Project Number: 1275-21000-164-00
Project Type: Appropriated

Start Date: May 14, 2003
End Date: May 13, 2008

Objective:
The objectives of this research are 1) to discover and map at least 3000 new single nucleotide polymorphisms (SNPs) in soybean 2) to assess the level of linkage disequilibrium in soybean germplasm, and 3) to examine the application of the SNP-based genetic map for the discovery of quantitative trait loci (QTL) via genetic association analysis of soybean germplasm accessions and via the application of the advanced backcross technique to genetic materials derived from exotic soybean germplasm.

Approach:
The discovery of SNP DNA markers will be undertaken using three approaches: 1) via the "resequencing" of homologous sequence tagged sites (STSs) from a set of six genetically diverse soybean genotypes, 2) via the in silico analysis of the existing EST sequence dataset which is derived from a number of genotypes, and 3) via the comparison of genomic sequence data from Medicago truncatula with soybean EST sequence data to permit the design of STSs from soybean EST data that amplify predicted introns soybean. Single base extension assays will be used for the genetic mapping of SNPs. Linkage disequilibrium (LD) in a number of regions across the soybean genome will be assessed via the analysis of SNPs in 24 diverse soybean germplasm accessions. Using the SNP markers that are developed and mapped, genetic Association Analysis will be applied to detect genes (quantitative trait loci, QTL) that control soybean seed size and seed protein concentration in a large collection of soybean germplasm lines. SNP DNA markers will also be used to detect yield and seed quality QTL in advanced backcross populations derived from (Glycine max)*3 x G. soja and (G. max)*2 x G. max.

Project Team

Cregan, Perry Yaklich, Robert

Project Annual Reports

FY 2003

Related National Programs

Plant, Microbial & Insect Genetic Res., Genomics, & Genetic Improv. I (301)   Plant Biological and Molecular Processes (302)

Related Projects

Microsatellite Marker Development & Construction of Microsatellite Allele Size Database    Development of Low-Saturated Substitutes for Partially Hydrogenated Soybean Oil    Elevating Seed Protein in the North Central Usa Soybean-Growing States    Single Nucleotide Polymorphism (Snp) Discovery & Mapping    Anchoring the Soybean Physical Map to the Soybean Genetic Map    Genetic Mapping and Applications of Snp DNA Markers in Soybean    Soybean Bac-Clone Identification Using Overgo Hybridization    Genetic Analysis to Create a Consensus Snp-Based Soybean Linkage Map    High Throughput Systems for Single Nucleotide Polymorphism Analysis