ARS | Publication request: Allele-Specific Transcription Factor Binding in Pig Calpastatin Promoter Regions

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: November 2, 2009
Publication Date: December 9, 2009
Repository URL: http://64.241.182.116/18/abstracts/P05n_PAGXVIII_607.html
Citation: Nonneman, Dan J., Lindholm-Perry, Amanda K., Shackelford, Steven D., King, D.Andy, Wheeler, Tommy L., Rohrer, Gary A. 2010. Allele-Specific Transcription Factor Binding in Pig Calpastatin Promoter Regions. Plant and Animal Genome Conference Proceedings XVIII. 1/9-13/2010. San Diego, CA. Abstract #P607.

Technical Abstract: The identification of predictive DNA markers for pork quality would allow U.S. pork producers and breeders to more quickly and efficiently select genetically superior animals for production of consistent, high quality meat. Genome scans have identified QTL for tenderness on pig chromosome 2 which have been fine-mapped to the calpastatin locus. The objectives of this study were to identify the causative sequence variation in calpastatin that likely affects tenderness in commercial-level pig populations and to develop definitive DNA markers that are predictive of pork tenderness for use in marker assisted selection programs. We resequenced the calpastatin regulatory and transcribed regions in pigs with divergently extreme shear force values in order to identify possible mutations that could affect tenderness. One hundred ninety-four single nucleotide polymorphisms (SNP) were identified in this sequence. We tested 130 polymorphisms in our research population and a subset (32) of these in samples of industry pigs for association with objective measures of tenderness. We identified five SNPs that were highly associated (p<0.000001) with pork tenderness in all of the populations studied, representing 2,826 pigs from four distinct populations. Twenty-nine SNP were found in transcription factor binding sites and gel shift assays were designed for 16 polymorphic sites, including the five SNPs that were the most significant in all populations. Five polymorphic sites demonstrated binding to nuclear extracts in gel shift assays and four of these were allele-specific in their ability to bind nuclear proteins. These SNPs were not in complete linkage disequilibrium with each other and may independently affect calpastatin expression. These markers should be predictive of pork tenderness in industry populations.