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Chi X.,Shandong Peanut Research Institute | Yang Q.,Shandong Peanut Research Institute | Pan L.,Shandong Peanut Research Institute | Chen M.,Shandong Peanut Research Institute | And 3 more authors.
Plant Cell Reports | Year: 2011

Fatty acid desaturases are responsible for the insertion of double bonds into pre-formed fatty acid chains in reactions that require oxygen and reducing equivalents. In this study, genes for FAB2, FAD2-2, FAD6 and SLD1, were cloned from peanut (Arachis hypogaea L.). The ORFs of the four genes were 1,221, 1,152, 1,329 and 1,347 bp in length, encoding 406, 383, 442 and 448 amino acids, respectively. The predicted amino acid sequences of AhFAB2, AhFAD2-2, AhFAD6, AhSLD1 shared high sequence identity of 79, 76.2, 73.4 and 61% to the corresponding ones in Arabidopsis, respectively. Heterologous expression in yeast was used to confirm the regioselectivity and the function of AhFAD2-2 and AhFAD6. Linoleic acid (18:2), normally not present in wild-type yeast cells, was detected in transformants of these two genes. Quantitative real-time RT-PCR analysis indicated that the transcript abundances of AhFAB2 and AhFAD2-1 were higher in seed than that in other tissues examined. On the other hand, transcript of AhFAD2-2, AhFAD6 and AhSLD1 showed higher abundances in leaves. In addition, these five genes showed different expression patterns during seed development. These results indicated that the five genes may have different biochemical functions during vegetative growth and seed development. © 2011 Springer-Verlag.


Chi X.,Shandong Peanut Research Institute | Hu R.,CAS Qingdao Institute of Bioenergy and Bioprocess Technology | Yang Q.,Shandong Peanut Research Institute | Zhang X.,Chinese Academy of Fishery Sciences | And 7 more authors.
Molecular Genetics and Genomics | Year: 2012

Quantitative real-time reverse transcription PCR (qRT-PCR), a sensitive technique for quantifying gene expression, depends on the stability of the reference gene(s) used for data normalization. Only a few studies on the reference genes have been done with peanut to date. In the present study, 14 potential reference genes in peanut were evaluated for their expression stability using the geNorm and NormFinder statistical algorithms. Expression stability was assessed by qRT-PCR across 32 biological samples, including various tissue types, seed developmental stages, salt and cold treatments. The results showed that the best-ranked references genes differed across the samples. UKN1, UKN2, TUA5 and ACT11 were the most stable across all the tested samples. A combination of ACT11, TUA5, UKN2, PEPKR1 and TIP41 would be appropriate as a reference panel for normalizing gene expression data across the various tissues tested, whereas the combination of TUA5 and UKN1 was the most suitable for seed developmental stages. TUA5 and EF1b exhibited the most stable expression under cold treatment. For salt-treated leaves, TUA5 and UKN2 were the most stably expressed and HDC and UKN1 for salt-treated roots. The relative gene expression level of peanut Cys 2/His 2-type zinc finger protein gene AhZFP1 was analyzed in order to validate the reference genes selected for this study. These results provide guidelines for the selection of reference genes under different experimental conditions and also a foundation for more accurate and widespread use of qRT-PCR in peanut gene analysis. © Springer-Verlag 2011.


Dong M.,Qingdao Agricultural University | Zhang X.,Chinese Academy of Fishery Sciences | Chi X.,Shandong Peanut Research Institute | Mou S.,State Oceanic Administration | And 4 more authors.
Current Genetics | Year: 2012

