Development of a 50,000 SNP Infinium assay for Genotyping the Soybean Germplasm Collection.

The USDA Soybean Germplasm Collection housed at the University of Illinois, Urbana consists of 19,719 soybean accessions collected from nearly 100 countries, but primarily from Asia, over the past 111 years.  Currently a project is underway to genotype all accessions from this germplasm collection with 50,000 SNP DNA markers to create a soybean HapMap.  We report the first step of this project which is the discovery of the 50,000 SNPs that will be used to genotype this germplasm collection.  Reduced representation libraries were created for seven soybean lines of which two make up high-resolution mapping populations.  The libraries were then sequenced with the Illumina Genome Analyzer.  The resulting sequence was then compared to the Department of Energy-Joint Genome Institute shotgun sequence of Williams 82 for high throughput SNP discovery which had a 90% validation rate.  A total of 60,800 SNPs were chosen that had an even distribution across the genome to be used for a soybean Infinium Assay which should convert into 50,000 working SNPs which will be used in genotyping the Germplasm Collection.  The development of this 50,000 SNP assay along with subsequent genotyping of the germplasm collection will be the first time for any crop that a resource of this magnitude will be available for breeders and researchers for mining such an extensive germplasm collection and to assist in understanding the variation contained within these 19,000 accessions.