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Title: Genome Wide Scan for Loci influencing Warner Bratzler Shear Force in Five Bos taurus Breeds

item McClure, Matthew
item RAMEY, H - University Of Missouri
item ROLF, M - University Of Missouri
item MCKAY, S - University Of Missouri
item WEABER, R - University Of Missouri
item SCHNABEL, R - University Of Missouri
item TAYLOR, J - University Of Missouri

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2011
Publication Date: 2/27/2012
Citation: Mcclure, M.C., Ramey, H.R., Rolf, M.M., Mckay, S.D., Weaber, R.L., Schnabel, R.D., Taylor, J.F. 2012. Genome Wide Scan for Loci influencing Warner Bratzler Shear Force in Five Bos taurus Breeds. Animal Genetics. DOI: 10.1111/j.1365-2052.2012.02323.x.

Interpretive Summary: Inadequate tenderness has consistently been identified in National Beef Quality Audits as a priority quality challenge because consumers consider tenderness to be the single most important component of meat quality and will substitute protein sources motivated by their dissatisfaction from the purchase of a tough cut. While quantitative trait loci (QTL) for Warner-Bratzler shear force (WBSF) measurements on the longissimus dorsi muscle have been identified on Bos taurus chromosomes 2, 4, 5, 7, 10, 15, 20, 25, and 29, DNA marker tests have been developed and commercialized only from calpastatin (CAST) on chromosome 7 and calpain 1 (CAPN1) on chromosome 29. To identify additional makers and regions that can be utilized by producers to improve tenderness a genome-wide association study for WBSF was performed by genotyping 3,360 animals from five breeds with 54,886 SNP. Thirty-nine regions associated with WBSF in at least three breeds were identified. Additionally, haplotypes in both CAPN1 and CAST were identified that explain a greater amount of WBSF variation than the current commercialized SNPs. This study shows on its own that high density SNP assays can be used to identify SNPs useful for in-breed diagnostics for predicting WBSF or other important traits, but a higher density assay is needed to identify SNP and haplotypes that will work consistently across B. taurus breeds due the genetic diversity between the breeds.

Technical Abstract: Genetic tests for beef tenderness are currently limited to single nucleotide polymorphisms (SNPs) within µ-calpain (CAPN1) and calpastatin (CAST) and explain little of the phenotypic variation in Warner-Bratzler shear force (WBSF). We performed a genome-wide association study for WBSF by genotyping 3,360 animals from five breeds with 54,790 BovineSNP50 and 96 putative SNPs located in CAPN1 or CAST. Within-breed analyses estimated SNP allele substitution effects by BLUP and variance components by REML under an animal model incorporating a genomic relationship matrix. By considering the 100 most strongly associated genomic regions within each breed, we identified only 39 regions associated with WBSF in at least three breeds suggesting that the within-breed analyses were underpowered, different QTL underlie variation between breeds, or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. Evaluation of linkage disequilibrium (LD) patterns in across two regions with high SNP density revealed three blocks in the CAST region and eight in the CAPN1 region that were conserved across breeds. Haplotypes from SNPs within these genes, each LD block, the most strongly associated SNPs within each block, and commercialized SNPs were analyzed for effects on WBSF. Breed specific and across breed haplotypes in CAST and CAPN1 were identified that better predict WBSF than do haplotypes based on commercialized SNPs which appear to not be causal variants. The most significant breed specific haplotype explained 0.3 to 10% more WBSF variation than the commercialized SNP in CAPN1 and 10 to 51% more in CAST.