Evaluation of Wild and Cultivated Soybean Genomic Resources for Genotype Variation and Identity

Abstract

Cultivated soybean has low genetic diversity due to a strong domestication bottleneck and selection in modern breeding. This lack of diversity limits the identification of genetic loci responsible for traits of interest to breeders. However, recent advancements in genotyping have resulted in an influx of genomic resources for soybean germplasm around the globe. In this thesis, the high-throughput SoySNP50K Chip genotyping of USDA Soybean Germplasm Collection was used to evaluate wild and cultivated soybean accessions for within-accession variation. Intervals of heterogeneity were found in 4% of the collection, representing 870 accessions (Supplemental Table S1.1). The SoySNP50K dataset was also used to compare genotype identity with a dataset of 106 resequenced soybean genomes. Although 78% unambiguous matches were found, some discrepancies in identity were detected. These analyses can be used to harness unutilized standing variation and maintain consistency across datasets to innovate and streamline international efforts for soybean improvement.