Evaluation of Four US Pig Breeds Using the Affymetrix Axiom Pig HD Array

A new pig high-density DNA microarray has recently been developed, the Affymetrix Axiom PigHD (PigHD), which includes over 650,000 single nucleotide polymorphisms (SNPs). We have used the PigHD array to evaluate samples from four US pig breeds, and compared genotype calls on the PigHD to those on the Illumina PorcineSNP60 Beadchip (SNP60), for markers common to both arrays. A total of 90 Yorkshire, 34 Landrace, 22 Hampshire, and 31 Duroc pigs from the National Swine Registry were genotyped using the PigHD chip, with 62 of the Yorkshire animals having been previously genotyped with the SNP60 chip. Across all 177 animals, 465,277 SNPs (high quality SNPs) exhibit good cluster resolution and at least 2 examples of the minor allele. Principle component analysis was done using a genetic relationship matrix derived from these high quality SNPs for all 177 animals, showing clear differentiation between breeds. High quality SNPs were matched between the PigHD and SNP60 platforms if they were annotated with the same physical position. Using 30,941 matched SNPs for 62 animals genotyped on both platforms, we observe noticeable differences in estimated allele frequencies between platforms, with 136 SNPs showing evidence that dosages of a different allele are being counted between platforms, thereby reversing the allelic count for those loci. Continuing work to provide estimates of global (genome-wide) and local (around loci of interest) linkage disequilibrium patterns using the enhanced resolution provided by the PigHD platform are ongoing.