège | Ren G.,Chinese Academy of Agricultural Sciences
Journal of Agricultural and Food Chemistry | Year: 2015

Diabetes mellitus is a metabolic disease characterized by hyperglycemia arising from defects in insulin secretion. This study investigated the effects of isoflavones in chickpea sprouts germinated in light (IGL) and isoflavones in chickpea seeds (ICS) on insulin resistance through their role in suppression of 3T3-L1 adipocyte differentiation. Results showed that IGL and ICS inhibit the differentiation of 3T3-L1 pre-adipocytes induced by differentiation medium in a dose-dependent manner, and the suppressive effect of IGL was stronger (p < 0.05) than that of ICS, evidenced by a decrease of Oil Red O staining and intracellular triacylglycerol content in the mature adipocytes. IGL and ICS also stimulated glucose uptake significantly (p < 0.05). Besides, IGL and ICS treatment caused a significant decrease in mRNA and protein expression levels of adipogenesis-related transcription factors peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT-enhancer-binding protein α (C/EBPα). Furthermore, the mRNA and protein expression levels of adipocyte fatty acid-binding protein (ap2), lipoprotein lipase (LPL), uncoupling protein-2 (UCP-2), and glucose transporter 4 (Glut4) in 3T3-L1 cells were also markedly down-regulated (p < 0.05). © 2015 American Chemical Society.


Du L.,Chinese Academy of Agricultural Sciences | Shen Y.,Louisiana State University | Zhang X.,Chinese Academy of Agricultural Sciences | Prinyawiwatkul W.,Louisiana State University | Xu Z.,Louisiana State University
Food Chemistry | Year: 2014

Miracle berry is known for its unique characteristic of modifying sour flavours to sweet. Twelve phenolics were identified and quantified in the miracle berry flesh at a level from 0.3 for kaempferol to 17.8 mg/100 g FW for epicatechin. Lutein and α-tocopherol were also quantified at a level of 0.4 and 5.8 mg/100 g FW, respectively. The TP and TF contents were 1448.3 GA and 9.9 QR mg Equiv/100 g FW for the flesh, respectively, compared with 306.7 GA and 3.8 mg QR mg Equiv/100 g FW of the seeds. The free radical scavenging and reducing percentage of the flesh extract was 96.3% and 32.5% in DPPH and ABTS assays, respectively. Additionally, the flesh extract had a high FRAP of 22.9 mmol/100 g. It significantly inhibited the oxidation of PUFA in fish oil as well. Thus, miracle berry could also serve as an antioxidant-rich fruit to provide health promoting function. © 2014 Published by Elsevier Ltd.


Shen Y.,Louisiana State University | Zhang X.,Chinese Academy of Agricultural Sciences | Prinyawiwatkul W.,Louisiana State University | Xu Z.,Louisiana State University
Food Chemistry | Year: 2014

A method for simultaneously determining four artificial food colourants [Red Nos. 2 (R2) and 40 (R40), Yellow Nos. 5 (Y5) and 6 (Y6)] and three carotenoids [lycopene, lutein, and β-carotene] was developed. They were successfully separated by the developed high pressure liquid chromatography (HPLC) method combined with a photo diode array detector. The detection limit (at signal to noise > 4) was from the lowest of 0.2 ng/mL for lutein to the highest of 50.0 ng/mL for R40. With a two-phase solvent and ultrasound-assisted extraction, the recoveries of the artificial and natural pigments in fifteen different types of food products were between 80.5-97.2% and 80.1-98.4%, respectively. This HPLC method with the ultrasound-assisted extraction protocol could be used as a sensitive and reliable analysis technique in simultaneously identifying and quantifying the reddish and yellowish pigments in different foods regardless of they are artificial food colourants or/and natural carotenoids. © 2014 Elsevier Ltd. All rights reserved.


Meng Y.,Chinese Academy of Agricultural Sciences | Li H.,Chinese Academy of Agricultural Sciences | Wang Q.,Chinese Academy of Agricultural Sciences | Wang Q.,University of California at Los Angeles | And 3 more authors.
Plant Cell | Year: 2013

Cryptochromes are blue light receptors that regulate light responses in plants, including various crops. The molecularmechanism of plant cryptochromes has been extensively investigated in Arabidopsis thaliana, but it has not been reported in any crop species. Here, we report a study of the mechanism of soybean (Glycine max) cryptochrome2 (CRY2a). We found that CRY2a regulates leaf senescence, which is a life history trait regulated by light and photoperiods via previously unknown mechanisms. We show that CRY2a undergoes blue light-dependent interaction with the soybean basic helix-loop-helix transcription activator CIB1 (for cryptochrome-interacting bHLH1) that specifically interacts with the E-box (CANNTG) DNA sequences. Analyses of transgenic soybean plants expressing an elevated or reduced level of the CRY2a or CIB1 demonstrate that CIB1 promotes leaf senescence, whereas CRY2a suppresses leaf senescence. Results of the gene expression and molecular interaction analyses support the hypothesis that CIB1 activates transcription of senescence-associated genes, such as WRKY DNA BINDING PROTEIN53b (WRKY53b), and leaf senescence. CIB1 interacts with the E-box-containing promoter sequences of the WRKY53b chromatin, whereas photoexcited CRY2a interacts with CIB1 to inhibit its DNA binding activity. These findings argue that CIBdependent transcriptional regulation is an evolutionarily conserved CRY-signaling mechanism in plants, and this mechanism is opted in evolution to mediate light regulation of different aspects of plant development in different plant species. © 2013 American Society of Plant Biologists. All rights reserved.


Xu Y.,Chinese Academy of Agricultural Sciences | Xu Y.,International Maize and Wheat Improvement Center
Theoretical and Applied Genetics | Year: 2016

Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept “envirotyping” is proposed, as a third “typing” technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts. © 2016 The Author(s)


Zhai Z.,Inner Mongolia University of Technology | Wu Y.,Chinese Academy of Agricultural Sciences | Wang C.,Inner Mongolia Agricultural University
Nongye Gongcheng Xuebao/Transactions of the Chinese Society of Agricultural Engineering | Year: 2012

In order to reveal the relationship between the motion pattern of the materials and power consumption and throwing efficiency of an impeller blower, and further reduce its power consumption and improve its throwing efficiency, the motion pattern of the materials moving along the throwing impeller was studied based on the high-speed camera technology combining with the theory analysis and virtual prototyping. Its dynamic equation was established and the moving pattern of the materials was numerically simulated in ADAMS. They can be applied to various mounting angle of the throwing impeller. Moreover, the equivalent friction coefficient obtained through regression analysis on the data acquired by the high speed camera was used to correct the dynamic equation and ADAMS simulation model for the sake of considering the interaction between the air flow and the materials as well as the interaction among the materials comprehensively. In addition, the optimal range of the material-throwing angle was established to be 60°-130°. All the results will play a significant role in carrying out the parametric optimization of the impeller blower in the future.


Zhang Z.,Renmin University of China | Zhao W.,Chinese Academy of Agricultural Sciences | Gu X.,Zhejiang GongShang University
Land Use Policy | Year: 2014

Land consolidation (LC) is essential for ensuring rural development and for increasing land use effectiveness. LC has been implemented in China since the mid-1990s in an attempt to increase available cropland area, reduce fragmentation and promote agricultural production capacity. The purpose of this study is to identify the changes resulting from the land consolidation project (LCP) implementation, and to develop a parametric approach to assess the resource-environment effects. This study could promote the LCP planning, and provide the support for the decision-making of the LC authorities. The Tianmen land consolidation project in Hubei Province of China was chosen as a case study. The results of the case study showed LCP implementation results in great changes in land use types and their proportions, connectivity of field-roads, irrigation systems and drainage systems, plot numbers, plot shape and plot size. These changes bring both positive and negative effects to region environmental and economic system. Positive effects were demonstrated in agricultural production capacity and agricultural production cost and the negative effects were expressed by the ecosystem services value, landscape diversity and human disturbance intensity. © 2013 Elsevier Ltd.


