Determining Genomic Regions Associated with Intramuscular Fat in Duroc Pigs

Intramuscular fat (IMF) content is an important trait affecting the quality of pork and consumer acceptance. Two Duroc populations (Iowa and Spain) selected for IMF were used to identify genomic regions associated with IMF. The effects of selection were analyzed between selected and control animals within each population using principal component analysis, genome wide association (GWAS) tests and F_ST to determine selection signatures using the porcine 60k SNP chip. Associations of IMF and gene markers were considerably correlated with F_ST measures across the genome, which revealed more than 120 marker-trait associations that have been affected by considerable selection or possibly random genetic drift. To further examine the effect of recent artificial selection on IMF, extended haplotype homozygosity (EHH)-based approaches were applied to account for the changes in haplotype frequency that may have originated from influential ancestors. Out of 14 candidate regions defined by GWAS and F_ST,  a total of 8 regions overlapped with at least 1 signature of selection detected by an EHH-based method, suggesting that EHH has been changed by recent selection for IMF, especially in the Iowa based lines. The disagreement between results from GWAS and signatures of selection reflects that selection programs could influence a limited number of loci affecting the genetic variation of IMF. Identifying the regions involved in selection for IMF will be useful to confirm the loci associated with IMF and to exploit markers showing association with the traits due to selection and not random drift for the future breeding plans.