Genome-wide Association Studies to Identify Quantitative Trait Loci and Positional Candidate Genes Affecting Meat Quality-related Traits in Pigs

Jae-Bong Lee1, Ji-Hoon Lim2, Hee-Bok Park2,*
Author Information & Copyright
1Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea.
2Department of Animal Resources Science, Kongju National University, Yesan 32439, Korea.
*Corresponding Author: Hee-Bok Park, Department of Animal Resources Science, Kongju National University, Yesan 32439, Korea, Republic of. E-mail:

© Copyright 2023 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


Meat quality comprises a set of key traits such as pH, meat color, water-holding capacity, tenderness and marbling. These traits are complex because they are affected by multiple genetic and environmental factors. The aim of this study was to investigate the molecular genetic basis underlying nine meat quality-related traits in a Yorkshire pig population using a genome-wide association study (GWAS) and subsequent biological pathway analysis. In total, 45,926 single nucleotide polymorphism (SNP) markers from 543 pigs were selected for the GWAS after quality control. Data were analyzed using a genome-wide efficient mixed model association (GEMMA) method. This linear mixed model-based approach identified two quantitative trait loci (QTLs) for meat color (b<sup>*</sup>) on chromosome 2 (SSC2) and one QTL for shear force on chromosome 8 (SSC8). These QTLs acted additively on the two phenotypes and explained 3.92-4.57% of the phenotypic variance of the traits of interest. The genes encoding <italic>HAUS8</italic> on SSC2 and an <italic>lncRNA</italic> on SSC8 were identified as positional candidate genes for these QTLs. The results of the biological pathway analysis revealed that positional candidate genes for meat color (b<sup>*</sup>) were enriched in pathways related to muscle development, muscle growth, intramuscular adipocyte differentiation, and lipid accumulation in muscle, whereas positional candidate genes for shear force were overrepresented in pathways related to cell growth, cell differentiation, and fatty acids synthesis. Further verification of these identified SNPs and genes in other independent populations could provide valuable information for understanding the variations in pork quality-related  traits.

Keywords: GWAS; meat quality-related traits; HAUS8; lncRNA; pig