A Survey of Single Nucleotide Polymorphisms Identified from Whole-Genome Sequencing and Their Functional Effect in the Porcine Genome

One of the key aims of livestock genetics and genomics research is to discover the genetic variants underlying economically important traits such as reproductive performance, feed efficiency, disease susceptibility, and product quality. Next generation sequencing has recently emerged as an economically feasible tool for assessing genomic variation among populations. Sequence variants, in contrast to currently used commercial SNP panels, are expected to allow direct estimation of the effects of causal mutations on a given trait, which could significantly boost the reliability of genomic predictions. Utilization of genome annotations may help in identifying SNPs that are more likely to affect the phenotype. Loss-of-function variants and others that disrupt or alter proteins coded by a gene, as well as variants that regulate protein production, likely have a greater effect on phenotype than other types of variation. Hence, narrowing our focus to these high impact variants may allow us to explain a significant amount of phenotypic variation, while reducing the number of SNPs that need to be analyzed. The objectives of this study were to identify SNPs from DNA sequence of 72 founders (12 Landrace boars, 12 Duroc boars, and 48 Yorkshire-Landrace composite sows) of a heavily phenotyped experimental swine herd at the U.S. Meat Animal Research Center and to predict the effects of these variants on gene function. Approximately 14 billion reads were generated by short-read sequencing on the Illumina HiSeq and NextSeq platforms. Sequence reads covered each pig’s genome at a mean of 6.1 fold (x) coverage. Individual coverage per animal ranged from 1.15x to 21.11x. We identified a total of 22,342,915 SNPs from the 72 sequenced genomes, of which 38% were listed in the National Center for Biotechnology Information genetic variation database (dbSNP), and a total of 49,105 overlapped with the 62,163 SNPs assayed by the PorcineSNP60 BeadChip. Variation was detected in coding sequence or untranslated regions (UTRs) of 18,753 of the 25,322 protein-coding genes annotated in the swine genome. A total of 162,000 SNPs were classified as high impact, which suggests that over 99% of the variation detected in our pigs could potentially be ignored, allowing us to focus on a much smaller number of SNPs during future analyses. Future work, including additional sequencing to impute sequence variants through our population and developing assays to directly genotype sequence variants, will aim to discover the extent to which these high impact variants affect economically important traits.