Porcine single nucleotide polymorphisms and their functional effect: an update

Authors: Keel, Brittney; Nonneman, Danny - Dan; Lindholm-Perry, Amanda; Oliver, William; Rohrer, Gary

Submitted to: BMC Research Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2018
Publication Date: 12/4/2018
Citation: Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. 2018. Porcine single nucleotide polymorphisms and their functional effect: an update. BMC Research Notes. 11:860. https://doi.org/10.1186/s13104-018-3973-6.
DOI: https://doi.org/10.1186/s13104-018-3973-6

Interpretive Summary: 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 resistance/susceptibility, and product quality. In order to understand the basis by which variation in DNA is associated with a particular phenotype, it is necessary to know whether that variant is functional, i.e. whether it alters the function of a gene or set of genes. ARS scientists have sequenced the genomes of 181 members of a heavily phenotyped experimental herd of swine and identified approximately 21 million variants. By utilizing the new and improved swine genome annotation, researchers found that only ~275,000 of these variants were expected to alter or disrupt the protein coded by a gene and or to regulate protein production. These are the variants that are likely to have a more significant effect on phenotypic variation and will be the focus of future analyses which will evaluate their effect on various performance traits. This work is the first step in identifying functional genetic markers that influence economically relevant traits in swine. Continued examination of these variants is expected to lead to the development of panels of functional genetic markers that will allow swine producers and breeders to be able to make more rapid genetic progress by including them into their selection decisions.

Technical Abstract: Objective: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was published in 2017. This communication extends our previous work not only by utilizing genomic sequence from additional animals, but also by the use of the newly released Sscrofa 11.1 reference genome. Results: A total of 26,850,263 high confidence SNP were identified, including 19,015,267 reported in our previously published results. Variation was detected in the coding sequence or untranslated regions (UTR) of 78% of the genes in the porcine genome: 1729 loss-of-function variants were predicted in 1162 genes, 12,686 genes contained 64,232 nonsynonymous variants, 250,403 variants were present in UTR of 15,739 genes, and 15,284 genes contained 90,939 synonymous variants. In total, approximately 316,000 SNP were classified as being of high to moderate impact (i.e. loss-of-function, nonsynonymous, or regulatory). These high to moderate impact SNP will be the focus of future genome-wide association studies.