Genome-wide association studies for feed efficiency, production and feeding behaviour traits in Canadian purebred Duroc pigs

This study aimed to identify potential genetic variants and candidate genes associated with feed efficiency (FE), production, and feeding behaviour traits in Canadian purebred Duroc pigs. Genome-wide association studies (GWAS) were conducted using 8,861 individuals and an imputed Affymetrix PigGen Canada 50K panel v2.0 using a linear mixed model (LMM) and a Bayesian B model. This analysis used an adjusted p-value threshold (ranging from 6.6 × 10-5 to 1.3 × 10-4) using false-discovery rate to determine significance. The number of significant SNPs identified for each trait was as follows: average daily gain (ADG, 48), daily feed intake (DFI, 85), feed conversion ratio (FCR, 101), residual feed intake (RFI, 37), residual gain (RG, 64), residual intake and gain (RIG, 55), backfat thickness (BF, 100), loin depth (LD, 6), Keibler ratio (KR, 0), total time spent eating per day (TPD, 7), and number of visits to the feeder per day (NVD, 6). Several traits (BF, DFI, FCR, RFI, RG, and RIG) showed strong overlapping signals on chromosomes 7 and 10 with 24 shared significant SNPs, indicating potential shared genetic mechanisms. These traits also had 71 overlapping candidate genes such as PACSIN1, PTCH1, ADIPOR1 and ITPR3, associated with glucose, lipid and cholesterol metabolism. Well known candidate genes in literature associated with growth and fatness such as MC4R and CDH20 were also identified to be associated with ADG, BF, FCR and DFI in this study. Gene Ontology enrichment analysis revealed a set of the candidate genes were involved in the gonadotropin-releasing hormone (GnRH) and the platelet-derived growth factor (PDGF) signaling pathways. Overall, this study contributed to understating the genetic architecture and provided a biological foundation for improving FE, production and feeding behaviour traits in Canadian Duroc pigs facilitating the selection of more efficient pigs.