Genome-wide Association Study For Yield And Quality Related Traits At R6 Stage In Soybean

Soybean(Glycine max),rich in both protein and oil,is one of the most important cash crops.According to the different harvest time and applications,it can be divided into seed/vegetable soybean.The former harvested after maturity is mainly employed for oil,soybean milk,tofu and other bean products.The latter,which were harvested at R6 stage when the pods are green and full filled with the seeds,is mainly served as a kind of bean vegetables.There are great differences in nutritional components between seed and vegetable soybean.The seed soybean mainly consists of protein and oil,while the vegetable soybean is not only rich in protein and oil,but also has plenty of starch,soluble sugar,vitamins and minerals.At present,the demand for vegetable soybean in the intermational market is ever-increasing and the quality requirement is getting higher and higher.However,the research on the genetic mechanism of soybean yield and quality traits is mainly aimed at the mature soybean in China.The research on the genetic mechanism of vegetable soybean is weak and starts late.Soybean germplasm resources have a wealth of geographical origins,and it possesses high genetic diversity and abundant allelic variations after intergenerational separation and reorganization.Using germplasm resources collection to study the complex quantitative traits,we can comprehensively analyze their genetic mechanisms,thus providing markers,genes and materials for breeding design.This dissertation mainly utilize 100-pod fresh weight,100-seed fresh weight,100-seed dry weight,kernel percent,number of seeds per pod,moisture content of fresh seeds associated with yield and oil,starch and soluble sugar content related to quality traits at R6 stage,as the research objects,based on the whole genome SNP and SNPLDBs,association analysis making use of mini core collection and cultivated soybean collection are conducted so as to identify the functional markers,candidate genes,excellent alleles and excellent germplasm resources of controlling the yield and quality at R6 stage.1.Genome-wide association study for yield-related traits of soybean mini-core collections at R6 stage.100-pod fresh weight,100-seed fresh weight,100-seed dry weight,kernel percent,seed number per pod and moisture content of fresh seeds are the main factors that determine the yield of vegetable soybean.In this study,genome-wide association analysis is conducted to identify the single-nucleotide polymorphisms(SNPs)associated with these yield related traits using 1514 SNPs(MAF>0.05)among soybean mini-core collections.The results are listed as following:(1)there exists extensive phenotypic variation among these research objects in soybean mini-core collections,and the corresponding analysis indicate that there are significant positive correlation among majority traits;(2)27,18,24,46,46 and 20 SNPs are prominently associated with 100-pod fresh weight,100-seed fresh weight,100-seed dry weight,kernel percent,seed number per pod and moisture content of fresh seeds under two year and mean enviroment condition,and ouly 13 SNPs are detected under all circumstances;(3)7 SNPs are found co-associated with two or three different traits,possibly due to the high correlation between characters;(4)11 of the 13 SNPs are found co-associated with soybean seed weight,oil content,protein content,pod maturity,number of seed per pod,seed length and other yield or quality related traits;(5)11 of the 13 SNPs are located in the CDS or 3'UTR regions of the genes,among which two genes,function is unknown,the products encoded by the remaining nine genes may be involved in the regulation of growth and development,stress resistance,photosynthesis,anylose synthesis,and gene expression.The identification of these significant SNPs and candidate genes will be beneficial to understand the genetic basis of Soybean yield at R6 stage and facilitate the pyramiding of favorable alleles for future high-yield breeding by marker-assisted selection in vegetable soybean.2.Genome-wide association study for yield-related traits of soybean cultivars at R6 stage.Yield is one of the most important traits for soybean breeding.However,the genetic basis of yield-related traits at R6 stage remains largely anbiguous in soybean.Association mapping has provided a robust approach to understand the genetic basis of complex agronomic traits in crops.The results are provided as following:(1)six yield-related traits(100-pod fresh weight,100-seed fresh weight,100-seed dry weight,Moisture content of fresh seed,Kernel percent and number of seeds per pod)of 133 cultivated soybeans are tested in two years with three replications.Abundant phenotypic and genetic diversities and significant correlations exist among these traits in this population,the heterability for all traits are high except Kermel percent and Number of seeds per pod,implying that these traits are mainly determined by genes;(2)correlation analysis displays that there is a significant positive correlation between some traits;(3)Population structure analysis shows that this population could be divided into two subpopulations,almost all of accessions from the south region are divided into the subpopulation 1,while the accessions from the north region are mainly divided into the subpopulation 2;(4)Genome-wide association studies are conducted for these traits using 82187 SNPs(MAF>0.05),a total of 124 SNPs are identified(2015,2016,the average across two years).Among these SNPs,35 SNPs are detected in all environments,and 6 SNPs are found co-associated with two-different traits,possibly due to the high correlation between characters;(5)35 identified SNPs are co-located with seed weight,seed length,pods maturity,seed protein,oil and oligosaccharides QTL reported before;(6)two SNPs,AX-90496773 and AX-904902902,which are closely associated with 100-pod fresh weight and moisture content of fresh seed,are located into the 2 haplotype blocks(34.5 kb?189.12 kb)of 5 and 16 chromosomes;(7)According to the significant SNP,functional annotation and expression of genes,six potential candidate genes for 100-pod fresh weight and Moisture content of fresh seed are identified in the LD blocks;(8)qRT-PCR analysis of the potential candidate genes shows that the expression levels of these genes are significantly different from aceessions with large phenotypic variation.This result suggests that the potential candidate genes are likely involved in the formation of 100-pod fresh weight and Moisture content of fresh seeds.All of these results will provide useful informantion for the function markers' development and the candidate genes9 explorations in vegetable soybean high-yield breeding prograns.3.Genome-wide association study for quality-related traits of soybean mini-core collections in R6 stage.In this study,a panel of 224 mini-core collections and 1378 SNPLDBs are employed to conduct the association analysis of soybean oil,starch and soluble sugar content at R6 stage.The results are presented as following:(1)abundant phenotypic and genetic diversities of these traits are found in this population.The distribution of phenotypic frequency is basically consistent with the normal distribution,indicating that it conforms to the characteristics of quantitative traits and is suitable for association analysis.;(2)the heritability of the three quality traits are low,ranging from 41.1%to 65.5%,suggesting that these traits are easily influenced by the environment;(3)based on the BLUP phenotype data(2015,2016),association analysis is conducted with the software RTM-GWAS,a total of 20,20 and 16 SNPLDBs for the three traits are identified,contributing to 0.83%?7.75%,0.95%?7.82%and 1.90%?5.94%variations for each SNPLDB,respectively.Among these SNPLDBs,32 SNPLDBs are Main-effect QTLs whose contribution to variation are more than 3%;(4)QTL-allele matrix illustrates that there are synergistic and reducing effect alleles in the mini-core collections,which provide useful information for the combination of excellent parents.