Zhang X.,Chinese Academy of Agricultural Sciences | Zhang X.,Louisiana State University | Shen Y.,Louisiana State University | Prinyawiwatkul W.,Louisiana State University | And 2 more authors.
Food Chemistry | Year: 2013

The antioxidant capabilities of anthocyanin and tocol extracts from black rice bran were evaluated using an emulsion system containing either cholesterol (1.0 mg/ml) or fish oil (10 mg/ml). The cholesterol oxidation product, 7-ketocholesterol, increased to 180.1 μg/ml in the control emulsion after 168 h of oxidation, while it was only 15.4 and 39.0 μg/ml in the emulsions containing 1 μg/ml of the anthocyanin and tocol extracts, respectively; but below 1.2 μg/ml in the emulsion having 5 μg/ml of anthocyanins or tocols. In the fish oil emulsion, over 80% of C20:5 and C22:6 were oxidised after a 48 h incubation at 37 °C, while they were retained above 38% and 65% in the emulsions containing 10 μg/ml of anthocyanins and tocols, respectively, and above 85% in the emulsion containing 20 μg/ml of anthocyanins or tocols. Compared with the tocols extract, the capability of the anthocyanin extract was relatively greater in stabilising cholesterol but lower in inhibiting fatty acids oxidation. © 2013 Elsevier Ltd. All rights reserved.


Yao H.,Zhejiang University | Gao Y.,Zhejiang University | Nicol G.W.,University of Aberdeen | Campbell C.D.,James Hutton Institute | And 6 more authors.
Applied and Environmental Microbiology | Year: 2011

Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammoniaoxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. © 2011, American Society for Microbiology.


Fan F.,Chinese Academy of Agricultural Sciences | Li Z.,Chinese Academy of Agricultural Sciences | Wakelin S.A.,Agresearch Ltd. | Yu W.,CAS Shenyang Institute of Applied Ecology | Liang Y.,Chinese Academy of Agricultural Sciences
Soil Biology and Biochemistry | Year: 2012

Nutrient inputs to soil can alter mineralization of organic matter and subsequently affect soil carbon levels. To understand how elemental interactions affect the biogeochemistry and storage of soil C, we examined soils receiving long-term applications of mineral fertilizer and manure-containing fertilizers. As cellulose is the dominant form of carbon entering arable soils, cellulolytic communities were monitored through enzymatic analysis, and characterization of the abundance (real-time PCR) and diversity (terminal restriction fragment length polymorphism, T-RFLP) of fungal cellobiohydrolases (cbhI) genes. The data showed that long-term mineral fertilization increased soil organic C and crop productivity, and reduced soil heterotrophic respiration and cellobiohydrolases (CBH) activity. Correspondingly, the diversity and community structure of cellulolytic fungi were substantially altered. The variation in cellulolytic fungi is mainly attributable to shifts in the proportion of Eurotiomycetes. In addition, CBH activity was significantly correlated with the diversity and community structure of cellulolytic fungi. These results suggest that enhanced C storage by mineral fertilizer addition occurs not only from extra organic carbon input, but may also be affected through the cellulose decomposing community in arable soil. © 2012 Elsevier Ltd.


Wang J.,Chinese Academy of Agricultural Sciences | Wang J.,Shandong University of Technology
Agriculture and Agricultural Science Procedia | Year: 2010

This paper provides empirical evidence of the determinants of food security, in which is expressed as a function of various factors, including the per capita disposable income of rural residents, food retail price index, agricultural disaster area, sown area and saving of urban and rural residents, using a dynamic panel data analysis from a sample of 27 provinces over 1985-2007 in China. This paper used POLS, FE (fixed effects), DIF-GMM (difference GMM) and SYS-GMM (system GMM) to estimate the relationship among all the variables. According to the results of SYS-GMM, we found that the climate change will affect the food security significantly in the current year, but food price had no influence on the food security in the current year in China. © 2010 Published by Elsevier B.V.


Du S.-J.,Tsinghua University | Dong C.-J.,Tsinghua University | Zhang B.,Tsinghua University | Lai T.-F.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Journal of Proteomics | Year: 2013

In this study, a comparative proteomic analysis was employed to identify fuzz fiber initiation-related proteins in wild-type diploid cotton (Gossypium arboreum L.) and its fuzzless mutant. Temporal changes in global proteomes were examined using 2-DE at five developmental time points for fuzz fiber initiation, and 71 differentially expressed protein species were identified by MS, 45 of which were preferentially accumulated in the wild-type. These proteins were assigned to several functional categories, mainly in cell response/signal transduction, redox homeostasis, protein metabolism and energy/carbohydrate metabolism. It was remarkable that more than ten key proteins with high-abundance were involved in gibberellic acid (GA) signaling and ROS scavenging, and increasing concentrations of active GAs and H2O2 were also detected approximately 5dpa in wild type ovules. Furthermore, in vivo GA and H2O2 treatments of ovules inside young bolls showed that these compounds can synergistically promote fuzz fiber initiation. Our findings not only described a dynamic protein network supporting fuzz initiation in diploid cotton fiber ovules, but also deepened our understanding of the molecular basis of cotton fiber initiation. Biological significance: Our study reported the identification of differentially expressed proteins in wild-type diploid cotton (G. arboreum L.) and its fuzzless mutant by comparative proteomic approach. In total, 71 protein species related to fuzz initiation were identified by MS. These proteins were assigned to several functional categories, mainly in energy/carbohydrate metabolism, protein metabolism, signal transduction, redox homeostasis etc. Importantly, a number of key proteins were found to be associated with GA signaling and ROS scavenging. In consistence with these findings, we detected the increase of GAs and H2O2 concentrations during fiber initiation, and our in vivo ovule experiments with GA and H2O2 injection and following microscopy observation of fuzz fiber initiation supported promoting effects of GA and H2O2 on cotton fiber initiation. These findings depicted a dynamic protein network supporting cotton fiber initiation in diploid cotton ovules. Our study is of major significance for understanding the molecular mechanisms controlling fuzz initiation and also provides a solid basis for further functional research of single nodes of this network in relation to cotton fiber initiation. © 2013 Elsevier B.V.


Tang K.,Tsinghua University | Dong C.,Chinese Academy of Agricultural Sciences | Liu J.,Tsinghua University
Science China Life Sciences | Year: 2016

The plant phospholipase D (PLD) plays versatile functions in multiple aspects of plant growth, development, and stress responses. However, until now, our knowledge concerning the PLD gene family members and their expression patterns in cotton has been limited. In this study, we performed for the first time the genome-wide analysis and expression profiling of PLD gene family in Gossypium arboretum, and finally, a total of 19 non-redundant PLD genes (GaPLDs) were identified. Based on the phylogenetic analysis, they were divided into six well-supported clades (α, β/γ, δ, ε, ζ and φ). Most of the GaPLD genes within the same clade showed the similar exon-intron organization and highly conserved motif structures. Additionally, the chromosomal distribution pattern revealed that GaPLD genes were unevenly distributed across 10 of the 13 cotton chromosomes. Segmental duplication is the major contributor to the expansion of GaPLD gene family and estimated to have occurred from 19.61 to 20.44 million years ago when a recent large-scale genome duplication occurred in cotton. Moreover, the expression profiling provides the functional divergence of GaPLD genes in cotton and provides some new light on the molecular mechanisms of GaPLDα1 and GaPLDδ2 in fiber development. © 2015, The Author(s).