Normalization based on inappropriate reference gene may lead to the reduction of the accuracy of RT-qPCR. Although determination of suitable reference genes is essential to RT-qPCR studies, reports on the evaluation of reference genes in Ulva linza, a ubiquitous green-tide forming alga, are lacking. The expression levels of ten candidate reference genes were analyzed in U. linza across different experimental treatments, and the best-ranked reference genes differed across the treatments. The most suitable reference genes were tubulin2 (TUB2) among different salinity and UV treatments. Histone 2 (H2) was stably expressed in different temperature and desiccation stress treatments. 18S rRNA exhibited better expression stability in different light intensity treatments. While all tested samples were considered, none of single gene was widely applicable as a reference gene. Moreover, using a combination of two genes as reference genes might improve the reliability of gene expression by RT-qPCR, and the combination of TUB1 and TUB2 was selected as ideal for all tested samples. The results suggest that assessing the stability of reference gene expression patterns, determining candidates, and testing their suitability are required for each experimental investigation. The results will guide the selection of reference genes for gene expression studies in U. linza. © 2011 Springer-Verlag.


Jiang X.-J.,CAS Institute of Zoology | Jiang X.-J.,Shandong Peanut Research Institute | Guo H.,CAS Institute of Zoology | Di C.,CAS Institute of Zoology | And 4 more authors.
Insect Biochemistry and Molecular Biology | Year: 2014

The olfactory system of moth species in subfamily Heliothinae is an attractive model to study the evolution of the pheromone reception because they show distinct differentiation in sex pheromone components or ratios that activate pheromone receptors (PRs). However, functional assessment of PRs in closely related species remains largely untried. Here we present a special cloning strategy to isolate full-length cDNAs encoding candidate odorant receptors (ORs) from Helicoverpa armigera (Harm) and Helicoverpa assulta (Hass) on the basis of Heliothis virescens ORs, and investigate the functional properties of PRs to determine how the evolution of moth PRs contribute to intraspecific mating choice and speciation extension. We cloned 11 OR orthologs from H.armigera and 10 from H.assulta. We functionally characterized the responses of PRs of both species to seven pheromone compounds using the heterologous expression system of Xenopus ooctyes. HassOR13 was found to be highly tuned to the sex pheromone component Z11-16:Ald, and unexpectedly, both HarmOR14b and HassOR16 were specific for Z9-14:Ald. However, HarmOR6 and HassOR6 showed much higher specificity to Z9-16:OH than to Z9-16:Ald or Z9-14:Ald. HarmOR11, HarmOR14a, HassOR11 and HassOR14b failed to respond to the tested chemicals. Based on our results and previous research, we can show that some PR orthologs from H.armigera, H.assulta and H.virescens such as OR13s have similar ligand selectivity, but others have different ligand specificity. The combined PR function and sex pheromone component analysis suggests that the evolution of PRs can meet species-specific demands. © 2014 Elsevier Ltd.


Hu R.,CAS Qingdao Institute of Bioenergy and Bioprocess Technology | Chi X.,Shandong Peanut Research Institute | Chai G.,CAS Qingdao Institute of Bioenergy and Bioprocess Technology | Kong Y.,University of Georgia | And 5 more authors.
PLoS ONE | Year: 2012

Background: Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. Principal Findings: In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I-IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. Conclusions: Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles. © 2012 Hu et al.


Xu H.-L.,International Nature Farming Research Center | Qin F.,International Nature Farming Research Center | Qin F.,Shandong Peanut Research Institute | Xu Q.,International Nature Farming Research Center | And 2 more authors.
Scientia Horticulturae | Year: 2011

