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

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Molecular Biology

Background:

• Improving carcass traits is crucial for pig breeding programs.
• Understanding the genetic basis of traits like iodine value, belly firmness, and fat deposition is essential for pork quality.

Purpose of the Study:

• To conduct a genome-wide association study (GWAS) to identify quantitative trait loci (QTLs) and genes associated with key pig carcass traits.
• To discover genetic markers for enhancing pork quality and fat composition in commercial pigs.

Main Methods:

• Whole-genome sequencing data from 1118 commercial pigs (Duroc sires and Yorkshire/Landrace F1 dams).
• Phenotypic measurements including iodine value, belly firmness, belly side fat, total side thickness, subcutaneous fat, and belly seam.
• Genotyping using low-pass sequencing (SkimSeq) and GWAS analysis with a linear mixed model (GCTA).

Main Results:

• A significant QTL on SSC15 (110.83-112.23 Mb) associated with iodine value, containing genes involved in fatty acid metabolism (e.g., COX15, SCD).
• Genes PNKD, VIL1, and PRKAG3 on SSC15 linked to belly firmness, impacting muscle structure and fat composition.
• Three QTLs for belly side fat identified on SSC1, SSC2, and SSC3, involving genes regulating fat deposition (e.g., SLC22A18, PHLDA2).

Conclusions:

• Novel molecular markers for iodine value, belly firmness, and belly fat have been identified.
• These markers can be integrated into selective breeding programs to enhance pork quality and fat distribution.
• The study advances the understanding of genetic mechanisms controlling carcass belly traits, aiding in meeting consumer preferences.