Li Y.,Cornell University | Li Y.,Chinese Academy of Agricultural Sciences | Romeis J.,ART Agroscope Reckenholz Tänikon | Wang P.,Cornell University | And 2 more authors.
PLoS ONE | Year: 2011

The ladybird beetle, Coleomegilla maculata (DeGeer), is a common and abundant predator in many cropping systems. Its larvae and adults are predaceous, feeding on aphids, thrips, lepidopteran larvae and plant tissues, such as pollen. Therefore, this species is exposed to insecticidal proteins expressed in insect-resistant, genetically engineered cotton expressing Cry proteins derived from Bacillus thuringiensis (Bt). A tritrophic bioassay was conduced to evaluate the potential impact of Cry2Ab- and Cry1Ac-expressing cotton on fitness parameters of C. maculata using Bt-susceptible and -resistant larvae of Trichoplusia ni as prey. Coleomegilla maculata survival, development time, adult weight and fecundity were not different when they were fed with resistant T. ni larvae reared on either Bt or control cotton. To ensure that C. maculata were not sensitive to the tested Cry toxins independent from the plant background and to add certainty to the hazard assessment, C. maculata larvae were fed artificial diet incorporated with Cry2Ab, Cry1Ac or both at >10 times higher concentrations than in cotton tissue. Artificial diet containing E-64 was included as a positive control. No differences were detected in any life-table parameters between Cry protein-containing diet treatments and the control diet. In contrast, larvae of C. maculata fed the E-64 could not develop to the pupal stage and the 7-d larval weight was significantly negatively affected. In both feeding assays, the stability and bioactivity of Cry proteins in the food sources were confirmed by ELISA and sensitive-insect bioassays. Our results show that C. maculata is not affected by Bt cotton and is not sensitive to Cry2Ab and Cry1Ac at concentrations exceeding the levels in Bt cotton, thus demonstrating that Bt cotton will pose a negligible risk to C. maculata. More importantly, this study demonstrates a comprehensive system for assessing the risk of genetically modified plants on non-target organisms.


Ma G.,Chinese Academy of Agricultural Sciences | Rudolf V.H.W.,Rice University | Ma C.-S.,Chinese Academy of Agricultural Sciences
Global Change Biology | Year: 2015

The frequency and magnitude of extreme events are predicted to increase under future climate change. Despite recent advancements, we still lack a detailed understanding of how changes in the frequency and amplitude of extreme climate events are linked to the temporal and spatial structure of natural communities. To answer this question, we used a combination of laboratory experiments, field experiments, and analysis of multi-year field observations to reveal the effects of extreme high temperature events on the demographic rates and relative dominance of three co-occurrence aphid species which differ in their transmission efficiency of different agricultural pathogens. We then linked the geographical shift in their relative dominance to frequent extreme high temperatures through a meta-analysis. We found that both frequency and amplitude of extreme high temperatures altered demographic rates of species. However, these effects were species-specific. Increasing the frequency and amplitude of extreme temperature events altered which species had the highest fitness. Importantly, this change in relative fitness of species was consistent with significant changes in the relative dominance of species in natural communities in a 1 year long field heating experiment and 6 year long field survey of natural populations. Finally, at a global spatial scale, we found the same relationship between relative abundance of species and frequency of extreme temperatures. Together, our results indicate that changes in frequency and amplitude of extreme high temperatures can alter the temporal and spatial structure of natural communities, and that these changes are driven by asymmetric effects of high temperatures on the demographic rates and fitness of species. They also highlight the importance of understanding how extreme events affect the life-history of species for predicting the impacts of climate change at the individual and community level, and emphasize the importance of using a broad range of approaches when studying climate change. © 2014 John Wiley & Sons Ltd.


Zhang J.,CAS Institute of Geology and Geophysics | Lu H.,CAS Institute of Geology and Geophysics | Wu N.,CAS Institute of Geology and Geophysics | Yang X.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | Diao X.,Chinese Academy of Agricultural Sciences
PLoS ONE | Year: 2011

Foxtail millet (Setaria italica) is one of the oldest domesticated cereal crops in Eurasia, but identifying foxtail millets, especially in charred grains, and differentiating it from its wild ancestor, green foxtail (Setaria viridis), in the archaeobotanical remains, is still problematic. Phytolithic analysis provides a meaningful method for identifying this important crop. In this paper, the silicon structure patterns in the glumes, lemmas, and paleas from inflorescence bracts in 16 modern plants of foxtail millet and green foxtail from China and Europe are examined using light microscopy with phase-contrast and a microscopic interferometer. Our research shows that the silicon structure of ΩIII from upper lemmas and paleas in foxtail millet and green foxtail can be correspondingly divided into two groups. The size of ΩIII type phytolith of foxtail millet is bigger than that from green foxtail. Discriminant function analysis reveals that 78.4% of data on foxtail millet and 76.9% of data on green foxtail are correctly classified. This means certain morphotypes of phytoliths are relatively reliable tools for distinguishing foxtail millet from green foxtail. Our results also revealed that the husk phytolith morphologies of foxtail millets from China and Eastern Europe are markedly different from those from Western Europe. Our research gives a meaningful method of separating foxtail millet and green foxtail. The implications of these findings for understanding the history of foxtail millet domestication and cultivation in ancient civilizations are significant. © 2011 Zhang et al.


Yao Y.,Chinese Academy of Agricultural Sciences | Sang W.,Chinese Academy of Agricultural Sciences | Zhou M.,Dong Zhimen Middle School | Ren G.,Chinese Academy of Agricultural Sciences
Journal of Agricultural and Food Chemistry | Year: 2010

Colored grains including red, purple, and black rice, purple corn, black barley, and black soybean contain anthocyanins. The present study was designed to (i) identify and quantify the individual anthocyanins and measure the total phenolic content (TPC), (ii) evaluate the antioxidant and a-glucosidase inhibitory activity, and (iii) correlate the TPC with total antioxidant activity and a-glucosidase inhibitory potency in these colored grains. The TPC was measured using a Folin-Ciocalteu assay, while the total antioxidant activity was determined by a method based on the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity. Among all of the studied colored grains, black rice possessed the highest TPC, which was 86 times greater than that of red rice. In addition, black rice had the highest total anthocyanin contents and a-glucosidase inhibitory activity. A significant positive correlation of the antioxidant activity and a-glucosidase inhibitory activity with total anthocyanin content and TPC was observed in this study. It is concluded that black rice possesses the highest antioxidant activity and a-glucosidase inhibitory among all of the colored grains tested and can be further explored as a functional food. © 2009 American Chemical Society.


Yin J.,Chinese Academy of Agricultural Sciences | Feng H.,Chinese Academy of Agricultural Sciences | Sun H.,Chinese Academy of Agricultural Sciences | Xi J.,Jilin University | And 2 more authors.
PLoS ONE | Year: 2012

Odorant binding proteins play a crucial role in transporting semiochemicals across the sensillum lymph to olfactory receptors within the insect antennal sensilla. In this study, the general odorant binding protein 2 gene was cloned from the antennae of Loxostege sticticalis, using reverse transcription PCR and rapid amplification of cDNA ends. Recombinant LstiGOBP2 was expressed in Escherichia coli and purified by Ni ion affinity chromatography. Real-time PCR assays indicated that LstiGOBP2 mRNA is expressed mainly in adult antennae, with expression levels differing with developmental age. Ligand-binding experiments using N-phenyl-naphthylamine (1-NPN) as a fluorescent probe demonstrated that the LstiGOBP2 protein has binding affinity to a broad range of odorants. Most importantly, trans-11-tetradecen-1-yl acetate, the pheromone component of Loxostege sticticalis, and trans-2-hexenal and cis-3-hexen-1-ol, the most abundant plant volatiles in essential oils extracted from host plants, had high binding affinities to LstiGOBP2 and elicited strong electrophysiological responses from the antennae of adults. © 2012 Yin et al.


