Mengchen Zhang

Proteomic analysis of elite soybean Jidou17 and its parents using iTRAQ-based quantitative approaches

BackgroundDerived from Hobbit as the female parent and Zao5241 as the male parent, the elite soybean cultivar Jidou17 is significantly higher yielding and shows enhanced qualities and stronger resistance to non-biological stress than its parents. The purpose of this study is to understand the difference in protein expression patterns between Jidou17 and its parental strains and to evaluate the parental contributions to its elite traits.ResultsLeaves (14 days old) from Jidou17 and its parental cultivars were analysed for differential expressed proteins using an iTRAQ-based (isobaric tags for relative and absolute quantitation) method. A total of 1269 proteins was detected, with 141 and 181 proteins in Jidou17 differing from its female and male parent, respectively. Functional classification and an enrichment analysis based on biological functions, biological processes, and cellular components revealed that all the differential proteins fell into many functional categories but that the number of proteins varied greatly for the different categories, with enrichment in specific categories. A pathway analysis indicated that the differentiated proteins were mainly classified into the ribosome assembly pathway. Protein expression clustering results showed that the expression profiles between Jidou17 and its female parent Hobbit were more similar than those between Jidou17 and its male parent Zao5241 and between the two parental strains. Therefore, the female parent Hobbit contributed more to the Jidou17 genotype.ConclusionsThis study applied a proven technique to study proteomics in 14-day-old soybean leaves and explored the depth and breadth of soybean protein research. The results provide new data for further understanding the mechanisms of elite cultivar development.

Evaluation of productivity and stability of elite summer soybean cultivars in multi-environment trials

Abstract Spring soybean cultivars produced in moderate climates currently represent almost the entire soybean industry; however, soybean production has the potential to be extended into the summer months in different regions of the world. It is critical to select the correct soybean cultivar for production in a specific environment. The purpose of this study was therefore to evaluate the productivity (yield) and stability of the current summer soybean cultivars in multi-environment trials in the Huang–Huai–Hai region, presently the largest summer soybean-producing region in the world, to determine which cultivars will be most successful for large scale production in this region, as well as those that should be used in future breeding efforts. A total of 94 summer soybean cultivars were grown in the three major soybean production provinces, i.e., Shandong, Henan, and Hebei, over 3 years (2008–2010). The GGEbiplot™ software provided a ‘genotype x genotype-by-environment interaction’ function to evaluate the importance of agronomic factors controlling the soybean yield of each cultivar across the nine different environments. Xudou10, Zhonghuang39, Lu93748-1 and Lu99-1 exhibited relatively high average yields. The stability among the high-yielding cultivars was ranked in decreasing order as Xudou10, Zheng99048, Jidou7, Yudou18, and Gaozuoxuan-1. Among all recorded factors, the pod number per plant was the most important factor controlling yield, followed by seed number per plant, effective branch number, and 100-seed weight, which positively affected soybean yield. In contrast, a higher bottom pod height, greater number of nodes on the main stem, and longer growth duration were negatively correlated with yield.

Genome-wide association mapping of resistance to Phytophthora sojae in a soybean [Glycine max (L.) Merr.] germplasm panel from maturity groups IV and V

Phytophthora sojae, an oomycete pathogen of soybean, causes stem and root rot, resulting in annual economic loss up to

Identifying and Validating a Quantitative Trait Locus on Chromosome 14 Underlying Stearic Acid in a Soybean Landrace

2 billion worldwide. Varieties with P. sojae resistance are environmental friendly to effectively reduce disease damages. In order to improve the resistance of P. sojae and broaden the genetic diversity in Southern soybean cultivars and germplasm in the U.S., we established a P. sojae resistance gene pool that has high genetic diversity, and explored genomic regions underlying the host resistance to P. sojae races 1, 3, 7, 17 and 25. A soybean germplasm panel from maturity groups (MGs) IV and V including 189 accessions originated from 10 countries were used in this study. The panel had a high genetic diversity compared to the 6,749 accessions from MGs IV and V in USDA Soybean Germplasm Collection. Based on disease evaluation dataset of these accessions inoculated with P. sojae races 1, 3, 7, 17 and 25, which are publically available, five accessions in this panel were resistant to all races. Genome-wide association analysis identified a total of 32 significant SNPs, which were clustered in resistance-associated genomic regions, among those, ss715619920 was only 3kb away from the gene Glyma.14g087500, a subtilisin protease. Gene expression analysis showed that the gene was down-regulated more than 4 fold (log2 fold > 2.2) in response to P. sojae infection. The identified molecular markers and genomic regions that are associated with the disease resistance in this gene pool will greatly assist the U.S. Southern soybean breeders in developing elite varieties with broad genetic background and P. sojae resistance.

