Genome-wide Association Study of Carcass Weight in Commercial Hanwoo Cattle

Overview

Journal Asian-Australas J Anim Sci

Specialty Veterinary Medicine

Date 2017 Nov 7

PMID 29103288

Citations 14

Authors

Zewdu Edea

Yeong Ho Jeoung

Sung-Sub Shin

Jaeul Ku

Sungbo Seo

Il-Hoi Kim

Sang-Wook Kim

Kwan-Suk Kim

Affiliations

Soon will be listed here.

Abstract

Objective: The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed.

Methods: Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10 (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests.

Results: By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds.

Conclusion: This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.

Citing Articles

Genome-Wide Detection of Copy Number Variations and Their Potential Association with Carcass and Meat Quality Traits in Pingliang Red Cattle.

Wang Y, Ma J, Wang J, Zhang L, Xu L, Chen Y Int J Mol Sci. 2024; 25(11).

PMID: 38891814 PMC: 11172001. DOI: 10.3390/ijms25115626.

Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan.

Nisa F, Naqvi R, Arshad F, Ilyas I, Asif M, Amin I Biochem Genet. 2024; 62(5):4137-4156.

PMID: 38664326 DOI: 10.1007/s10528-024-10809-2.

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle.

Sheet S, Jang S, Kim J, Park W, Kim D Sci Rep. 2024; 14(1):315.

PMID: 38172605 PMC: 10764957. DOI: 10.1038/s41598-023-51037-9.

Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding.

Lee D, Kim Y, Dinh P, Chung Y, Lee D, Kim Y Genes (Basel). 2023; 14(10).

PMID: 37895191 PMC: 10606632. DOI: 10.3390/genes14101839.

Genome-Wide Association Study to Identify QTL for Carcass Traits in Korean Hanwoo Cattle.

Alam M, Haque M, Iqbal A, Lee Y, Ha J, Jin S Animals (Basel). 2023; 13(17).

PMID: 37685003 PMC: 10486602. DOI: 10.3390/ani13172737.

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