Characterization of genetic heterogeneity within accessions in the USDA soybean germplasm collection

Soybean breeding relies on the use of wild (Glycine soja Sieb. and Zucc.) and domesticated [Glycine max (L.) Merr.] germplasm for trait improvement. Soybeans are self-pollinating and accessions can be maintained as pure lines, however within-accession genetic variation has been observed in previous studies of some landraces and elite cultivars. The objective of this study was to characterize within-line variation in the accessions housed in the USDA Soybean Germplasm Collection. This collection includes over 20,000 accessions, each previously genotyped using the SoySNP50K Chip. Each SoySNP50K genotype was developed by pooling approximately three individuals per accession. Therefore, clusters of SNPs called as heterozygous within an accession can be inferred to represent putative regions of heterogeneity between the three individuals sampled. In this study, we found high-probability intervals of heterogeneity in 4% of the collection, representing 870 accessions. Heterogeneous loci were found on every chromosome and, collectively, covered 98.4% of the soybean genome and 99% of the gene models. Sanger sequencing confirmed regions of genomic heterogeneity among a subset of ten accessions. This dataset provides useful information and considerations for users of crop germplasm seed banks. Furthermore, the heterogeneous accessions and/or loci represent a unique genetic resource that is immediately available for forward and reverse genetics studies.