Discovery of 14.6 Million SNP in a Mixed Breed Swine Population

The USMARC has developed, and extensively phenotyped, a population of swine that was created by crossing 24 founding boars, 12 each of the Duroc and Landrace breeds with Landrace/Yorkshire sows. Four to six hundred litters of pigs were produced yearly for 10 years. Recent advances in genomics have allowed the genotyping of this population to become commensurate to the phenotyping. The Illumina PorcineSNP60 beadchip was run on 2976 of these animals. To improve the density of markers, 72 animals were chosen for whole genome sequencing with an Illumina HiSeq, yielding paired-end 2x100bp reads. The reads were mapped to build 10.2 of the swine genome resulting in a total of 40X coverage for the Duroc boars, 35X for the Landrace boars and 127X for the 48 sows. Alternate alleles that were observed at least twice on each strand were collected for a total of 14,606,666 SNP. This resource provides the opportunity for imputation and identification of functional alleles for trait associations in this population.

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