Liu X.,Chinese Academy of Agricultural Sciences | Xu J.,Chinese Academy of Agricultural Sciences | Dong F.,Chinese Academy of Agricultural Sciences | Li Y.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Analytical and Bioanalytical Chemistry | Year: 2011

The new analytical method using Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) procedure for simultaneous determination of diacylhydrazine insecticide residues in fruits and vegetables was developed using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). The four insecticides (tebufenozide, methoxfenozide, chromafenozide, and halofenozide) were extracted from six fruit and vegetable matrices using acetonitrile and subsequently cleaned up using primary secondary amine (PSA) or octadecylsilane (C18) as sorbent prior to UPLC-MS/MS analysis. The determination of the target compounds was achieved in less than 3.0 min using an electrospray ionization source in positive mode (ESI+) for tebufenozide, methoxfenozide, and halofenozide and in negative mode (ESI-) for chromafenozide. The limits of detection were below 0.6 μg kg -1, while the limit of quantification did not exceed 2 μg kg -1 in different matrices. The QuEChERS procedure by using two sorbents (PSA and C18) and the matrix-matched standards gave satisfactory recoveries and relative standard deviation (RSD) values in different matrices at four spiked levels (0.01, 0.05, 0.1, and 1 mg kg -1). The overall average recoveries for this method in apple, grape, cucumber, tomato, cabbage, and spinach at four levels ranged from 74.2% to 112.5% with RSDs in the range of 1.4-13.8% (n∈=∈5) for all analytes. This study provides a theoretical basis for China to draw up maximum residue limits and analytical method for diacylhydrazine insecticide in vegetables and fruits. © 2011 Springer-Verlag.


Chen W.,Chinese Academy of Agricultural Sciences | Guo S.,Anhui Academy of Agricultural Sciences
Nongye Gongcheng Xuebao/Transactions of the Chinese Society of Agricultural Engineering | Year: 2013

This paper analyzes the development trends of frontier technology for agricultural informatization including five aspects of agricultural sensor technology, precision farming technology, agricultural robot technology, agricultural internet of things technology, and agricultural information service technology. It also discusses the existing problems in the development of frontier technology for agricultural informatization in China and proposes corresponding countermeasures. Firstly, the paper introduces the frontier techniques for agricultural informatization. For advanced agricultural sensor technology, three types of techniques are described, namely life information sensing technique, environmental information sensing technique, and comprehensive information collecting technique. For precision farming technology and intelligent equipment, onboard farmland information collection technique, precision farming positioning and controlling technique, decision model and prescription generating technique, and precise implementation technique are described. For agricultural intelligent robot technology, terrestrial mobile platform navigation and control technique and action planning technique are introduced. For agricultural internet of things technology and equipment, several issues are discussed including the sophisticated monitoring and scheduling of resources, ecological environment monitoring and management, agricultural product quality safety traceability, etc. For agricultural information service technology, frontier techniques and applications for agricultural remote sensing and agricultural information resource value-added services are evaluated. Major problems existed in the development of agricultural informatization technology in China are also discussed. For agricultural sensor technology, the existing problems include that the agricultural information dynamic sensing technique needs to be improved, advanced agricultural sensor technique and industry development are not perfect, and agricultural sensor after-sales supports arenot sufficient. For precision farming technology and intelligent equipment, China has not had its 3S technical support system that is suitable for agricultural applications and its intelligent equipment research and development is not sufficient. For agricultural robot technology, the research direction selection is very subjective, and the research content mainly focuses on the planting industry. Leading robot research agencies rarely involve the agriculture domain. For the industrialization of agricultural robot, related domestic patents are not sufficient and foreign companies take a large market share. For agricultural internet of things technology and equipment, there are also some problems in the technology standard, security, industrialization, application and promotion. For agricultural information services, agricultural remote sensor practicality needs to be improved, software development capability is not sufficient, and the service targets are not well trained. Finally, suggestions are proposed as countermeasures to the existing problems. Agricultural information technology innovation needs to be accelerated. Major engineering projects need to be established to support the informatization development. Subsidies for agricultural informatization need to be implemented. Agricultural informatization standards and evaluation system need to be improved. Researches show that agricultural sensor technology is the basis of agricultural information acquisition and informatization. Precision farming technology represents today's advanced level of agricultural equipment. Agricultural robot technology is an important research direction for agricultural intelligent equipment in the future. Agricultural internet of things technology is an effective means of agricultural supervision and quality monitoring. Agricultural information service technology is more and more focusing on the key technical problems of cloud storage, cloud computing, cloud service and mobile internet in agricultural information services.


Li J.,Chinese Academy of Agricultural Sciences | Dong F.,Chinese Academy of Agricultural Sciences | Xu J.,Chinese Academy of Agricultural Sciences | Liu X.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Analytica Chimica Acta | Year: 2011

A rapid and effective method for enantioselective determination of simeconazole enantiomers in food products (cucumber, tomato, apple, pear, wheat and rice) has been developed. The enantiomers were resolved by capillary gas chromatography (GC) using a commercial chiral column (BGB-172) and a temperature program from 150°C (held for 1min) and then raised at 10°Cmin -1 to 240°C (held for 10min). This enantioselective gas chromatographic separation was combined with a clean-up/enrichment procedure based on the modification of QuEChERS (quick, easy, cheap, effective, rugged and safe) method. Co-extractives were removed with graphitized carbon black/primary secondary amine (GCB/PSA) solid-phase extraction (SPE) cartridges using acetonitrile:toluene (3:1, v/v) as eluent. Gas chromatography/ion trap mass spectrometry (GC-ITMS) with electron ionization (EI) was then used for qualitative and quantitative determination of the simeconazole enantiomers. Two precursor-to-product ion transitions (m/z 121-101 and 195-153) with the best signal intensity were chosen to build the multiple-reaction monitoring (MRM) acquisition method. The limits of detection for each enantiomer of simeconazole in six food products ranged between 0.4 and 0.9μgkg -1, which were much lower than maximum residue levels (MRLs) established by Japan. The methodology was successfully applied for the enantioselective analysis of simeconazole enantiomers in real samples, indicating its efficacy in investigating the environmental stereochemistry of simeconazole in food matrix. © 2011 Elsevier B.V.


Yao Y.,Chinese Academy of Agricultural Sciences | Sang W.,Chinese Academy of Agricultural Sciences | Zhou M.,Dong Zhimen Middle School | Ren G.,Chinese Academy of Agricultural Sciences
Journal of Food Science | Year: 2010

Eleven cultivars of celery, belonging to 2 species, were collected and analyzed for their phenolic compound composition and antioxidant activities. Major phenolic acids identified in the extracts of these celeries were caffeic acid, p-coumaric acid, and ferulic acid, while the identified flavonoids were apigenin, luteolin, and kaempferol. The contents of total phenolics were measured using a Folin-Ciocalteu assay and the total antioxidant capacity was estimated by the 1, 1-diphenyl-2-picrylhydrazyl radical (DPPH) and 2, 2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS· +) methods. Apigenin was the major flavonoid in these samples and the most abundant phenolic acid was p-coumaric acid. Many of the investigated cultivars had high levels of phenolics and exhibited high antioxidant capacity. Among these 11 cultivars, Shengjie celery had the highest antioxidant activity whereas Tropica had the lowest. An extremely significant positive correlation between the antioxidant activity and the contents of total flavonoids, total phenolic acids, or total phenolics was observed in this study. © 2009 Institute of Food Technologists ®.


Liu W.,Chinese Academy of Agricultural Sciences | Liu J.,Hunan Agricultural University | Triplett L.,Colorado State University | Leach J.E.,Colorado State University | And 2 more authors.
Annual Review of Phytopathology | Year: 2014

Rice feeds more than half of the world's population. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, and bacterial blight, caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae, are major constraints to rice production worldwide. Genome sequencing and extensive molecular analysis has led to the identification of many new pathogen-associated molecular patterns (PAMPs) and avirulence and virulence effectors in both pathogens, as well as effector targets and receptors in the rice host. Characterization of these effectors, host targets, and resistance genes has provided new insight into innate immunity in plants. Some of the new findings, such as the binding activity of X. oryzae transcriptional activator-like (TAL) effectors to specific rice genomic sequences, are being used for the development of effective disease control methods and genome modification tools. This review summarizes the recent progress toward understanding the recognition and signaling events that govern rice innate immunity. ©2014 by Annual Reviews. All rights reserved.


