Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population

Abstract

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.

Prediction of hub genes associated with intramuscular fat content in Nelore cattle

“…The fact that PDE4D was downregulated in HIF animals may increase the intracellular cAMP through the regulation of other genes and thus may contribute to an increase in IF content and maintain immune homeostasis of Nelore cattle. PDE4D was previously related with marbling score in a commercial Hanwoo cattle population from genome-wide association study (GWAS) [64].…”

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

“…The PIK3R1 gene has been associated with an increased milk protein fraction at peak lactation [ 38 ]. The PDE4D gene has been reported to increase meat marbling in studies on Nellore and Hanwoo cattle [ 39 ]. Genes related to immunity and environmental resistance have been identified on BTA20; for example, the candidate gene CD180 is associated with the animal’s ability to deal with pathogens in Brahman and Angus cattle [ 40 ].…”

Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population

“…To estimate the contribution of the genome-wide significant SNPs to the genetic variance based on the GRM calculated from all eligible SNPs, the percentage of genetic contribution ( ) accounted for by each SNP was calculated using the following formula ( Sudrajad et al, 2016 ; Bhuiyan et al, 2018 ): where p and q are the observed allele frequencies for the SNP in the current population, is the additive effect of the SNP, and is the additive genetic variance for a given trait estimated in the linear mixed model.…”