Project Number: 1275-21000-263-26
Project Type: Reimbursable

Start Date: Apr 01, 2008
End Date: Mar 31, 2009

Objective:
The first objective is the development of DNA markers known as Single Nucleotide Polymorphisms or SNPs using the Solexa 1G Genetic Analyzer. The second objective is to apply a panel of 1536 SNP markers to determine the positions of genes that control high and stable seed protein content in soybean breeding lines. The third objective is to complete the selection and analysis of 50,000 SNPs using the Solexa 1G Genetic Analyzer and to select an optimized set of 1536 SNPs.

Approach:
SNP DNA marker discovery will proceed using the whole genome sequence of the Williams 82 variety that has been generated by the Department of Energy, Joint Genome Institute (JGI) combined with the use of the newest generation of DNA sequencing technology: the Solexa 1G Genetic Analyzer. Reduced representation libraries of six soybean genotypes (Minsoy, Noir 1, Archer, Peking, Evans, and Essex) will be sequenced using the Solexa 1G Genetic Analyzer and aligned with the Williams 82 whole genome sequence for SNP discovery and to roughly define SNP allele frequency. Selected SNPs will be genetically mapped in a large population of 1000 recombinant inbred lines. A selected set of SNP DNA markers will be used to define the genome positions of genes that control the level of protein in the soybean seed using progeny from 60 different soybean crosses. Finally, based upon the SNP discovery and genetic mapping, an optimized set of SNPs will be identified that are evenly distributed across the 20 soybean chromosomes and which are maximally polymorphic.