Genome Wide Association Studies (GWAS) Identify QTL on SSC2 and SSC17 Affecting Loin Peak Shear Force in Crossbred Commercial Pigs

PLoS One. 2016 Feb 22;11(2):e0145082. doi: 10.1371/journal.pone.0145082. eCollection 2016.

Abstract

Of all the meat quality traits, tenderness is considered the most important with regard to eating quality and market value. In this study we have utilised genome wide association studies (GWAS) for peak shear force (PSF) of loin muscle as a measure of tenderness for 1,976 crossbred commercial pigs, genotyped for 42,721 informative SNPs using the Illumina PorcineSNP60 Beadchip. Four 1 Mb genomic regions, three on SSC2 (at 4 Mb, 5 Mb and 109 Mb) and one on SSC17 (at 20 Mb), were detected which collectively explained about 15.30% and 3.07% of the total genetic and phenotypic variance for PSF respectively. Markers ASGA0008566, ASGA0008695, DRGA0003285 and ASGA0075615 in the four regions were strongly associated with the effects. Analysis of the reference genome sequence in the region with the most important SNPs for SSC2_5 identified FRMD8, SLC25A45 and LTBP3 as potential candidate genes for meat tenderness on the basis of functional annotation of these genes. The region SSC2_109 was close to a previously reported candidate gene CAST; however, the very weak LD between DRGA0003285 (the best marker representing region SSC2_109) and CAST indicated the potential for additional genes which are distinct from, or interact with, CAST to affect meat tenderness. Limited information of known genes in regions SSC2_109 and SSC17_20 restricts further analysis. Re-sequencing of these regions for informative animals may help to resolve the molecular architecture and identify new candidate genes and causative mutations affecting this trait. These findings contribute significantly to our knowledge of the genomic regions affecting pork shear force and will potentially lead to new insights into the molecular mechanisms regulating meat tenderness.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Female
  • Genome-Wide Association Study / methods*
  • Genotype
  • Male
  • Meat / analysis*
  • Quantitative Trait Loci / genetics*
  • Swine

Grants and funding

GP acknowledges the financial support from Natural Sciences and Engineering Research Council of Canada (NSERC) CRDPJ 379911: www.nserc-crsng.gc.ca; Hypor Inc. www.hypor.com/; Genesus Inc. www.genesus.com/; and CZ and GP Mitacs Elevate Program IT03418: https://www.mitacs.ca/en/progra,s/elevate. The industry funders (Hypor Inc. and Genesus Inc.) provided support in the form of salaries for authors (PC, RAK, and NB), and data collection at the commercial units, but did not have any additional role in the study design and analysis, or decision to publish. The specific roles of these authors are articulated in the “author contributions” section. The other funders did not have any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.