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

Shota Nishimura,Tatsuo Fujita,Akiko Takasuga,Toshio Watanabe,Kazunori Mizoshita,Yoshikazu Sugimoto,Ken Tatsuda,Naoto Watanabe

doi:10.1186/1471-2156-13-40

Abstract

BackgroundSignificant 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.ResultsBonferroni-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.ConclusionThe 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.

Highlights

Significant quantitative trait loci (QTL) for carcass weight were previously mapped on several chromosomes in Japanese Black half-sib families
Snelling et al [5] detected the strongest association on Bovine chromosome(s) (BTA) 6 and others on BTAs 7, 10, 11, 14, 20, and 23 that reached a Bonferroni-corrected significance level using more than 2500 crossbred beef cattle, they did not indicate the portion of heritability that could be accounted for by the associated single nucleotide polymorphism (SNP)
The analysis was performed using EMMAX software [13], which is based on a linear mixed model approach using a genetic relationship matrix estimated by highdensity SNP genotypes to model the correlation between the phenotypes of the sample subjects

Summary

Introduction

Significant quantitative trait loci (QTL) for carcass weight were previously mapped on several chromosomes in Japanese Black half-sib families. We previously performed bovine quantitative trait locus (QTL) mapping using Japanese Black paternal half-sib families and detected significant linkages with carcass. The association corresponded to the loci for human adult height, including PLAG1, MOS, CHCHD7, RDHE2, RPS20, LYN, TGS1, and PENK [7,10] They identified a highly significantly associated SNP in a putative polyadenylation signal of RPS20. Karim et al [11], recently identified causative variations influencing bovine stature in the PLAG1-CHCHD7 intergenic region This QTL influences body weight and the quantitative trait nucleotides (QTN) modulate the expression of the surrounding genes, including PLAG1 [11], whose knockout in mice causes dwarfism in the absence of other symptoms [12]. The CW-1 QTL that we narrowed down [2] locates approximately 2.5-Mb apart from the variations on RPS20 or PLAG1-CHCHD7

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Discussion

Conclusion