McClure MC, Ramey HR, Rolf MM, McKay SD, Decker JE, Chapple RH, Kim JW, Taxis TM, Weaber RL, Schnabel RD, Taylor JF. Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.
Anim Genet 2012;
43:662-73. [PMID:
22497286 PMCID:
PMC3506923 DOI:
10.1111/j.1365-2052.2012.02323.x]
[Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2011] [Indexed: 01/09/2023]
Abstract
We performed a genome-wide association study for Warner–Bratzler shear
force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five
breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms
(SNPs) within μ-calpain [HUGO nomenclature
calpain 1, (mu/I) large subunit; CAPN1]
and calpastatin (CAST). Within- and
across-breed analyses estimated SNP allele substitution effects (ASEs) by
genomic best linear unbiased prediction (GBLUP) and variance components by
restricted maximum likelihood under an animal model incorporating a genomic
relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were
moderately correlated (0.31–0.66) with those from the individual
within-breed analyses, indicating that prediction equations for molecular
estimates of breeding value developed from across-breed analyses should be
effective for genomic selection within breeds. We identified 79 genomic regions
associated with WBSF in at least three breeds, but only eight were detected in
all five breeds, suggesting that the within-breed analyses were underpowered,
that different quantitative trait loci (QTL) underlie variation between breeds
or that the BovineSNP50 SNP density is insufficient to detect common QTL among
breeds. In the across-breed analysis, CAPN1 was followed by
CAST as the most strongly associated WBSF QTL genome-wide,
and associations with both were detected in all five breeds. We show that none
of the four commercialized CAST and CAPN1SNP
diagnostics are causal for associations with WBSF, and we putatively fine-map
the CAPN1 causal mutation to a 4581-bp region. We estimate that
variation in CAST and CAPN1 explains 1.02 and
1.85% of the phenotypic variation in WBSF respectively.
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