Project Number: 1275-21000-263-27
Project Type: Reimbursable

Start Date: Jun 01, 2008
End Date: May 31, 2011

Objective:
The first objective is to design a 50,000 Single Nucleotide Polymorphism (SNP) Illumina Infinium assay and use it to analyze each of the 18,603 cultivated and 1116 wild soybean accessions from the USDA Soybean Germplasm Collection and to genetically map these SNPs. Another objective is to characterize all the common molecular variation available to soybean breeders in the USDA Germplasm Collection. The third objective is to use these molecular data to provide the basis of a system to initiate the application of ¿Association Analysis¿ for gene discovery in soybean.

Approach:
A 50,000 SNP Illumina Infinium assay will be designed and produced with SNPs and surrounding DNA sequence information we will discover and supply to Illumina Inc. This information will be used by Illumina to design a 50,000 SNP Infinium chip. The SNPs will be selected from SNPs discovered in ongoing research in the laboratory using the Solexa high throughput DNA sequencer. This high-throughput sequencing capability will allow us to discover SNPs polymorphic between the parental lines of Essex x Williams 82 or Williams 82 x PI 468916. The SNPs to populate the 50,000 Infinium chip will be selected to be evenly spaced throughout the genome as determined by the DOE-JGI whole genome sequence of soybean and to be mappable in one of the two mapping populations. In addition, in the case of at least 80% of the SNPs chosen, both SNP alleles must be present in the set of diverse soybean lines (Minsoy, Noir 1, Evans, Archer, Peking, and PI 209332) as determined by the sequence analysis using the Illumina Genome Analyzer. DNA of the entire USDA germplasm collection of 18,603 cultivated and 1116 wild soybeans as well as many other adapted cultivars will be extracted and analyzed with the 50,000 SNP Infinium chip. These DNA marker data will be used to create a database which will be accessible to soybean researchers. The data will be used to create a high resolution genome map of the 20 soybean chromosomes as well as to begin to apply genetic Association Analysis for the discovery of genes controlling important traits including biotic and abiotic stress resistance, seed quality and productivity.