Genome wide association analysis for residual feed intake in Danish Duroc boars

This aim of this study was to identify genomic regions controlling feed efficiency defined by 2 estimated residual feed intake (RFI) measures in Danish Duroc boars. RFI1 was calculated based on regression of individual average daily feed intake (30-100 kg) on initial test weight and average daily gain (30-100 kg). RFI2 was the same as RFI1 except that it was also regressed on backfat (BF). A total of 868 boars had phenotypic and genotype (i.e. Illumina Porcine SNP60 BeadChip) records. A total of 33945 SNPs were available for genome wide association studies (GWAS) after quality control. Deregressed EBVs were used as response variables in GWAS implemented in the R-GenABEL package. A total of 16 and 17 loci were significantly associated (p < 5×10-4) with RFI1 and RFI2, respectively. 12 SNPs were in common implying the existence of common genetic mechanisms. A mutation (A/G) at locus ALGA0098358 on CPVL gene on SSC18 was highly associated with both RFI1 (p = 1.8×10-4) and RFI2 (p = 4.5×10-5). Moreover, the genomic region 30.5-31.5Mb on SSC1 contained high numbers of significant SNPs (8 loci) for both RFIs. The SNPs within region of MAP3K5 on SSC1, GTF2IRD2 on SSC3, and WDR70 on SSC16 may be interesting markers for both RFIs. The ANKRD6 on SSC1, CADM1 on SSC9 and RHBDD1 on SSC15 were distinct markers for each RFI1 and RFI2, respectively. Further systems genetics investigations were carried out to reveal functional importance of genes and haplotypes on candidate chromosomes with high numbers of significant SNPs. This study enhanced our biological knowledge of the genes and variants controlling RFIs and might contribute to genetic improvement for feed efficiency traits in pigs