Cheng F.,Chinese Academy of Agricultural Sciences | Mandakova T.,Masaryk University | Wu J.,Chinese Academy of Agricultural Sciences | Xie Q.,CAS Institute of Genetics and Developmental Biology | And 2 more authors.
Plant Cell | Year: 2013

The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers. © 2013 American Society of Plant Biologists. All rights reserved.


Liu N.,Jiangnan University | Fan F.,Chinese Academy of Agricultural Sciences | Qiu D.,Chinese Academy of Agricultural Sciences | Jiang L.,Jiangnan University
Fungal Genetics and Biology | Year: 2013

Fusarium head blight (FHB) is a worldwide devastating disease of wheat, barley and other small grain cereals and caused primarily by Fusarium graminearum. Carbendazim (MBC) is one of the fungicides widely used to control FHB in China. In the present study, we have identified the F. graminearum locus FGSG_04220 as the sequence homolog for Saccharomyces cerevisiae ScSWI6, named FgSWI6 hereafter. Deletion of FgSWI6 causes mycelium of F. graminearum become sensitive to MBC in liquid medium. In addition, deletion of FgSWI6 reduces mycelial growth as well as production and development of conidia. F. graminearum cells lacking FgSWI6 show reduced production efficiency and sizes of perithecia as well as a defect in the production of ascus and ascospore. FgSWI6 is required for the cellulose utilization, lithium tolerance and deoxynivalenol (DON) production of this pathogen. Furthermore, deletion of FgSWI6 significantly attenuates the virulence of F. graminearum on wheat. Therefore, FgSwi6p plays an important role in growth and development of the economically important fungal pathogen F. graminearum as well as its resistance to MBC. © 2013 Elsevier Inc.


Duan Y.,Chinese Academy of Sciences | Duan Y.,Chinese Academy of Agricultural Sciences | Li F.,Chinese Academy of Sciences | Li L.,Chinese Academy of Sciences | And 4 more authors.
British Journal of Nutrition | Year: 2014

The objective of the present study was to investigate the optimal dietary n-6:n-3 PUFA ratios that regulate lipid metabolism and inflammation in pigs. A total of ninety-six cross-bred (Large White × Landrace) growing-finishing pigs (73·8 (sem 1·6) kg) were chosen and fed one of the four isoenergetic diets with n-6:n-3 PUFA ratios of 1:1, 2·5:1, 5:1 and 10:1. The growth performance of pigs fed the diet with an n-6:n-3 PUFA ratio of 5:1 was the best, but the group fed the diet with an n-6:n-3 PUFA ratio of 1:1 had the highest muscle mass and the lowest adipose tissue mass (P< 0·05). The concentrations of IL-6 and IL-1β of pigs fed the diet with an n-6:n-3 PUFA ratio of 1:1 were decreased compared with those of the other groups (P< 0·05). The concentration of adiponectin of pigs fed the diet with an n-6:n-3 PUFA ratio of 1:1 was also markedly decreased, but the concentration of leptin was increased compared with that of the groups fed the diets with n-6:n-3 PUFA ratios of 5:1 and 10:1 (P< 0·05). Additionally, the optimal dietary ratios of n-6:n-3 PUFA of 1:1 and 5:1 markedly suppressed the expression levels of lipid metabolism-related genes and proteins such as phosphoinositide-3-kinase-α, fatty acid transport protein-1 and PPARγ. They also significantly suppressed the expression levels of the inflammatory cytokines IL-1β, TNF-α and IL-6. The results indicated that the optimal n-6:n-3 PUFA ratios of 1:1 and 5:1 exerted beneficial effects on lipid metabolism and inflammatory system, leading to the availability of more energy and nutrients for high performance and homeostatic pathways. © 2013 The Authors.


Du J.,London School of Hygiene and Tropical Medicine | Du J.,Chinese Academy of Agricultural Sciences | Bhattacharya B.,London School of Hygiene and Tropical Medicine | Ward T.H.,London School of Hygiene and Tropical Medicine | Roy P.,London School of Hygiene and Tropical Medicine
Journal of Virology | Year: 2014

Bluetongue virus (BTV), a member of the Orbivirus genus in the Reoviridae family, is a double-capsid insect-borne virus enclosing a genome of 10 double-stranded RNA segments. Like those of other members of the family, BTV virions are nonenveloped particles containing two architecturally complex capsids. The two proteins of the outer capsid, VP2 and VP5, are involved in BTV entry and in the delivery of the transcriptionally active core to the cell cytoplasm. Although the importance of the endocytic pathway in BTV entry has been reported, detailed analyses of entry and the role of each protein in virus trafficking have not been possible due to the lack of availability of a tagged virus. Here, for the first time, we report on the successful manipulation of a segmented genome of a nonenveloped capsid virus by the introduction of tags that were subsequently fluorescently visualized in infected cells. The genetically engineered fluorescent BTV particles were observed to enter live cells immediately after virus adsorption. Further, we showed the separation of VP2 from VP5 during virus entry and confirmed that while VP2 is shed from virions in early endosomes, virus particles still consisting of VP5 were trafficked sequentially from early to late endosomes. Since BTV infects both mammalian and insect cells, the generation of tagged viruses will allow visualization of the trafficking of BTV farther downstream in different host cells. In addition, the tagging technology has potential for transferable application to other nonenveloped complex viruses. © 2014, American Society for Microbiology.


Song J.B.,Nanjing Agricultural University | Huang S.Q.,Nanjing Agricultural University | Huang S.Q.,Chinese Academy of Agricultural Sciences | Dalmay T.,University of East Anglia | Yang Z.M.,Nanjing Agricultural University
Plant and Cell Physiology | Year: 2012

The present study identified Arabidopsis miR394 and its target, an F-box (SKP1-Cullin/CDC53-F-box) gene At1g27340 (here referred to as LEAF CURLING RESPONSIVENESS, LCR), for regulation of leaf curling-related morphology. The loss-of-function lcr mutants exhibit pleiotropic defects with semi-dwarfism, altered leaf shape and a shorter stem. Overexpression of an miR394-resistant version of LCR under the 35S promoter (35S:m5LCR) and target mimicry MIM394 resulted in a curled-down leaf defect. Conversely, transgenic plants overexpressing 35S:MIR394a/b display a curled-up leaf phenotype. Detailed analyses show that there is a certain level of LCR that is optimal for leaf morphology, but lower or higher levels lead to abnormal leaf development, indicating that expression of miR394 in the leaf lamina is necessary for proper leaf morphology. Because the phytohormone auxin plays a crucial role in leaf morphogenesis and patterning, the DR5-GUS reporter gene was used to monitor the auxin response. We show that DR5 expression patterns in lcr and 35S::m5LCR plants were significantly different from those in the wild type. Also, overexpression of LCR in 35S::m5LCR plants drastically decreased the expression of the auxin-responsive genes IAA3, AXR3 and IAMT1, whereas increased expression of the genes was found in 35S::MIR394a plants. These results indicate that miR394 and its target LCR are involved in the regulation of leaf development. © 2012 The Author.


Wang J.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | Rothausen S.G.S.A.,University of East Anglia | Conway D.,University of East Anglia | Zhang L.,CAS Beijing Institute of Geographic Sciences and Nature Resources Research | And 3 more authors.
Environmental Research Letters | Year: 2012

China is the worlds largest emitter of greenhouse gases (GHGs) and the agricultural sector in China is responsible for 1720% of annual emissions and 62% of total freshwater use. Groundwater abstraction in China has increased rapidly from 10km3yr1 in the 1950s to more than 100km 3yr1 in the 2000s, such that roughly 70% of the irrigated area in northern China is now groundwater-fed. Pumping of water for irrigation is one of the most energy consuming on-farm processes; however, to date this source of GHG emissions in China and elsewhere has been relatively neglected. We derive the first detailed estimate of GHG emissions from groundwater pumping for irrigation in China, using extensive village survey data from 11 provinces, broadly representative of the situation during the mid-2000s. The 11 provinces cover roughly half of Chinas irrigated cropland and we upscale to the national level using government statistics for the remaining 20 provinces. Our results show emissions of 33.1MtCO2e, just over half a per cent of the national total. Groundwater abstraction represents an important source of GHG emissions that has been rapidly increasing and which at present is largely unregulated. Water scarcity in China is already driving policies to improve water conservation. These results suggest that significant potential exists to promote the co-benefits of water and energy saving in order to meet national planning targets. © 2012 IOP Publishing Ltd.


