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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE EFFICIENCY OF SWINE PRODUCTION AND PRODUCT QUALITY

Location: Reproduction Research

Title: Predictive markers in calpastatin for tenderness in commercial pig populations

Authors
item Nonneman, Danny
item Lindholm-Perry, Amanda
item Shackelford, Steven
item King, David
item Wheeler, Tommy
item Rohrer, Gary
item Bierman, Chad -
item Schneider, James
item Miller, Rhonda -
item Zerby, Henry -
item Moeller, Steven -

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 21, 2011
Publication Date: September 1, 2011
Citation: Nonneman, D.J., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Rohrer, G.A., Bierman, C.D., Schneider, J.F., Miller, R.K., Zerby, H., Moeller, S.J. 2011. Predictive markers in calpastatin for tenderness in commercial pig populations. Journal of Animal Science. 89:2663-2672.

Interpretive Summary: 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. Improvement in the genetic potential of swine populations to efficiently convert feed into lean, palatable pork will provide long-term economic returns to the producer. By predicting cooked meat tenderness genetic potential, such technology could be used by packers to ensure product quality and more efficiently determine optimal use of pork. The objectives of this proposal 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. Because the calpastatin gene lies under QTL for tenderness in different resource populations and markers in calpastatin are highly associated with tenderness traits, we sequenced the regulatory regions of the calpastatin gene in pigs with divergently extreme shear-force values in order to identify possible mutations that could affect tenderness. We tested these polymorphisms in our research population and samples of industry pigs for association with objective measures of tenderness. From this study we have identified 5 genetic markers that were highly associated with pork tenderness in all of the populations studied representing 2,826 pigs from four distinct populations. These markers should be predictive of pork tenderness in industry populations.

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 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 and twenty-nine SNPs were found in transcription factor binding sites. We tested 130 polymorphisms in our research population and a subset (40) 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. Gel shift assays were designed for these SNPs and 11 other polymorphic sites. Five sites demonstrated a gel shift when probes were incubated with nuclear extract from muscle, heart or testis. Four of these sites, a Sp1 site around nucleotides 12979 and 12980, a potential Tef site at nucleotide 25587, an unknown site at nucleotide 48699, and Mef-2/TATA sites with SNPs at positions 49223 and 49228 were allele-specific in binding nuclear proteins. The allele frequencies for the tender alleles were similar (0.11-0.36) in the four different commercial populations. Allele frequencies in purebred animals, however, varied greatly in Chinese and European Wild Boar breeds. The alleles associated with more tender meat were fixed in a small sample of Berkshire. 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.

Last Modified: 4/19/2014