55. Genome-wide Association Studies of Resilience Traits in Canadian Duroc Pigs.

Abstract Pigs are a valuable source of high-quality protein, lipids and other essential nutrients for many human populations worldwide. Key production traits, including growth, welfare and meat quality, can be compromised through environmental stressors, disease challenges or changes in management conditions. Resilience is described as tolerance to such disturbances or rapid recovery of performance after exposure to such environmental stressors. Variations in feed intake and duration quantified using quantile regression (QR), root mean square error (RMSE) and coefficient of variation (CV) provide robust and non-invasive indicators of resilience. Resilience traits, being moderately correlated with growth and feed efficiency, make them a promising candidate for inclusion in breeding goals. However, underlying genetic mechanisms regulating these traits remain poorly understood. Thus, this study conducted genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) and candidate genes linked to the QR, RMSE and CV of feed intake (QRFI, RMSEFI, CVFI) and time spent at the feeder per day (QRTPD, RMSETPD, CVTPD) in Canadian purebred Duroc pigs. Increased understanding of the biological basis behind resilience can enhance genomic selection and overall production efficiency through increased tolerance to external stressors. Feeding data was collected from 13 PIC farms across Quebec, Canada using electronic automatic FIRE feeders. All phenotypes were adjusted by extracting the residuals from fitted linear mixed models that accounted for herd-year-season, sex, age, random common litter effects, and random pen effects. Genotyping was performed from various SNP panels, then imputed to the Affymetrix PigGen Canada 60K panel v2.0 using FImpute 3.0 software. GWAS was conducted using Genomic Best Linear Unbiased Prediction (GBLUP) with a final dataset of 38,121 SNPs corresponding to 9,485 animals. The significance threshold was adjusted using False Discovery Rate with a level of 0.01. Annotated genes located within 500 kbp of the significant SNP were used for Gene Ontology (GO) analysis using PANTHER. The numbers of significant SNPs identified were 44, 1, 13, 21, 55, and 16 for QRFI, QRTPD, RMSEFI, RMSETPD, CVFI and CVTPD, respectively, with strong signals on Sus scrofa (SSC) chromosomes 1 and 10. Prominent candidate genes included melanocortin 4 receptor (MC4R) and cadherin 20 (CDH20), with MC4R being a well-known candidate gene associated with feed intake, growth, and fatness in pigs but also obesity and lipid metabolism in humans. Likewise, CDH20 is also associated with fat metabolism, adipogenesis and various primal cut traits such as backfat, loin fat, and ham fat in pigs. Overlapping GO terms for both traits included transcription factor binding, cellular anatomical entity, and biological regulation. Overall, this study identified key genomic regions and candidate genes previously associated with growth and feed intake, leading to the enhancement of the current state of knowledge on the internal mechanisms underlying resilience traits.