Survey of SNPs in Pig Immune Genes by Exome Enrichment

It is conceivable that many immune and disease-related traits are associated with polymorphisms (SNPs, insertions/deletions and CNVs) in immune genes. Detection of polymorphisms in pig immune genes conferring an advantage to disease resistance is beneficial to breeding aiming at disease resistance of pigs and improvement of livestock productivity. We conducted comprehensive exploration of polymorphisms of immune genes in pigs of four breeds (Landrace, Large White, Duroc and Berkshire), which are representative in Japanese livestock, by exome enrichment and sequencing using a next-generation sequencer. We extracted 760 immunity-related genes that had description of exon-intron structure in the pig genome assembly Sscrofa10.1 in GenBank and designed 120-mer “baits” to enrich exonic sequences of the CDS of the extracted immune genes. Equal amounts of genomic DNA of eight animals derived from each breed were mixed and DNA corresponding to the CDS of the immune genes was concentrated. Paired-end sequencing of the concentrated genomic DNA by an Illumina GAIIx sequencer and mapping of the sequencing reads thus obtained on the latest pig genome assembly Sscrofa10.2 showed 500 to 1300 reliable (≥ 30× read depth) polymorphisms in the CDS of the immune genes among the animals in each breed. The sum of the polymorphisms among all of the animals thus sequenced was approximately 2300. The polymorphisms detected here will be valuable resources to investigate association between immune-related traits and particular genomic regions in pigs.