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United States Department of Agriculture

Agricultural Research Service

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Research Project: Genomic Analysis of the Toxin Sensitivity Genes Snn3-B1 and Snn3-D1 in Wheat

Location: Cereal Crops Research

Project Number: 3060-21000-037-22
Project Type: Specific Cooperative Agreement

Start Date: Jul 01, 2011
End Date: Jun 30, 2016

Objective:
1) Develop saturated molecular marker-based linkage maps of the genomic regions harboring the Snn3-B1 and Snn3-D1 loci; 2) Develop high-resolution marker-based linkage maps of the Snn3-B1 and Snn3-D1 loci; 3) Determine feasibility of cloning the Snn3-B1 and Snn3-D1 genes using a map-based approach; and 4) Develop markers suitable for marker-assisted selection against the Snn3-B1 and Snn3-D1 genes.

Approach:
Appropriate low-resolution mapping populations segregating for the Snn3-B1 and Snn3-D1 genes will be developed and phenotyped for reaction to the Stagonospora nodorum host-selective toxin SnTox3. The low-resolution populations will then be used to develop saturated genetic linkage maps of chromosome arms 5BS and 5DS, which are known to harbor the Snn3-B1 and Snn3-D1 genes, respectively. Sources of DNA-based markers for saturation mapping will include simple sequence repeats, expressed sequence tags identified based on available deletion mapping data and colinearity of the genomic regions with rice and Brachypodium, and other PCR-based markers. Markers flanking the target genes will be used to screen large segregating populations consisting of at least 3,000 individuals for high-resolution mapping. Plants harboring recombination events between the flanking markers will be further evaluated with markers that cosegregate with the Snn3 genes and scored for reaction to SnTox3. The most tightly flanking PCR-based markers will then be used to screen available BAC libraries to identify BAC clones and/or BAC contigs at the Snn3 loci. Physical to genetic distance ratios will be evaluated to determine the feasibility of cloning the Snn3 genes using a map-based approach. PCR-based markers tightly linked to the Snn3 genes will also be tested for their utility in marker-assisted selection schemes by evaluating genotypes of at least 100 wheat varieties and comparing the frequencies of marker alleles and response to SnTox3.

Last Modified: 12/21/2014
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