Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs

The improvement of carcass traits is a key focus in pig genetic breeding programs. To identify quantitative trait loci (QTLs) and genes linked to key carcass traits, we conducted a genome-wide association study (GWAS) using whole-genome sequencing data from 1118 commercial pigs (Duroc sires and Yorkshire/Landrace F1 dams). This study focused on six phenotypes: iodine value, belly firmness, belly side fat, total side thickness (belly SThK), belly subcutaneous fat (Subq), and belly seam. Phenotypes were measured using image analysis, DEXA, and fatty acid profiling, and genotyping was performed using low-pass sequencing (SkimSeq). After quality control, 18,911,793 single nucleotide polymorphisms (SNPs) were retained for further analysis. A GWAS was conducted using a linear mixed model implemented in GCTA. Key findings include a significant QTL on SSC15 (110.83-112.23 Mb), which is associated with the iodine value, containing genes such as <i>COX15</i>, <i>CHUK</i>, <i>SCD</i>, and <i>HIF1AN</i>, which have known roles in fatty acid metabolism. Additionally, <i>PNKD</i>, <i>VIL1</i>, and <i>PRKAG3</i> (120.74-121.88 Mb on SSC15) were linked to belly firmness, influencing muscle structure and fat composition. Three QTLs for belly side fat were identified on SSC1, SSC2, and SSC3, highlighting genes like <i>SLC22A18</i>, <i>PHLDA2</i>, and <i>OSBPL5</i>, which regulate fat deposition and lipid metabolism. The results provide novel molecular markers that can be incorporated into selective breeding programs to improve pork quality, fat distribution, and meat composition. These findings enhance our understanding of the genetic mechanisms underlying carcass belly traits while offering tools to improve pork quality, optimize fat composition, and align with consumer preferences in the meat production industry.