Investigation of GWAS variants associated with loin depth in commercial pigs

Suzanne Desire, Martin Johnsson, Roger Ros-Freixedes, Ching-Yi Chen, william o herring, Gregor Gorjanc, Richard Mellanby, Melissa Jungnickel

Research output: Contribution to conferencePaperpeer-review

Abstract / Description of output

Genome wide associate studies (GWAS) aim to identify genomic regions implicated in phenotype expression, but identifying true causative variants is difficult. Pig combined annotation dependent depletion (pCADD) scores may provide a straight-forward method of prioritising causal variants identified by GWAS. This study aimed to test using pCADD to identify candidate variants using loin depth in four pig lines. Three main regions on SSC7, 9, and 16 were identified in both maternal and terminal lines and have been found to be associated with carcass traits in previous studies. Two genomic regions were identified in maternal lines only, with SNPs within MC4R and PIK3C2A identified as the most likely causative variants. Several of the candidate SNPs have plausible biological links to muscle-related phenotypes, however further work is required to determine whether these are true causal variants.
Original languageEnglish
Publication statusPublished - 8 Jul 2022
EventWorld Congress on Genetics Applied to Livestock - Rotterdam, Netherlands
Duration: 3 Jul 20228 Jul 2022


ConferenceWorld Congress on Genetics Applied to Livestock
Abbreviated titleWCGALP
Internet address


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