Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

Residual feed intake (RFI) is the difference between the observed feed intake and the expected feed requirements for an animal’s growth and maintenance. Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed using SNP genotypes from the Illumina PorcineSNP60 BeadChip on 1,400 pigs from ISU-RFI selection lines. Various statistical methods including allele frequency differences between lines, a Bayesian approach using GenSel software, and frequentist approaches for single SNP and haplotype analyses using PLINK software were applied to find SNPs and genomic regions associated with the traits. Frequentist approaches showed no significant associations (except for LMA) after genomic control and accounting for FDR. Bayesian methods found at least two associations for each trait at a false positive probability of 0.5. RFI selection lines at generation 8 mainly differed in allele frequencies at SNP within 0.05Mb of genes that regulate insulin and leptin functions. Bayesian WGAS identified associations for genomic regions that contain insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI; energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG; fat metabolism genes (e.g., ACOXL, AEBP1) with BF; and skeletal myogenesis genes (e.g., KLHL31) with LMA. Important genomic regions associated with RFI and related traits allow for future validation studies prior to their incorporation in marker assisted selection programs. Funding support from Pfizer Animal Health, National Pork Board, Iowa Pork Producers Association and CIAG are appreciated.