title: Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan.
authors.forename: Shota
authors.initials: S
authors.lastname: Nishimura
authors.forename: Toshio
authors.initials: T
authors.lastname: Watanabe
authors.forename: Kazunori
authors.initials: K
authors.lastname: Mizoshita
authors.forename: Ken
authors.initials: K
authors.lastname: Tatsuda
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Fujita
authors.forename: Naoto
authors.initials: N
authors.lastname: Watanabe
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Sugimoto
authors.forename: Akiko
authors.initials: A
authors.lastname: Takasuga
mesh_terms: D000818:Animals; D049628:Body Size / Q000235:genetics*; D001835:Body Weight / Q000235:genetics*; D002417:Cattle / Q000033:anatomy & histology* / Q000235:genetics*; D002874:Chromosome Mapping / Q000662:veterinary*; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D040641:Quantitative Trait Loci