Wang H.-Y.,Chinese Academy of Agricultural Sciences | Fan B.-Q.,Chinese Academy of Agricultural Sciences | Li C.-H.,Chinese Research Academy of Environmental Sciences | Liu S.,Chinese Academy of Agricultural Sciences | Li M.,Chinese Academy of Agricultural Sciences
Bioresource Technology | Year: 2011

The effects of biosurfactant rhamnolipid (RL) and chemical surfactant Triton X-100 on the production of cellulases and xylanase from Penicillium expansum (P. expansum) in untreated, acid- and alkali-pretreated wheat straw submerged fermentations were studied, and the influences on the activity and stability of Cellulase R-10 were also investigated. The results showed that RL and Triton X-100 enhanced the activities of cellulases and xylanase to different extents and the stimulatory effects of RL were superior to those of Triton X-100. During the peak enzyme production phase, RL (60. RE. mg/l) increased cellulases activities by 25.5-102.9%, in which the raise of the same enzyme in acid-pretreated straw broths was the most. It was found that the reducing sugars by hydrolyzing wheat straw with Cellulase R-100 were not visibly increased after adding RL. However, it distinctly protected Cellulase R-10 from degradation or inactivation, keeping the reducing sugars yield at about 17%. © 2011.


Xiong W.,Chinese Academy of Agricultural Sciences | Holman I.,Cranfield University | Lin E.,Chinese Academy of Agricultural Sciences | Conway D.,University of East Anglia | And 2 more authors.
Environmental Research Letters | Year: 2012

There is increasing evidence of crop yield response to recent global warming, yet there is poor understanding of the relative contributions of different climatic variables to changes in crop production. Using a spatially calibrated crop model with cultivars and crop inputs held constant for the year 2000, we simulate idealized national cereal production during the period 1961-2010 under different combinations of observed climate and CO2 forcings. With increasing CO2 and all climate forcings, production shows a slight and insignificant change (-0.9% between 1961 and 2010); however, without CO2 the combined climate forcings decrease production (-8.6%). Changing one climate variable at a time, whilst holding the other variables constant at 1961 values, observed warming has virtually no overall effect on production (0.01%), precipitation decreases it by 1.2% and radiation decreases it by 7.0%. The effects are management and crop dependent, with decreasing radiation responsible for reduced irrigated crop production, and precipitation for variability in rain-fed crop production. Rice is the most sensitive crop, with the largest decline (-12.4%) in simulated production. Wheat shows reduced yield (-9.7%) owing to climate factors, whilst offset by CO 2 fertilization (overall change 0.9%). Maize shows insignificant change (-1.2%) and moderate increase in production (2.6%), respectively. These model results suggest that decreasing radiation due to increasing aerosol concentration and other atmospheric pollutants has had a greater effect on crop production than warming trends in China. This underscores the need for crop-climate studies to resolve better the effects of radiation on crop yield and examine climate model projections of radiation in greater detail. © 2012 IOP Publishing Ltd.


Su Y.,Xinjiang University | Liang Y.,Chinese Academy of Agricultural Sciences
Journal of Hazardous Materials | Year: 2013

The foliar uptake and downward translocation of trichloroethylene (TCE) and 1,2,3-trichlorobenzene (TCB) in wheat, corn, and tomato seedlings were investigated following 2-48-h exposure of the plant shoots to vapor-contaminated air. The results showed that both TCE and TCB could be rapidly transported from air to plant rhizosphere solution through the foliar uptake and downward transport; the TCE and TCB concentrations in rhizosphere solutions increased with exposure time and external contaminant concentration. Among the three plant species studied, the TCE and TCB downward transport followed the order of wheat>tomato>corn. The transport efficiency of TCE by the three plants was far greater than that of TCB. With a 24-h uptake time, the amounts of TCE transported into the rhizosphere solution by wheat, tomato, and corn seedlings were 2.39±0.42, 1.50±0.22 and 1.45±0.08μg TCE per gram of fresh weight biomass, respectively, when the initial external TCE concentration was set at 12mgl-1. In a 48-h uptake experiment with corn seedlings, the TCE concentration in the rhizosphere solutions was lower in the TCE-TCB mixture system than in the single TCE system, whereas there was no significant difference in TCB concentration between the single TCB and TCE-TCB mixture systems at 48h. The downward transport processes of TCE were inhibited, while those of TCB were enhanced in the mixed contaminant system within a 48-h uptake time. © 2013 Elsevier B.V.


Li H.,Chinese Academy of Agricultural Sciences | Qiu J.,Chinese Academy of Agricultural Sciences | Wang L.,Chinese Academy of Agricultural Sciences | Tang H.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Agriculture, Ecosystems and Environment | Year: 2010

Agricultural production plays an important role in affecting atmospheric greenhouse gas concentrations. Field measurements were conducted in Quzhou County, Hebei Province in the North China Plains to quantify carbon dioxide (CO2) and nitrous oxide (N2O) emissions from a winter wheat-maize rotation field, a common cropping system across the Chinese agricultural regions. The observed flux data in conjunction with the local climate, soil and management information were utilized to test a process-based model, Denitrification-Decomposition or DNDC, for its applicability for the cropping system. The validated DNDC was then used for predicting impacts of three management alternatives (i.e., no-till, increased crop residue incorporation and reduced fertilizer application rate) on CO2 and N2O emissions from the target field. Results from the simulations indicated that (1) CO2 emissions were significantly affected by temperature, initial SOC, tillage method, and quantity and quality of the organic matter added in the soils; (2) increases in temperature, initial SOC, total fertilizer N input, and manure amendment substantially increased N2O emissions; and (3) temperature, initial SOC, tillage, and quantity and quality of the organic matter added in the soil all had significant effects on global warming. Finally, five 50-year scenarios were simulated with DNDC to predict their long-term impacts on crop yield, soil C dynamics, nitrate leaching losses, and N2O emissions. The modelled results suggested that implementation of manure amendment or crop residue incorporation instead of increased fertilizer application rates would more efficiently mitigate GHG emissions from the tested agro-ecosystem. The multi-impacts provided a sound basis for comprehensive assessments on the management alternatives. © 2009 Elsevier B.V. All rights reserved.


Liu W.,Chinese Academy of Agricultural Sciences | Liu J.,Chinese Academy of Agricultural Sciences | Liu J.,Hunan Agricultural University | Ning Y.,Chinese Academy of Agricultural Sciences | And 5 more authors.
Molecular Plant | Year: 2013

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most destructive diseases of rice worldwide. The rice-M. oryzae pathosystem has become a model in the study of plant-fungal interactions because of its scientific advancement and economic importance. Recent studies have identified a number of new pathogen-associated molecular patterns (PAMPs) and effectors from the blast fungus that trigger rice immune responses upon perception. Interaction analyses between avirulence effectors and their cognate resistance proteins have provided new insights into the molecular basis of plant-fungal interactions. In this review, we summarize the recent research on the characterization of those genes in both M. oryzae and rice that are important for the PAMP- and effector-triggered immunity recognition and signaling processes. We also discuss future directions for research that will further our understanding of this pathosystem.© 2012 The Author.


