Genomic Resources for Next Generation Breeding Strategies in Soybean.

Natural genetic variation in plant genetic resources provides a foundation for plant breeders to develop new and improved cultivars with desirable characteristics. Large scale sequencing of soybean genomes and transcriptomes helped us to discover the extent and distribution of genetic diversity in soybean gene pools, and its relationship to yield, disease resistance, and quality traits. At the same time, development of several reference genomes representing spectrum of soybean evolution and domestication makes these studies more significant. Core sets of soybean germplasm including both cultivated and wild types were selected based on an initial diversity analysis of the entire USDA germplasm collection for re-sequencing. We have conducted comparative genome analysis of wild type, land races, and elite cultivars of soybean and provided insights of genome evolution, diversity and genomic bottlenecks. Analysis of putative domestication sweeps, including the genomic regions associated with artificial selection identified genes involved in artificial selection during domestication from landraces to elite cultivars. The application of this matrix of genomic variants strengthen the analysis of genotype-to-phenotype relationships. Also, utilization of the SNP resources from soybean germplasm sequences with optimal coverage will have significant impact on designing of genomic imputation methodologies for breeding strategies including genomic section. The information on genome-wide genetic variation and domestication, along with genotype-phenotype association studies provide a valuable resource for trait dissection and marker discovery towards formulating next generation breeding strategies.