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. 2023 Mar;65(2):311-323.
doi: 10.5187/jast.2022.e110. Epub 2023 Mar 31.

Genome-wide association studies on collagen contents trait for meat quality in Hanwoo

KyeongHye Won  1 , Dohyun Kim  1 , Inho Hwang  2 , Hak-Kyo Lee  1   3 , Jae-Don Oh  1
Affiliations

Genome-wide association studies on collagen contents trait for meat quality in Hanwoo

KyeongHye Won et al. J Anim Sci Technol. 2023 Mar.

Abstract

Beef consumers valued meat quality traits such as texture, tenderness, juiciness, flavor, and meat color that determining consumers' purchasing decision. Most research on meat quality has focused on marbling, a key characteristic related to meat eating quality. However, other important traits such as meat texture, tenderness, and color have not much studied in cattle. Among these traits, meat tenderness and texture of cattle are among the most important factors affecting quality evaluation of consumers. Collagen is the main component of connective tissues.It greatly affects meat tenderness. The objective of this study was to determine significant variants and candidate genes associated with collagen contents trait (total collagen) through genome-wide association studies (GWAS). Phenotypic and genomic data from 135 Hanwoo were used. The BLUPF90 family program and GRAMMAR method for GWAS were applied in this study. A total of 73 potential single nucleotide polymorphisms (SNPs) showed significant associations with collagen content. They were located in or near 108 candidate genes. TMEM135 and ME3 genes were identified to have the most significant SNPs associated with collagen contents trait. Data indicated that these genes were related to collagen. Biological processes and pathways for the prediction of biological functions of candidate genes were confirmed. We found that candidate genes were involved in positive regulation of CREB transcription factor activity and actin cytoskeleton related to tenderness and texture of beef. Three genes (CRTC3, MYO1C and MYLK4) belonging to these biological functions were related to tenderness. These results provide a basis for improving genomic characteristics of Hanwoo for the production of tender beef. Furthermore, they could be used they could be used as an index to select desired traits for consumers.

Keywords: Collagen; Genome-wide association studies (GWAS); Hanwoo; Meat quality; Single nucleotide polymorphisms (SNPs); Tenderness.

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Conflict of interest statement

No potential conflict of interest relevant to this article was reported.

Figures

Fig. 1.
Fig. 1.. Flow chart related to GWAS analysis using genomic and phenotypic data.
IBS, identity by state; QC, quality control; GWAS, genome-wide association studies; GWAS, genome-wide association studies; SNPs, single nucleotide polymorphisms; QQ, quantile-quantile.
Fig. 2.
Fig. 2.. The QQ-plot for the studied total collagen contents trait.
The dotted line represents the 95% concentration band under the null hypothesis no association between trait and SNPs. The green dots represent the p-values. QQ, quantile-quantile; SNPs, single nucleotide polymorphisms.
Fig. 3.
Fig. 3.. The Manhattan plot of SNP effects for GWAS analysis using GRAMMAR methods in PLINK.
SNP, single nucleotide polymorphism; GWAS, genome-wide association studies.
Fig. 4.
Fig. 4.. The Manhattan plot of GWAS for total collagen contents trait with significance thresholds indicated at −log10P > 1 × 10−3.
The orange dots represent significant SNPs associated with total collagen contents trait. GWAS, genome-wide association studies; SNPs, single nucleotide polymorphisms.
See this image and copyright information in PMC

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