Tao C.,Chinese Academy of Agricultural Sciences | Tao C.,U.S. Center for Disease Control and Prevention | Li G.,Chinese Academy of Agricultural Sciences
Letters in Applied Microbiology | Year: 2014

We developed an immunochromatographic test strip using colloidal gold-coated staphylococcal protein A (SPA) for the detection of rabies antibody in canine serum samples. The recombinantly expressed rabies virus phosphoprotein (RV-P) and the anti-staphylococcal protein A (anti-SPA) polyclonal antibody were coated on the test (T) and control (C) lines on a nitrocellulose membrane, respectively. This layout is designed such that the polyclonal antibody in canine serum is captured by the colloidal gold-SPA conjugates, before the rabies antibody complex is specifically selected by the RV-P deposited on the T line, forming a 'sandwich' pattern. Unbound excess colloidal SPA then proceeds to the control line where SPA specifically interacts with the anti-SPA antibody, producing a red precipitation at the C line, indicating the validity of the strip. We tested 165 canine serum samples with the strips, and the results were compared with those obtained using ELISA. The specificity and sensitivity of ICTS were found to be 93·1 and 92·2%, respectively. As a rapid technique, not demanding expensive instrumentation, the strip offers potential in disease monitoring, especially in rabies-endemic developing countries. © 2014 The Society for Applied Microbiology.


Han X.,Chinese Academy of Agricultural Sciences | Kim J.-Y.,Gyeongsang National University
Molecular Plant | Year: 2016

Intercellular and supracellular communications through plasmodesmata are involved in vital processes for plant development and physiological responses. Micro- and macromolecules, including hormones, RNA, and proteins, serve as biological information vectors that traffic through the plasmodesmata between cells. Previous studies demonstrated that the plasmodesmata are elaborately regulated, whereby a long queue of multiple signaling molecules forms. However, the mechanism by which these signals are coupled or coordinated in terms of simultaneous transport in a single channel remains a puzzle. In the last few years, several phytohormones that could function as both non-cell-autonomous signals and plasmodesmal regulators have been disclosed. Plasmodesmal regulators such as auxin, salicylic acid, reactive oxygen species, gibberellic acids, chitin, and jasmonic acid could regulate intercellular trafficking by adjusting plasmodesmal permeability. Here, callose, along with β-glucan synthase and β-glucanase, plays a critical role in regulating plasmodesmal permeability. Interestingly, most of the previously identified regulators are capable of diffusing through the plasmodesmata. Given the small sizes of these molecules, the plasmodesmata are prominent intercellular channels that allow diffusion-based movement of those signaling molecules. Obviously, intercellular communication is under the control of a major mechanism, named a feedback loop, at the plasmodesmata, which mediates complicated biological behaviors. Prospective research on the mechanism of coupling micromolecules at the plasmodesmata for developmental signaling and nutrient provision will help us to understand how plants coordinate their development and photosynthetic assimilation, which is important for agriculture. © 2016 The Author.


News Article | December 1, 2015
Site: phys.org

Boyalife Group and its partners are building the giant plant in the northern Chinese port of Tianjin, where it is due to go into production within the next seven months and aims for an output of one million cloned cows a year by 2020. But cattle are only the beginning of chief executive Xu Xiaochun's ambitions. In the factory pipeline are also thoroughbred racehorses, as well as pet and police dogs, specialised in searching and sniffing. Boyalife is already working with its South Korean partner Sooam and the Chinese Academy of Sciences to improve primate cloning capacity to create better test animals for disease research. And it is a short biological step from monkeys to humans—potentially raising a host of moral and ethical controversies. "The technology is already there," Xu said. "If this is allowed, I don't think there are other companies better than Boyalife that make better technology." The firm does not currently engage in human cloning activities, Xu said, adding that it has to be "self-restrained" because of possible adverse reaction. But social values can change, he pointed out, citing changing views of homosexuality and suggesting that in time humans could have more choices about their own reproduction. "Unfortunately, currently, the only way to have a child is to have it be half its mum, half its dad," he said. "Maybe in the future you have three choices instead of one," he went on. "You either have fifty-fifty, or you have a choice of having the genetics 100 percent from Daddy or 100 percent from Mummy. This is only a choice." Xu, 44, went to university in Canada and the US, and has previously worked for US pharmaceutical giant Pfizer, and in drug development. Presenting cloning as a safeguard of biodiversity, the Tianjin facility will house a gene bank capable of holding up to approximately five million cell samples frozen in liquid nitrogen—a catalogue of the world's endangered species for future regeneration. Boyalife's South Korean partner Sooam is already working on a project to bring the woolly mammoth back from extinction by cloning cells preserved for thousands of years in the Siberian permafrost. Sooam founder Hwang Woo-Suk was a national hero with his own postage stamp before being embroiled in controversy a decade ago after his claims to be the first in the world to clone a human embryo were discredited. Hwang, who created Snuppy, the world's first cloned dog, in 2005, lost his university position, had two major papers retracted, and was accused of crimes ranging from violation of bioethics laws to embezzling research funds. Earlier this year he was quoted in South Korea's Dong-A Ilbo newspaper saying that his firm was planning a cloning joint venture in China "because of South Korea's bioethics law that prohibits the use of human eggs". "We have decided to locate the facilities in China in case we enter the phase of applying the technology to human bodies," he was quoted as saying. For now, Xu seeks to become the world's first purveyor of "cloned" beef, breeding genetically identical super-cattle that he promises will taste like Kobe and allow butchers to "slaughter less and produce more" to meet the demands of China's booming middle class. Cloning differs from genetic modification, but its application to animals would enable the firm to homogenise its output. "Everything in the supermarket looks good—it's almost all shiny, good-looking, and uniformly shaped. For animals, we weren't able to do that in the past. But with our cloning factory, we choose to do so now," Xu said. "Remember, this is a food. We want it to be uniform, very consistent, very premium quality," he added. There is controversy over whether cloned beef is safe for human consumption—research by the US Food and Drug Adminstration says that it is, but the European parliament has backed a ban on cloned animals and products in the food chain. The UN's Food and Agriculture Organization has yet to review the issue. Han Lanzhi, a GMO safety specialist at the Chinese Academy of Agricultural Sciences, said Boyalife's claims about the safety, scope and timeline of their operations were alarming—and implausible. "To get approval for the safety of cloned animals would be a very drawn-out process, so when I heard this news, I felt very surprised," she said. "There must be strong regulation because as a company pursuing its own interests, they could very easily do other things in the future," she added. Xu sought to be reassuring, telling AFP: "We want the public to see that cloning is really not that crazy, that scientists aren't weird, dressed in lab coats, hiding behind a sealed door doing weird experiments."


