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Hao D.,Jiangsu Yanjiang Institute of Agricultural science | Xue L.,Jiangsu Yanjiang Institute of Agricultural science | Xue L.,Jiangsu Collaborative Innovation Center for Modern Crop Production | Yuan J.,Jiangsu Collaborative Innovation Center for Modern Crop Production | And 9 more authors.
Molecular Breeding | Year: 2017

Starch paste viscosity properties are widely used as important indicators for quality estimation in waxy maize. To elucidate the genetic basis of paste viscosity characteristics of waxy maize, seven parameters from the rapid visco analyzer (RVA) profile were analyzed for quantitative trait loci (QTLs) in this study, using a recombinant inbred line population derived from a cross between the inbred lines Tongxi5 and Hengbai522. A high-density linkage map was constructed using 2703 bin markers, covering 1876.20 cM of the whole genome with an average genetic distance of 0.73 cM between adjacent bin markers. Seventy-two QTLs were detected for RVA parameters across 3 years, of which 17 could be identified in 2 years, and 6 identified in all 3 years. Eight QTL clusters were observed to be co-associated with two or more RVA parameters. Three major QTLs, qPV4-1, qTV4-1, and qFV5-2, which explained over 10% of the phenotypic variation, were stably mapped to the chromosomes 4 or 5 in all years. Based on functional annotations, two genes were considered as potential candidate genes for the identified major QTLs. The QTLs and candidate genes identified in this study will be useful for further understanding of the genetic architecture of starch paste viscosity characteristics in waxy maize, and may facilitate molecular breeding for grain quality improvement in breeding programs, and simultaneously provide a basis for cloning of the genes underlying these QTLs. © 2017, Springer Science+Business Media Dordrecht.


Song Y.,Anhui Agricultural University | Rui Y.,China Agricultural University | Bedane G.,University of Queensland | Li J.,Anhui Agricultural University | Li J.,Jiangsu Collaborative Innovation Center for Modern Crop Production
PLoS ONE | Year: 2016

Improving crop productivity through higher plant density requires a detailed understanding of organ development in response to increased interplant competition. The objective of this paper is thus to investigate the characteristics of organ development under increased interplant competition. A field experiment was conducted to investigate organ development across 4 maize plant densities i.e. 2, 6, 12 and 20 plants m-2 (referred to PD2, PD6, PD12 and PD20 respectively). In response to increased interplant competition, lengths of both laminae and sheaths increased in lower phytomers, but decreased in upper phytomers. Sheath extension appeared to be less sensitive to increased interplant competition than lamina extension. Extension of laminae and internodes responded to increased plant density as soon as onset of mild interplant competition, but did not respond any further to severe competition. Both lamina width and internode diameter were reduced due to a smaller growth rate in response to increased plant density. Overall, this study identified that organ expansion rate can be taken as the key morphological factor to determine the degree of interplant competition. © 2016 Song 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.


He H.,Anhui Agricultural University | Wu L.,Anhui Agricultural University | Yang R.,Shihezi University | Ma F.,Shihezi University | And 2 more authors.
Nongye Jixie Xuebao/Transactions of the Chinese Society for Agricultural Machinery | Year: 2016

To investigate the effects of water regimes on yield formation, photosynthetic characteristics and transpiration efficiency of rice plants in arid region, plot experiments were conducted in 2011 and 2012 in Shihezi City with three water treatments, including flooding irrigation (W1), controlled irrigation technology (W2) and aerobic rice (W3). The results showed that there was no significant difference for net photosynthetic rate (Pn) in W1 and W2 treatments before anthesis, but W1 treatment was 11.29%~20.91% higher than W2 treatment, and 38.65%~52.03% higher than W3 treatment after anthesis across both years. Further analysis indicated that little difference of the parameters of Pn, carboxylation efficiency, saturation light intensity, and compensation light intensity were existed in W1 and W2 treatments in saturated soil moisture, the lower Pn in W2 and W3 treatments than that in W1 treatment was mainly due to significantly decreased Pn in W2 and W3 treatments when soil water content was unsaturated in 2011 and 2012 (p<0.05). Moreover, the diurnal changes of Pn was higher in W1 treatment than that in W2 and W3 treatments during whole observed times, and the difference was greater on forenoon (before 12:00) than on afternoon (after 14:00) among treatments. Finally, the grain yield in W2 and W3 treatments only decreased by 4.43%~18.72% and 31.23%~39.45% when compared with W1 treatment considering both years. The transpiration efficiency in W2 treatment was always significantly greater than that in W1 and W3 treatments during whole growth stages in both years (p<0.05). Generally speaking, the W2 treatment performs high grain yield and high water use efficiency in arid region, meanwhile, the grain yield in W2 treatment could be increased when improving photosynthetic produce ability in the afternoon at grain-filling stage. © 2016, Chinese Society of Agricultural Machinery. All right reserved.


