Validation of Whole Genome Association Analyses for Residual Feed Intake in the Pig

Residual feed intake (RFI) is defined as the difference between the amount of feed an animal consumes and the feed requirement for its growth and maintenance, with the most efficient pigs having negative RFI. Using Bayesian variable selection methods, a genomic association study for RFI had previously been performed using genotypes from the Porcine SNP60 beadChip on 730 animals from generations 0, 4, 5 and 6 from the ISU low RFI selection and control lines. That previous study reported genome regions on SSC2 having large effects on RFI. In this validation study, data from 312 additional animals from generations 4 and 7 of the ISU-RFI lines were combined with the earlier data, totaling 1,042 animals. With the same model as used in the earlier analyses, the combined data showed associations of RFI on SSC2 but in different genomic regions than the previous results. A region on SSC3 which had small effects in the previous analyses, showed the largest effects in the combined data. Furthermore, new regions on SSC4 and 9 now appear to be associated with RFI using this combined data. The difference between the previous and current results might be due to increased power from more animals or from an additional generation of selection. Excluding line from the model did not affect results for the important genomic regions on SSC2, 3, 4, and 9 but identified additional regions on SSC14, 15 and 17. These associated genomic regions will be confirmed by further statistical analyses.