News Article | April 7, 2016
Site: www.greencarcongress.com

« Volvo Cars plans to launch large-scale autonomous driving experiment in China; 100 cars on public roads | Main | NASA, Boeing designing truss-braced wing expected to reduce aircraft fuel consumption and emissions by 50% » The green microalga Botryococcus braunii is considered a promising biofuel feedstock producer due to its prodigious accumulation of hydrocarbon oils that can be converted into fuels. Now, a team led by researchers from Texas A&M AgriLife Research has identified the first committed step in the biosynthesis of hydrocarbon oil in B. braunii and has described a new enzyme which carries out this reaction. The study, published as an open-access paper in the current issue of the journal Nature Communications, could enable scientists to use the enzyme in a plant to make large amounts of fuel-grade oil, according to Dr. Tim Devarenne, AgriLife Research biochemist in College Station and lead scientist on the team. Devarenne’s lab has been studying the concept of making fuel from algae on a $2-million National Science Foundation grant for four years. The colony-forming green microalga B. braunii is an exciting candidate for biofuel feedstock production, as it produces up to 61% of its dry weight as liquid hydrocarbon oils. These hydrocarbons are produced inside the cells of the colony, seen as intracellular oil bodies and secreted into the colony extracellular matrix where the majority of the hydrocarbons are stored. Most importantly, catalytic hydrocracking of hydrocarbons from this alga results in petroleum-equivalent fuels of gasoline, kerosene and diesel. Intriguingly, geologic evidence also shows a direct contribution of this alga to the formation of currently used fossil fuel deposits around the globe. Despite the aforementioned advantages of B. braunii, its use for biofuel feedstock production is hindered by a slow growth rate and the lack of transformation systems to achieve targeted genetic modification. Thus, the identification of B. braunii hydrocarbon biosynthetic pathways and associated genes/enzymes can provide options for metabolically engineering these pathways into heterologous hosts with better growth characteristics and the ability to be genetically manipulated. This would then allow the development of improved versions of hydrocarbon biosynthetic enzymes, to direct production towards the most commercially desirable products. Devarenne’s lab has been trying to understand how Botryococcus braunii makes the liquid hydrocarbons—i.e., what genes and pathways are involved—so the genes can be manipulated to make more oil, possibly by transferring those genes into a land plant such as tobacco, or maybe other algae that grow very quickly. It takes about a week for one Botryococcus cell to double into two cells, whereas a faster growing algae—but one that doesn't make a lot of oil—can double in about six hours, Devarenne said. The researchers targeted deciphering the biochemical pathway for making the hydrocarbon oil, which is called lycopadiene. They discovered a gene called lycopaoctaene synthase (LOS). The enzyme encoded by the LOS gene is able to initiate the production of the oil. A closer look at the LOS enzyme revealed that the enzyme is “promiscuous” in that it is capable of mixing several substrates to make different products. Devarenne explained that’s not only different from other enzymes that are similar to LOS, but it’s important because most enzymes like LOS only use a 15-carbon substrate. In terms of fuel, it's better to start with a higher carbon number molecule. The team determined the sequence of all the actively working genes of the organism under hydrocarbon producing conditions. Bioinformatic analysis of this sequence information was then able to pinpoint a gene that might have the appropriate activity to initiate hydrocarbon biosynthesis. Even when the genes are more fully understood, scientists will have to find the right host organism to express the genes, optimize that expression and try to get them to produce as much of the oil as possible. The project included Devarenne’s graduate student Hem Thapa and colleague Mandar Naik at Texas A&M University in College Station, along with Shigeru Okada and Kentaro Takada from the University of Tokyo in Japan, Istvan Molnar from the University of Arizona’s College of Agriculture and Life Sciences and Yuquan Xu from the Chinese Academy of Agricultural Sciences.


Wang H.,Hong Kong Baptist University | Wang H.,Donald Danforth Plant Science Center | Lu Y.,Chinese Academy of Agricultural Sciences | Jiang T.,Hong Kong Baptist University | And 4 more authors.
Plant Journal | Year: 2013

Pollen formation is a complex developmental process that has been extensively investigated to unravel underlying fundamental developmental mechanisms and for genetic manipulation of the male-sterility trait for hybrid crop production. Here we describe identification of AtPUB4, a U-box/ARM repeat-containing E3 ubiquitin ligase, as a novel player in male fertility in Arabidopsis. Loss of AtPUB4 function causes hypertrophic growth of the tapetum layer. The Atpub4 mutation also leads to incomplete degeneration of the tapetal cells and strikingly abnormal exine structures of pollen grains. As a result, although the Atpub4 mutant produces viable pollen, the pollen grains adhere to each other and to the remnants of incompletely degenerated tapetal cells, and do not properly disperse from dehisced anthers for successful pollination. We found that the male-sterility phenotype caused by the Atpub4 mutation is temperature-dependent: the mutant plants are sterile when grown at 22°C but are partially fertile at 16°C. Our study also indicates that the AtPUB4-mediated pathway acts in parallel with the brassinosteroid pathway in controlling developmental fates of the tapetal cells to ensure male fertility. © 2013 The Authors The Plant Journal © 2013 Blackwell Publishing Ltd.


Wang H.,Hong Kong Baptist University | Wang H.,Fudan University | Lu Y.,Hong Kong Baptist University | Lu Y.,Chinese Academy of Agricultural Sciences | And 5 more authors.
Plant Journal | Year: 2013

AtNUDT7 was reported to be a negative regulator of EDS1-mediated immunity in Arabidopsis. However, the underlying molecular and genetic mechanism of the AtNUDT7-regulated defense pathway remains elusive. Here we report that AtNUDT7 and its closest paralog AtNUDT6 function as novel negative regulators of SNC1, a TIR-NB-LRR-type R gene. SNC1 is upregulated at transcriptional and possibly post-transcriptional levels in nudt6-2 nudt7. The nudt6-2 nudt7 double mutant exhibits autoimmune phenotypes that are modulated by temperature and fully dependent on EDS1. The nudt6-2 nudt7 mutation causes EDS1 nuclear accumulation shortly after the establishment of autoimmunity caused by the temperature shift. We found that a low ammonium/nitrate ratio in growth media leads to a higher level of nitrite-dependent nitric oxide (NO) production in nudt6-2 nudt7, and NO acts in a positive feedback loop with EDS1 to promote the autoimmunity. The low ammonium/nitrate ratio also enhances autoimmunity in snc1-1 and cpr1, two other autoimmune mutants in Arabidopsis. Our study indicates that Arabidopsis senses the ammonium/nitrate ratio as an input signal to determine the amplitude of the EDS1-mediated defense response, probably through the modulation of NO production. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.


Koch H.,ETH Zurich | Koch H.,Yale University | Abrol D.P.,Sher-e-Kashmir University of Agricultural Sciences and Technology | Li J.,Chinese Academy of Agricultural Sciences | Schmid-Hempel P.,ETH Zurich
Molecular Ecology | Year: 2013

The animal gut is a habitat for diverse communities of microorganisms (microbiota). Honeybees and bumblebees have recently been shown to harbour a distinct and species poor microbiota, which may confer protection against parasites. Here, we investigate diversity, host specificity and transmission mode of two of the most common, yet poorly known, gut bacteria of honeybees and bumblebees: Snodgrassella alvi (Betaproteobacteria) and Gilliamella apicola (Gammaproteobacteria). We analysed 16S rRNA gene sequences of these bacteria from diverse bee host species across most of the honeybee and bumblebee phylogenetic diversity from North America, Europe and Asia. These focal bacteria were present in 92% of bumblebee species and all honeybee species but were found to be absent in the two related corbiculate bee tribes, the stingless bees (Meliponini) and orchid bees (Euglossini). Both Snodgrassella alvi and Gilliamella apicola phylogenies show significant topological congruence with the phylogeny of their bee hosts, albeit with a considerable degree of putative host switches. Furthermore, we found that phylogenetic distances between Gilliamella apicola samples correlated with the geographical distance between sampling locations. This tentatively suggests that the environmental transmission rate, as set by geographical distance, affects the distribution of G. apicola infections. We show experimentally that both bacterial taxa can be vertically transmitted from the mother colony to daughter queens, and social contact with nest mates after emergence from the pupa greatly facilitates this transmission. Therefore, sociality may play an important role in vertical transmission and opens up the potential for co-evolution or at least a close association of gut bacteria with their hosts. © 2013 Blackwell Publishing Ltd.


Liu Q.,Chinese Academy of Agricultural Sciences | Liu Q.,Academy of Military Medical science | Cao L.,Academy of Military Medical science | Cao L.,Jilin Academy of Animal Husbandry and Veterinary Medicine | Zhu X.-Q.,Chinese Academy of Agricultural Sciences
International Journal of Infectious Diseases | Year: 2014

Emerging and re-emerging zoonoses are a significant public health concern and cause considerable socioeconomic problems globally. The emergence of severe acute respiratory syndrome (SARS), highly pathogenic avian influenza (HPAI) H5N1, avian influenza H7N9, and severe fever with thrombocytopenia syndrome (SFTS), and the re-emergence of rabies, brucellosis, and other zoonoses have had a significant effect on the national economy and public health in China, and have affected other countries. Contributing factors that continue to affect emerging and re-emerging zoonoses in China include social and environmental factors and microbial evolution, such as population growth, urbanization, deforestation, livestock production, food safety, climate change, and pathogen mutation. The Chinese government has devised new strategies and has taken measures to deal with the challenges of these diseases, including the issuing of laws and regulations, establishment of disease reporting systems, implementation of special projects for major infectious diseases, interdisciplina