Jia H.,Nanjing Agricultural University | Shao M.,Nanjing Agricultural University | He Y.,Nanjing Agricultural University | Guan R.,Nanjing Agricultural University | And 3 more authors.
PLoS ONE | Year: 2015

Salt stress limits plant growth and crop productivity and is an increasing threat to agriculture worldwide. In this study, proteomic and physiological responses of Brassica napus leaves under salt stress were investigated. Seedlings under salt treatment showed growth inhibition and photosynthesis reduction. A comparative proteomic analysis of seedling leaves exposed to 200 mM NaCl for 24 h, 48 h and 72 h was conducted. Fortyfour protein spots were differentially accumulated upon NaCl treatment and 42 of them were identified, including several novel salt-responsive proteins. To determine the functional roles of these proteins in salt adaptation, their dynamic changes in abundance were analyzed. The results suggested that the up-accumulated proteins, which were associated with protein metabolism, damage repair and defense response, might contribute to the alleviation of the deleterious effect of salt stress on chlorophyll biosynthesis, photosynthesis, energy synthesis and respiration in Brassica napus leaves. This study will lead to a better understanding of the molecular basis of salt stress adaptation in Brassica napus and provides a basis for genetic engineering of plants with improved salt tolerance in the future. © 2015 Jia 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.


Lin Z.,Nanjing Agricultural University | Zhang X.,Nanjing Agricultural University | Yang X.,Nanjing Agricultural University | Li G.,Nanjing Agricultural University | And 6 more authors.
BMC Plant Biology | Year: 2014

Background: Grain chalkiness is a complex trait adversely affecting appearance and milling quality, and therefore has been one of principal targets for rice improvement. Eliminating chalkiness from rice has been a daunting task due to the complex interaction between genotype and environment and the lack of molecular markers. In addition, the molecular mechanisms underlying grain chalkiness formation are still imperfectly understood.Results: We identified a notched-belly mutant (DY1102) with high percentage of white-belly, which only occurs in the bottom part proximal to the embryo. Using this mutant, a novel comparison system that can minimize the effect of genetic background and growing environment was developed. An iTRAQ-based comparative display of the proteins between the bottom chalky part and the upper translucent part of grains of DY1102 was performed. A total of 113 proteins responsible for chalkiness formation was identified. Among them, 70 proteins are up-regulated and 43 down-regulated. Approximately half of these differentially expressed proteins involved in central metabolic or regulatory pathways including carbohydrate metabolism (especially cell wall synthesis) and protein synthesis, folding and degradation, providing proteomic confirmation of the notion that chalkiness formation involves diverse but delicately regulated pathways. Protein metabolism was the most abundant category, accounting for 27.4% of the total differentially expressed proteins. In addition, down regulation of PDIL 2-3 and BiP was detected in the chalky tissue, indicating the important role of protein metabolism in grain chalkiness formation.Conclusions: Using this novel comparison system, our comprehensive survey of endosperm proteomics in the notched-belly mutant provides a valuable proteomic resource for the characterization of pathways contributing to chalkiness formation at molecular and biochemical levels. © 2014 Lin et al.; licensee BioMed Central Ltd.