Partial root zone drying (PRD) has been used as a technique in the production of many crops. However, the extent or duration of the drying treatment would change the effect and the mechanisms in terms of plant water relations are not clear enough. The aim of this research was to evaluate the PRD effect with shorter or longer drying duration in a potato crop and elucidate the mechanisms based on plant water relations. Potato (Solanum tuberosum L. cv. May Queen) was grown in experimental plots under plastic rainout shelters. Three treatments: (1) whole-season PRD, (2) early-season PRD for 8 weeks and then return to normal irrigation for the remainder of the season and (3) normal irrigation as control, were arranged in a Latin square design in 9 plots. Water was supplied by drip irrigation to one side of the potato row once every 5 days on average, and the other side of the row was allowed to dry for 15 days, and then the irrigation line was moved to the dry side and the wet side allowed to dry. Pressure-volume curves were used to analyze the osmotic adjustment induced by PRD and a modified mathematic equation, -Ψ-1=ΨFT-1-πs+a-1[ζ0-β(1-ζ)-ζap]e-α(1-ζ)+πs+a-1[ζ0-β(1-ζ)-ζap] was used to compare the pressure-volume relations. As shown by the results, tuber yield and photosynthetic activity were increased by the early-season PRD treatment, but not by the whole-season PRD treatment because the whole-season PRD treatment reduced the leaf area index. By analyzing the pressure-volume curves, it was found that osmotic adjustment occurred and the turgor potential was higher in potato leaves in the PRD treatments. The fraction of water in the cell symplasm was higher and that in apoplasm was smaller in PRD-treated potato leaves. Both the osmotic potential and relative water content at the point of incipient plasmolysis were lower in potato leaves in the PRD treatments, suggesting that the plants in the PRD plots were more resistant to water stress, which was also confirmed by the analysis of transpiration declining curve of excised leaves. In conclusion, the PRD treatment was effective in improving potato tuber yield, but early-season treatment rather than the whole-season treatment should be adopted. © 2011 Elsevier B.V.


Kong Q.,Ocean University of China | Shan S.,Shandong Peanut Research Institute | Liu Q.,Ocean University of China | Wang X.,Ocean University of China | Yu F.,Ocean University of China
International Journal of Food Microbiology | Year: 2010

A strain of marine Bacillus megaterium isolated from the Yellow Sea of East China was evaluated for its activity in reducing postharvest decay of peanut kernels caused by Aspergillus flavus in in vitro and in vivo tests. The results showed that the concentrations of antagonist had a significant effect on biocontrol effectiveness in vivo: when the concentration of the washed bacteria cell suspension was used at 1×109CFU/ml, the percentage rate of rot of peanut kernels was 31.67%±2.89%, which was markedly lower than that treated with water (the control) after 7days of incubation at 28°C. The results also showed that unwashed cell culture of B. megaterium was as effective as the washed cell suspension, and better biocontrol was obtained when longer incubation time of B. megaterium was applied. When the incubation time of B. megaterium was 60-h, the rate of decay declined to 41.67%±2.89%. Furthermore, relative to the expression of 18S rRNA, the mRNA abundances of aflR gene and aflS gene in the experiment group were 0.28±0.03 and 0.024±0.005 respectively, indicating that this strain of B. megaterium could significantly reduce the biosynthesis of aflatoxins and expression of aflR gene and aflS gene (p<0.01). To the best of our knowledge, this is a first report demonstrating that the marine bacterium B. megaterium could be used as a biocontrol agent against postharvest fungal disease caused by A. flavus. © 2010 Elsevier B.V.


Sun J.,Shandong Peanut Research Institute | Liu S.-f.,Shandong Peanut Research Institute | Zhang C.-s.,Shandong Peanut Research Institute | Yu L.-n.,Shandong Peanut Research Institute | And 3 more authors.
PLoS ONE | Year: 2012

