Genome-wide association study identifies major loci for carcass weight on BTA14 in Hanwoo (Korean cattle)

Seung Hwan Lee; Bong Hwan Choi; Dajeong Lim; Cedric Gondro; Young Min Cho; Chang Gwon Dang; Aditi Sharma; Gul Won Jang; Kyung Tai Lee; Duhak Yoon; Hak Kyo Lee; Seong Heum Yeon; Boh Suk Yang; Hee Seol Kang; Seong Koo Hong

doi:10.1371/journal.pone.0074677

Genome-wide association study identifies major loci for carcass weight on BTA14 in Hanwoo (Korean cattle)

PLoS One. 2013 Oct 7;8(10):e74677. doi: 10.1371/journal.pone.0074677. eCollection 2013.

Authors

Seung Hwan Lee¹, Bong Hwan Choi, Dajeong Lim, Cedric Gondro, Young Min Cho, Chang Gwon Dang, Aditi Sharma, Gul Won Jang, Kyung Tai Lee, Duhak Yoon, Hak Kyo Lee, Seong Heum Yeon, Boh Suk Yang, Hee Seol Kang, Seong Koo Hong

Affiliation

¹ Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang, Korea.

Abstract

This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10(-6)) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was BTB-01280026 (P = 4.02×10(-11)), located in the 25 Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were Hapmap27934-BTC-065223 (P = 4.04×10(-11)) in 25.2 Mb, BTB-01143580 (P = 6.35×10(-11)) in 24.3 Mb, Hapmap30932-BTC-011225 (P = 5.92×10(-10)) in 24.8 Mb, Hapmap27112-BTC-063342 (P = 5.18×10(-9)) in 25.4 Mb, and Hapmap24414-BTC-073009 (P = 7.38×10(-8)) in 25.4 Mb, all on BTA 14. One SNP (BTB-01143580; P = 6.35×10(-11)) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP (BTB-01280026; P = 4.02×10(-11)) had 16.96 kg of allele substitution effect, and the second most significant SNP (Hapmap27934-BTC-065223; P = 4.04×10(-11)) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Animals
Body Weight / genetics*
Cattle
Genome-Wide Association Study
Male
Polymorphism, Single Nucleotide*
Quantitative Trait Loci*

Grants and funding

This study was supported by awards from the AGENDA project (grant no. PJ907008062012) and Molecular Breeding program (PJ0081882012) of Next Generation BIOGREEN21 project in the National Institute of Animal Science, RDA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.