Open Access Research article

Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle

Shota Nishimura1, Toshio Watanabe15, Kazunori Mizoshita2, Ken Tatsuda3, Tatsuo Fujita4, Naoto Watanabe4, Yoshikazu Sugimoto1 and Akiko Takasuga15*

Author Affiliations

1 Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan

2 Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima, 899-8212, Japan

3 Hyogo Prefectural Institute of Agriculture, Forestry & Fisheries, Befu, Kasai, Hyogo, 679-0198, Japan

4 Oita Prefectural Institute of Animal Industry, Kuju, Takeda, Oita, 878-0201, Japan

5 National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan

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BMC Genetics 2012, 13:40  doi:10.1186/1471-2156-13-40

Published: 20 May 2012



Significant quantitative trait loci (QTL) for carcass weight were previously mapped on several chromosomes in Japanese Black half-sib families. Two QTL, CW-1 and CW-2, were narrowed down to 1.1-Mb and 591-kb regions, respectively. Recent advances in genomic tools allowed us to perform a genome-wide association study (GWAS) in cattle to detect associations in a general population and estimate their effect size. Here, we performed a GWAS for carcass weight using 1156 Japanese Black steers.


Bonferroni-corrected genome-wide significant associations were detected in three chromosomal regions on bovine chromosomes (BTA) 6, 8, and 14. The associated single nucleotide polymorphisms (SNP) on BTA 6 were in linkage disequilibrium with the SNP encoding NCAPG Ile442Met, which was previously identified as a candidate quantitative trait nucleotide for CW-2. In contrast, the most highly associated SNP on BTA 14 was located 2.3-Mb centromeric from the previously identified CW-1 region. Linkage disequilibrium mapping led to a revision of the CW-1 region within a 0.9-Mb interval around the associated SNP, and targeted resequencing followed by association analysis highlighted the quantitative trait nucleotides for bovine stature in the PLAG1-CHCHD7 intergenic region. The association on BTA 8 was accounted for by two SNP on the BovineSNP50 BeadChip and corresponded to CW-3, which was simultaneously detected by linkage analyses using half-sib families. The allele substitution effects of CW-1, CW-2, and CW-3 were 28.4, 35.3, and 35.0 kg per allele, respectively.


The GWAS revealed the genetic architecture underlying carcass weight variation in Japanese Black cattle in which three major QTL accounted for approximately one-third of the genetic variance.

GWAS; QTL; Carcass weight; Body size; Body weight; Growth trait; Cattle