High-Throughput SNP Analysis in Soybean.

High-throughput SNP detection technology is revolutionizing QTL mapping and germplasm characterization in crop research.  We have developed two different platforms for high-throughput SNP detection in soybean.  The first platform is the Universal Soy Linkage Panel 1.0 which was developed from a total of 3,049 total SNPs of which we have selected 1,536 SNPs which could be genotyped on a universal linkage panel over three days on 192 DNA samples.  This 1,536 Universal Soy Linkage Panel is currently being used by a collaborative group to genotype 17,000 DNA samples to create high density genetic maps on numerous QTL populations segregating for numerous disease resistance, seed quality and agronomic quantitative traits.  The second platform is the Illumina Infinium Assay designed from a total of 60,800 SNPs with a uniform physical distribution across the genome.  It is expected the Soy Infinium Assay will convert into at least 50,000 working SNP markers (50K chip) which can be assayed on 288 DNA samples over a three day period.  This 50K chip will be used to genotype two high resolution mapping populations, each of which consists of 1,000 recombinant inbred lines, and to genotype the USDA Soybean Germplasm Collection maintained at Urbana, Illinois which consists of 19,854 soybean and wild soybean accessions collected from nearly 100 countries, but primarily from Asia, over more than 120 years.  Together these two platforms are changing the way soybean researchers are able to quickly identify alleles that can be used for soybean improvement.