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Title: Service and research for Molecular Marker Development in the USDA-ARS Western Regional Small Grains Genotyping Laboratory

Author
item Ling, Peng
item Garland-Campbell, Kimberly
item Little, Lynn
item Skinner, Daniel

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2005
Publication Date: 1/1/2006
Citation: Ling, P., Garland Campbell, K.A., Little, L.M., Skinner, D.Z. 2006. Service and research for molecular marker development in the usda-ars western regional small grains genotyping laboratory. Plant and Animal Genome Abstracts, page 14, #P203. Plant Animal Genome Conference XIV. January 14-18, 2006. San Diego, CA.

Interpretive Summary:

Technical Abstract: The Western Regional Small Grain Genotyping Laboratory is offering collaborative genotyping services to assist the marker assisted selection for wheat and barley cultivar development in Western region. Commonly known molecular markers are routinely used. Effective and versatile genomic technology is used to develop robust high-density and high-throughput markers that can be effectively deployed for closely related elite germplasm. Affymetrix Wheat GeneChips was used to identify Single Feature Polymorphisms (SFPs), which would allow us to screening the whole "gene rich space" for Single Nucleotide Polymorphisms (SNPs) in parallel, including polymorphisms generated during mRNA processes. mRNA of "Eltan" and "Oregon feed Wheat (ORFW)" were probed to the Affymetrix Wheat GeneChips. The perfect matches (PM) of gene probes were evaluated. Nearly 1,000 folds differences were found at different genes expression level between these two genotypes. Total of 948 genes were categorized as SFPs. In general, there were approximately 3.2% of genes were found significantly different at various gene expression levels for these two genotypes. A total of 96 oligo probes were initially generated from selected SFPs, and were subjected to custom oligo array for the transcriptome mapping. Polymorphisms identified in this study would provide a rich source of candidate gene markers for marker-assisted breeding and for mapping wheat genes associated with different phenotypic traits such as cold tolerance, salt tolerance and other environmental stress tolerances. Molecular marker genotyping will increasingly provide more efficient information to crop breeders so that marker-assisted selection can be used in breeding programs to incorporate more valuable traits.