Identification of novel genetic sources for agronomic and quality traits in soybean using multi-trait allele specific genic marker assays

Natural allelic variation among the genes governing various agronomic and quality traits of plant provides opportunity to develop desirable plant type in crops. In soybean [Glycine max (L.) Merr.], natural allelic variation is known for many functionally characterized genes conferring superior phenotype for their respective governing trait. Exploring this natural allelic variation in germplasm pool through gene based allele specific multiplex marker genotyping is one way to identify and combine the alleles of multiple traits in desired genetic background. Using known alleles of 15 genes governing 10 different agronomic and quality traits, we have developed two multi-trait allele specific genic marker assays of 22-plex and 7-plex alleles. These two multi-trait allele specific genic marker assays were used to genotype a large set of diverse soybean germplasm accessions, which identified several novel genetic sources of rare alleles conferring superior or desirable phenotype. Selected genetic sources of rare alleles for days to flowering and maturity, hard-seededness, pod shattering and oleic acid content were validated phenotypically. Genotyping and phenotyping in a multi-parent advanced generation intercross population validated the utility of multi-trait allele specific genic marker assays in marker assisted selection of multiple traits from multiple parents. The novel genetic sources identified in this study will help in the selection of parents with multiple desirable traits for hybridization. The multi-trait allele specific genic marker assays developed will speed up selection of multiple traits in routine soybean breeding programmes for cultivar development and improvement.