A genome-wide association scan in pig identifies novel regions associated with feed efficiency trait

Feed conversion ratio (FCR) is an economically important trait in pigs and feed accounts for a significant proportion of the costs involved in pig production. In this study we used a high density SNP chip panel, Porcine SNP60 BeadChip, to identify association between FCR and SNP markers and to study the genetic architecture of the trait. After quality control, a total of 30,847 SNPs that could be mapped to the 18 porcine autosomes (SSC) following the pig genome assembly 10.2, were used in the analyses. Deregressed estimated breeding value was used as the response variable. A total of 3,071 Duroc pigs had both FCR data and genotype data. The linkage disequilibrium (r2) between adjacent markers was 0.56. Two association mapping approaches were used: linear mixed model (LMM) based on single locus regression analysis and a Bayesian variable selection approach (BVS). A total of 79 significant (p < 0.0001) SNP associations on six chromosomes were identified by LMM analyses. Out of these, ten SNPs crossed the genome-wide significance threshold. These ten SNPs were all located on the chromosomes 4 and 14. In the BVS analysis, a total of 44 SNPs located on 12 chromosomes had posterior probability more than or equal to 0.05, i.e. Bayes factor ≥ 10. Thirteen SNPs were identified both by LMM and BVS. These 13 SNPs were located on four chromosomes 4, 7, 8 and 14. Hypoxia inducible factor 1, alpha subunit inhibitor (HIF1AN) and Ladybird homeobox 1 (LBX1) are two possible candidate genes affecting FCR on chromosomes 4 and 14, respectively. The study provides a list of SNPs associated with FCR and also offers valuable information on the genetic architecture and candidate genes for this trait