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United States Department of Agriculture

Agricultural Research Service


Location: Corn, Soybean and Wheat Quality Research

2012 Annual Report

1a. Objectives (from AD-416):
Develop SNP markers for soybean aphid resistance genes for marker assisted breeding for the Rag2 gene.

1b. Approach (from AD-416):
SNP (single nucleotide polymorphism) markers will be identified in the genomic regions of the aphid resistance genes using appropriate RIL mapping populations and near isogenic lines. The Solexa sequencing and Illumina and other genotyping platforms will be used for mapping the SNPs.

3. Progress Report:
More than 20 new single nucleotide polymorphism (SNP) markers within 500 Kb of the Rag2 gene in PI 243540 were developed and more than 1500 BC6F2 soybean lines were screened to find recombinants. Project progress since inception: The Rag2 gene was first fine mapped using 400 recombinant inbred line (RIL) of the FG05 x PI 243540. We mapped 7 simple sequence repeat (SSR) and 10 SNP markers in a 3 cM region flanking the Rag2 gene on linkage group F. Phenotyping of the RILs was completed in May 2010, and genotyping of the Rag2 region was done by December. The phenotypes of 10 lines needed to be confirmed before the new high-density map was finalized. More than 2000 backcross lines were then genotyped with markers within the 3 cM region and recombinants were confirmed by phenotyping and the Rag2 region was narrowed in a window of <200 kilo bases (kb). Three more polymorphic SNP markers were identified and mapped to narrow down the Rag2 region to a less than 150 kb flanking region. A SNP marker within 100 kb for high-throughput marker assisted selection was also developed using melting curve analysis on LightCycler 480. Fifty SSR markers within the 150 kb region were tested in 2012 on 2500 more backcross lines and four recombinants were identified to narrow down the Rag2 gene in a less than 50 kb window. This finding will be confirmed by phenotyping the four recombinants and the results will be published. This project enhances/expands on objective 2B (Characterize and map aphid resistance genes in three soybean plant introductions) of the parent project.

4. Accomplishments

Last Modified: 08/15/2017
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