Identification of a major quantitative trait locus underlying salt tolerance in ‘Jidou 12’ soybean cultivar

ABSTRACT Stearic acid (ST) is one of the saturated fatty acids (FAs) in soybean [Glycine max (L.) Merr.] oil; lowering ST content may be helpful to reduce the potential health risks. In this study, recombinant inbred lines (RILs) derived from “Jidou 12” × “Heidou” cross were used to identify the QTL underlying ST content. As a result, two quantitative trait loci (QTL), designated as qSTE_6_1 and qSTE_14_1, were identified. The QTL qSTE_14_1 was also validated using residual heterozygous lines (RHLs) derived from the RILs. Analysis of the RHLs showed that two simple sequence repeats (SSR) markers, BARCSOYSSR_14_1033 and BARCSOYSSR_14_1079, located on chromosome 14, were tightly linked with qSTE_14_1 and could explain 50.2% and 43.1% of ST content variance at two locations. The allele from “Heidou” decreased the ST content from 3.28% to 2.92% at one location and from 3.55% to 3.01% at the other location. No significant effect of qSTE_14_1 on other FA contents was detected at either location. This study will assist in creating cultivars with lower ST.

iTRAQ protein profile analysis of developmental dynamics in soybean [Glycine max (L.) Merr.] leaves

BackgroundIdentification of the quantitative trait locus (QTL) underlying salt tolerance is a prerequisite for marker-assisted selection in the salt-tolerant breeding process.MethodsIn this study, the recombinant inbred lines derived from the salt-tolerant elite soybean cultivar ‘Jidou 12’ and the salt-sensitive elite cultivar ‘Ji NF 58’ were used to identify the QTL associated with salt tolerance, using both salt tolerance rating (STR) and leaf chlorophyll content (SPAD) as indicators.ResultsA major salt-tolerant QTL, which was flanked by SSR markers GMABAB and Barcsoyssr_03_1421 on chromosome 3, was identified based on single-marker regression, single trait composite interval mapping, and multiple interval mapping analysis. For STR, the LOD ranged from 19.8 to 20.1; R2 ranged from 44.3 to 44.7%; and the additive effect ranged from 0.876 to 0.885 among the three mapping methods. For SPAD, the LOD ranged from 10.6 to 11.0; R2 ranged from 27.0 to 27.6%; and the additive effect ranged from 1.634 to 1.679 among the three mapping methods.ConclusionsIn this study, a major QTL conditioning salt tolerance on chromosome 3 was identified. The DNA markers closely associated with the QTLs might be useful in marker-assisted selection for soybean salt tolerance improvement in Huanghuaihai, China.

Population Structure and Association Analysis of Traits in Summer Soybeans

Zao5241 is an elite soybean [Glycine max (L.) Merr.] line and backbone parent. In this study, we employed iTRAQ to analyze the proteomes and protein expression profiles of Zao5241 during leaf development. We identified 1,245 proteins in all experiments, of which only 45 had been previously annotated. Among overlapping proteins between three biological replicates, 598 proteins with 2 unique peptides identified were reliably quantified. The protein datasets were classified into 36 GO functional terms, and the photosynthesis term was most significantly enriched. A total of 113 proteins were defined as being differentially expressed during leaf development; 41 proteins were found to be differently expressed between two and four week old leaves, and 84 proteins were found to be differently expressed between two and six week old leaves, respectively. Cluster analysis of the data revealed dynamic proteomes. Proteins annotated as electron carrier activity were greatly enriched in the peak expression profiles, and photosynthesis proteins were negatively modulated along the whole time course. This dataset will serve as the foundation for a systems biology approach to understanding photosynthetic development.

iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate.

ABSTRACT The summer soybeans (Glycine max (L.) Merr.) in Hebei Province, China, which have adapted to different environments, show extraordinarily rich genetic diversity and extensive species variation. The objectives of this study were to analyze the population structure of summer soybean using simple sequence repeat (SSR) markers and to identify the SSR markers associated with specific traits. A set of 135 SSR markers was used to analyze 50 soybean cultivars, of which 47 cultivars were from 10 breeding institutions in Hebei Province and three cultivars were introductions from the United States. Software tools, the TASSEL, DARwin, and STRUCTURE, were used to analyze linkage disequilibrium (LD) and genetic structure. In addition, an association analysis between the molecular markers and the phenotypic values of 15 agronomic and quality traits was performed. The yield-related agronomic traits included plant height, bottom pod height, effective branch number, number of nodes on main stem, pod number per plant, seed number per plant, one-seed pods, two-seed pods, three-seed pods, four-seed pods, seed weight per plant, 100-seed weight, and yield. The quality traits included crude protein content and crude fat content. The following results were obtained from the analysis. First, principal component analysis (PCA) indicated that a significant correlation existed between the cultivar distribution and the breeding institutions or breeding areas. Second, 63.86% of pairs of SSR loci exhibited certain levels of LD. The fragment between loci Satt557 and Satt371 in the C2 LG had a genetic distance of 33.29 cM and featured strong LD (r2 > 0.33). Third, the genetic-structure analysis revealed that the population was composed of two subpopulations, which related to their parental pedigrees. In addition, 70 SSR markers were found to be associated with 13 agronomic traits; 49 SSR markers have not been reported previously. The SSR markers identified in this study could potentially be used in marker-assisted breeding to accelerate genetic improvement of soybean for yield and quality.