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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #247221

Title: Association of Functional SNPs in Pig Calpastatin Regulatory Regions with Tenderness

item Nonneman, Danny - Dan
item Lindholm-Perry, Amanda
item Shackelford, Steven
item King, David - Andy
item Wheeler, Tommy
item Rohrer, Gary
item BIERMAN, CHAD - Babcock Genetics
item MILLER, RHONDA - Texas A&M University
item ZERBY, HENRY - The Ohio State University
item MOELLER, STEVEN - The Ohio State University

Submitted to: Midwestern Section of the American Society of Animal Science
Publication Type: Abstract Only
Publication Acceptance Date: 11/2/2009
Publication Date: 3/15/2010
Citation: Nonneman, D.J., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Rohrer, G.A., Bierman, C., Miller, R.K., Zerby, H., Moeller, S.J. 2010. Association of Functional SNPs in Pig Calpastatin Regulatory Regions with Tenderness. Proc., Midwestern Section of the American Society of Animal Science Meeting. March 15-17, 2010. Des Moines, IA. Abstract #34. p. 11-12.

Interpretive Summary:

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 three of these were allele-specific in their ability to bind nuclear proteins. These SNPs were not in linkage disequilibrium with each other and may independently affect calpastatin expression. These markers should be predictive of pork tenderness in industry populations.