Wang Y.,Nanjing Agricultural University | Wang Y.,Jiangsu Collaborative Innovation Center for Modern Crop Production | He J.,Nanjing Agricultural University | Yang L.,Nanjing Agricultural University | And 9 more authors.
Theoretical and Applied Genetics | Year: 2016

Key message: A saturated map was constructed using SNP markers to fine-map aBrassica napusdominant locus for dwarf mutant onto a 152-kb interval of chromosome A09 containing 14 genes.Abstract: Major dwarf loci in crops may play important roles in crop improvement and developmental genetics. The present study investigated and fine-mapped a Brassica napus dwarf-dominant locus BnDWF1. Plants carrying the BnDWF1 locus in populations derived from ‘zhongshuang11’ and Bndwf1 have deep-green leaves and dwarf architecture that differ sharply from tall plants with normal green leaves. BnDWF1, as a major locus controlling plant height, showed a very high heritability (0.91–0.95). To map this locus, a high-density single-nucleotide polymorphism map was constructed, and the BnDWF1 locus was mapped at an interval between single-nucleotide polymorphism markers, M19704 and M19695, on linkage group A09 of B. napus, with five co-segregating single-nucleotide polymorphism markers. Furthermore, fine mapping narrowed the interval harboring BnDWF1 to 152 kb in length in B. napus. This interval contains 14 annotated or predicted genes, seven of which are candidates responsible for the dwarf trait. This study provides an effective foundation for the study of plant height regulation and plant type breeding in B. napus. © 2016 Springer-Verlag Berlin Heidelberg


Xu J.,Nanjing Agricultural University | Xu J.,Key Laboratory of Crop Physiology and Ecology in Southern China | Zha M.,Nanjing Agricultural University | Zha M.,Key Laboratory of Crop Physiology and Ecology in Southern China | And 12 more authors.
Plant Cell Reports | Year: 2015

Key message: Nitrogen availability and cytokinin could promote shoot branching in rice, whereas auxin and strigolactone inhibited it. The interaction between nitrogen availability and the three hormones is discussed. Abstract: Rice shoot branching is strongly affected by nitrogen availability and the plant hormones auxin, cytokinin, and strigolactone; however, the interaction of them in the regulation of rice shoot branching remains a subject of debate. In the present study, nitrogen and the three hormones were used to regulate rice tiller bud growth in the indica rice variety Yangdao 6. Both nitrogen and CK promoted shoot branching in rice, whereas auxin and SL inhibited it. We used HPLC to determine the amounts of endogenous IAA and CK, and we used quantitative real-time PCR analysis to quantify the expression levels of several genes. Nitrogen enhanced the amount of CK by promoting the expression levels of OsIPTs in nodes. In addition, both nitrogen and CK downregulated the expression of genes related to SL synthesis in root and nodes, implying that the inhibition of SL synthesis by nitrogen may occur at least partially through the CK pathway. SL did not significantly reduce the amount of CK or the expression levels of OsIPT genes, but it did significantly reduce the amount of auxin and the auxin transport capacity in nodes. Auxin itself inhibited CK synthesis and promoted SL synthesis in nodes rather than in roots. Furthermore, we found that CK and SL quickly reduced and increased the expression of FC1 in buds, respectively, implying that FC1 might be a common target for the CK and SL pathways. Nitrogen and auxin delayed expression change patterns of FC1, potentially by changing the downstream signals for CK and SL. © 2015, Springer-Verlag Berlin Heidelberg.


Tang W.,Nanjing Agricultural University | Tang W.,Jiangsu Collaborative Innovation Center for Modern Crop Production | Wu T.,Nanjing Agricultural University | Ye J.,CAS Institute of Microbiology | And 9 more authors.
BMC Plant Biology | Year: 2016