Fruits of Broussonetia papyrifera from South China were analyzed for their total chemical composition, and antioxidant activities in ethanol and aqueous extracts. In the fruit of this plant, the crude protein, crude fat and carbohydrates was 7.08%, 3.72% and 64.73% of dry weight, respectively. The crude protein, crude fat and carbohydrates were 15.71%, 20.51% and 36.09% of dry weight, respectively. Fatty acid and amino acid composition of the fruit were analyzed. Unsaturated fatty acid concentration was 70.6% of the total fatty acids. The percentage of the essential amino acids (EAAs) was 40.60% of the total amino acids. Furthermore, B. papyrifera fruit are rich in many mineral elements and vitamins. Total phenolic content was assessed using the Folin-Ciocalteau assay, whereas antioxidant activities were assessed by measuring the ability of the two extracts to scavenge DPPH radicals, inhibit peroxidation, and chelate ferric ions. Their reducing power was also assessed. Results indicated that the aqueous extract of B. papyrifera was a more potent reducing agent and radical-scavenger than the ethanol extract. GC-MS analysis of the ethanol extract showed the presence of some acid-containing compounds. The changes in total phenolic content and antioxidant capacity in B. papyrifera from four different regions grown under normal conditions were assessed. The antioxidant activity of different extracts was positively associated with their total phenolic content. These results suggest that the fruit of B. papyrifera could be used in dietary supplement preparations, or as a food additive, for nutritional gain, or to prevent oxidation in food products. © 2012 Sun et al.


Wang J.,Nanjing Agricultural University | Yang X.,Nanjing Agricultural University | Xu H.,Peking Union Medical College | Chi X.,Shandong Peanut Research Institute | And 2 more authors.
Gene | Year: 2012

The microRNAs are a new class of small non-coding endogenous RNAs with lengths of approximately ~ 21 nt. MicroRNAs perform their biological function via the degradation of the target mRNAs or by inhibiting protein translation. Until recently, only limited numbers of miRNAs were identified in Brassica oleracea, a vegetable widely cultivated around the world. In present study, 193 potential miRNA candidates were identified from 17 expressed sequence tag (ESTs) and 152 genome survey sequences (GSSs) in B. oleracea. These miRNA candidates were classified into 70 families using a well-defined comparative genome-based computational analysis. Most miRNAs belong to the miRNA169, miR5021, miR156 and miR158 families. Of these, 36 miRNA families are firstly found in Brassica species. Around 1393 B. oleracea genes were predicted as candidate targets of 175 miRNAs. The mutual relationship between miRNAs and the candidate target genes was verified by checking differentially expression levels using quantitative real-time polymerase chain reaction (qRT-PCR) and 5' RLM-RACE analyses. These target genes participate in multiple biological and metabolic processes, including signal transduction, stress response, and plant development. Gene Ontology analysis shows that the 818, 514, and 265 target genes are involved in molecular functions, biological processes, and cellular component respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis suggests that these miRNAs might regulate 186 metabolic pathways, including those of lipid, energy, starch and sucrose, fatty acid and nitrogen. © 2012 Elsevier B.V.


Chi X.,Shandong Peanut Research Institute | Yang Q.,Shandong Peanut Research Institute | Chen X.,Guangdong Academy of Agricultural Sciences | Wang J.,Shandong Peanut Research Institute | And 7 more authors.
PLoS ONE | Year: 2011

Background: MicroRNAs (miRNAs) are noncoding RNAs of approximately 21 nt that regulate gene expression in plants post-transcriptionally by endonucleolytic cleavage or translational inhibition. miRNAs play essential roles in numerous developmental and physiological processes and many of them are conserved across species. Extensive studies of miRNAs have been done in a few model plants; however, less is known about the diversity of these regulatory RNAs in peanut (Arachis hypogaea L.), one of the most important oilseed crops cultivated worldwide. Results: A library of small RNA from peanut was constructed for deep sequencing. In addition to 126 known miRNAs from 33 families, 25 novel peanut miRNAs were identified. The miRNA* sequences of four novel miRNAs were discovered, providing additional evidence for the existence of miRNAs. Twenty of the novel miRNAs were considered to be species-specific because no homolog has been found for other plant species. qRT-PCR was used to analyze the expression of seven miRNAs in different tissues and in seed at different developmental stages and some showed tissue- and/or growth stage-specific expression. Furthermore, potential targets of these putative miRNAs were predicted on the basis of the sequence homology search. Conclusions: We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library. This study of the identification and characterization of miRNAs in peanut can initiate further study on peanut miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in peanut. © 2011 Chi et al.

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