Project Number: 1275-21000-263-07
Project Type: Reimbursable

Start Date: Aug 01, 2007
End Date: Sep 30, 2009

Objective:
The first objective is to analyze each of 2290 cultivated and 300 wild soybean genotypes with 1536 single nucleotide polymorphism (SNP) DNA markers using the Illumina BeadStation 500. The second objective is to use the DNA marker data to define the ¿subpopulations¿ that exist in the soybean germplasm Core Collection and to determine which subpopulations are represented in 100 commodity type soybean cultivars. The third objective is to use the DNA marker data to identify those lines with pest resistance that are most likely to be genetically distinct for the genes controlling resistance.

Approach:
DNA will be isolated from leaf tissue of 10-15 plants each of the 1690 members of the USDA Soybean Core Collection. In addition, DNA will be similarly isolated from leaf tissue of 500 soybean lines with known pest resistance, 100 commodity type commercial cultivars, and 300 accessions of the wild soybean. From the 4000 SNP-containing sequence tagged sites discovered in the Soybean Genomics and Improvement Laboratory, 1536 SNPs will be selected to use to analyze the 2290 cultivated soybean and 300 wild soybean genotypes. The 1536 SNPs will be selected based upon their even distribution across the 20 soybean linkage groups. These SNPs will be included in the design of an Illumina Oligo Pool Array to allow the concurrent assay of the 1536 SNPs using the Illumina GoldenGate assay on the Illumina BeadStation 500. The resulting SNP allele data on each of the cultivated and wild soybean genotypes will permit estimates of genetic diversity and the definition of population structure or sub-populations within the cultivated soybean genotypes. Those subpopulations that are not represented in current commodity cultivars will provide a pool of untapped genetic variability that can be exploited for genetic advance for abiotic and biotic stress resistance, seed quality traits and productivity.