Background: Single-nucleotide polymorphisms (SNPs) have become the genetic markers of choice in various genetic, ecological, and evolutionary studies. Genotyping-by-sequencing (GBS) is a next-generation-sequencing based method that takes advantage of reduced representation to enable high-throughput genotyping using a large number of SNP markers. Results: In the present study, the distribution of non-redundant SNPs in the parents of 12 rice recombination line populations was evaluated through GBS. A total of 45 Gigabites of nucleotide sequences conservatively provided satisfactory genotyping of rice SNPs. By assembling to the genomes of reference genomes of japonica Nipponbare, we detected 22,682 polymorphic SNPs that may be utilized for QTL/gene mapping with the Recombinant Inbred Lines (RIL) populations derived from these parental lines. Meanwhile, we identified polymorphic SNPs with large effects on protein-coding and miRNA genes. To validate the effect of the polymorphic SNPs, we further investigated a SNP (chr4:28,894,757) at the miRNA binding site in the 3'-UTR region of the locus Os4g48460, which is associated with rice seed size. Os4g48460 encodes a putative cytochrome P450, CYP704A3. Direct degradation of the 3'-UTR of the CYP704A3 gene by a miRNA (osa-miRf10422-akr) was validated by in planta mRNA degradation assay. We also showed that rice seeds of longer lengths may be produced by downregulating CYP704A3 via RNAi. Conclusions: Our study has identified the genome-wide SNPs by GBS of the parental varieties of RIL populations and identified CYP704A3, a miRNA-regulated gene that is responsible for rice seed length. © 2016 Tang et al.


Liu W.,Zhejiang University | Li W.,Zhejiang University | He Q.,Zhejiang University | Daud M.K.,Zhejiang University | And 5 more authors.
PLoS ONE | Year: 2015

To produce unsaturated fatty acids, membrane-bound fatty acid desaturases (FADs) can be exploited to introduce double bonds into the acyl chains of fatty acids. In this study, 19 membrane-bound FAD genes were identified in Gossypium raimondii through database searches and were classified into four different subfamilies based on phylogenetic analysis. All 19 membrane-bound FAD proteins shared three highly conserved histidine boxes, except for GrFAD2.1, which lost the third histidine box in the C-terminal region. In the G. raimondii genome, tandem duplication might have led to the increasing size of the FAD2 cluster in the Omega Desaturase subfamily, whereas segmental duplication appeared to be the dominant mechanism for the expansion of the Sphingolipid and Front-end Desaturase subfamilies. Gene expression analysis showed that seven membrane-bound FAD genes were significantly up-regulated and that five genes were greatly suppressed in G. raimondii leaves exposed to low temperature conditions. © 2015 Liu et al.


Wang F.,Zhejiang University | Liu J.,Zhejiang University | Liu J.,Jiangsu Collaborative Innovation Center for Modern Crop Production | Chen M.,China National Rice Research Institute | And 8 more authors.
PLoS ONE | Year: 2016

D1 protein in the PSII reaction center is the major target of photodamage, and it exhibits the highest turnover rate among all the thylakoid proteins. In this paper, rice psf (premature senescence of flag leaves) mutant and its wild type were used to investigate the genotypedependent alteration in PSII photo-damage and D1 protein turnover during leaf senescence and its relation to ABA accumulation in senescent leaves. The symptom and extent of leaf senescence of the psf mutant appeared to be sunlight-dependent under natural field condition. The psf also displayed significantly higher levels of ABA accumulation in senescent leaves than the wild type. However, the premature senescence lesion of psf leaves could be alleviated by shaded treatment, concomitantly with the strikingly suppressed ABA level in the shaded areas of flag leaves. The change in ABA concentration contributed to the regulation of shade-delayed leaf senescence. The participation of ABA in the timing of senescence initiation and in the subsequent rate of leaf senescence was closely associated with PSII photodamage and D1 protein turnover during leaf senescence, in which the transcriptional expression of several key genes (psbA, psbB, psbC and OsFtsH2) involved in D1 protein biosynthesis and PSII repair cycle was seriously suppressed by the significantly increased ABA level. This response resulted in the low rate of D1 protein synthesis and impaired repair recovery in the presence of ABA. The psf showed evidently decreased D1 protein amount in the senescent leaves. Both the inhibition of de novo synthesized D1 protein and the slow rate of proteolytic removal for the photodamaged D1 protein was among the most crucial steps for the linkage between light-dependent leaf senescence and the varying ABA concentration in psf mutant leaves. OsFtsH2 transcriptional expression possibly played an important role in the regulation of D1 protein turnover and PSII repair cycle in relation to ABA mediated leaf senescence. © 2016 Wang 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.

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