Selection of a Core Set of Cultivated and Wild Soybean Germplasm based on the SoySNP50K Illumina Beadchip Assay

Based on a dataset with 18,489 G. max and 1,168 G. soja accessions in the USDA collection genotyped with the SoySNP50K Illumina Beadchip SNP assay containing >50,000 SNPs, we identified a total of 30% and 23% of the accessions with similarity greater than 99.9% in the G. soja and G. max collections, respectively, among which, 8% of the Glycine soja and 9% of the G. max accessions were 100% identical to at least one other accession.  In order to select core sets of accessions for cultivated and wild soybean, pair-wise genetic distances among all accessions within the G.max and G. soja accessions were calculated and were used to classify the accessions into a pre-defined number of clusters (core size).  The accessions to be included in the core collection within each cluster was determined by a number of factors, such as rank of genetic distance to other accessions, previous use of the accessions and their public availability.  The goal for the soybean core collection is to choose approximately 1,420 G. max accessions and 115 G. soja accessions which will contain >90% of the diversity of the entire G. max and G. soja collections, respectively.  The accessions in the core sets are expected to be used for a whole genome sequencing project at the University of Missouri.  In addition, the core sets will facilitate genome-wide association analysis, parent selection, and efficient use of diversity in soybean germplasm.