Association Analysis between Agronomic-Processing Traits and SSR Markers and Genetic Dissection of Specific Accessions in Chinese Wild Soybean Population

Abstract

Association analysis is potential in genetic dissection of germplasm accessions and breeding materials for designing crosses and improving selection efficiencies. The present study was aimed at finding elite QTLs/alleles as well as their carriers through genetic dissection of agronomic-processing traits in Chinese annual wild soybean (Glycine soja Sieb. et Zucc.) population for improvement and broadening the genetic background of modern soybean cultivars. The genotypic data of 204 simple-sequence repeat (SSR) markers on 174 wild accessions sampled from and evenly distributed in all the wild soybean eco-regions in China were used and analyzed for association with six agronomic and processing traits under TASSEL GLM (general linear model) program based on the population structure analysis. The QTLs significantly associated with the traits were analyzed further for their allele effects. The results showed: (1) Fifty-one SSR loci (times) associated with the six agronomic-processing traits were identified in the wild population. There were a few markers/loci associated with two or more traits simultaneously, which might be the genetic bases of correlation among the traits. Sixteen of fifty-one associated loci (times) were in agreement with mapped QTLs from linkage mapping procedure. (2)There existed only a few association loci in wild population coincided with those in landrace and released cultivar populations, indicating the difference of genetic structure among the three kinds of populations. (3) A set of elite alleles of detected loci and their carrier materials were screened out. Alleles for loci associated with several traits had different phenotypic effects in different traits, e.g. GMES5532a-A332 had positive phenotypic effect for both 100-seed weight and seedling death rate under submergence, while GMES5532a-A344 had negative effect on 100-seed weight but positive effect on seedling death rate under submergence. (4)There showed great difference of the genetic structure among the tested materials with extreme phenotypic value. The extreme accessions possessed the alleles with bigger effects, such as N23349 containing four alleles with bigger positive effects having its 100-seed weight as high as 9.08 g, while N23387 containing four alleles with bigger negative effects having its 100-seed weight only 0.75 g. The above results implied that association mapping could offer further genetic information complementary to linkage mapping, especially the information of multiple alleles of QTL on whole genome could be used in cross design for pyramiding elite alleles and marker-assisted selection in breeding for soybean.