Abstract
Carcass traits of beef cattle have been genetically improved to increase yield of high quality meat. Genome-wide association study (GWAS) is a powerful method to identify genetic variants associated with carcass traits. For the 770K genotyped SNPs from 1141 Chinese Simmental cattle, we used the compressed mixed linear model (CMLM) to perform a genome-wide association study for knuckle, biceps and shank of beef carcass traits. Seventeen significantly associated SNPs were found, which are located on BTA6, BTA14 and BTA15. Interestingly, one pleiotropic quantitative trait nucleotide (QTN), named BovineHD1400007259 (p < 10−8) within the well-known gene region PLAG1-CHCHD7 on BTA14, was found to govern variation of the knuckle, biceps and shank traits. The QTN accounted for 8.6% of phenotypic variance for biceps. In addition, 16 more SNPs distributed on BTA14 were detected as being associated with the carcass traits.
Highlights
Genome-wide association studies (GWAS) have enabled us to detect many genetic variants associated with quantitative traits in human [1] and farm animals [2]
Previous studies had mapped several QTLs for carcass weights on BTA 6, 8 and 14, where one quantitative trait nucleotide (QTN) was detected on BTA 6 and related to the encoding of NCAPG Ile442Met and the others were identified within gene PLAG1-CHCHD7 in the region on BTA14 [16]
Hot carcass weight, adjusted fat thickness, marbling, rib eye area and slice shear force have been analyzed with PLINK to obtain estimated breeding values (EBV) in genetic evaluation using multivariate animal models [18]
Summary
Genome-wide association studies (GWAS) have enabled us to detect many genetic variants associated with quantitative traits in human [1] and farm animals [2]. Previous studies had mapped several QTLs for carcass weights on BTA 6, 8 and 14, where one QTN was detected on BTA 6 and related to the encoding of NCAPG Ile442Met and the others were identified within gene PLAG1-CHCHD7 in the region on BTA14 [16]. The association of gene PLAG1 with carcass weight was found in Hanwoo steers [17]. Gene NCAPG-LCORL was found to be associated with carcass traits in multi-breed beef cattle [18]. Both PLAG1 and NCAPG were found to segregate in Japanese Black steers [6]. Previous studies revealed that five SNPs within or near four genes, including HS3ST1, DVL1, PRKCQ
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