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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #360176

Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

Title: Cataloguing genetic variants in commercial swine

item Keel, Brittney
item Nonneman, Danny - Dan
item Rohrer, Gary

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/19/2018
Publication Date: 1/16/2019
Citation: Keel, B.N., Nonneman, D.J., Rohrer, G.A. 2019. Cataloguing genetic variants in commercial swine [abstract]. In: Plant & Animal Genome Conference Proceedings XXVII, 12-16 January 2019, San Diego, CA. pg. 216. W1046. Available:

Interpretive Summary:

Technical Abstract: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) and copy number variations (CNV) were identified from whole genome sequence of 240 pigs. In this work, we utilized whole genome sequence from 240 members of a heavily phenotyped swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the founding boars (12 Duroc and 12 Landrace), 48 of the founding Yorkshire-Landrace composite sows, 109 composite animals from generations 4 through 9, 29 composite animals from generation 15, and 30 purebred industry boars (15 Landrace and 15 Yorkshire) used as sires in generations 10 through 15. Sequence reads were mapped to Sscrofa 11.1 reference genome. A total of 26,850,263 high confidence SNP and 3,716 copy number variable regions (CNVR) were identified. Variation was detected in the coding sequence or untranslated regions (UTR) of 78% of the genes in the porcine genome: 1,729 loss-of-function variants were predicted in 1,162 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. CNVR covered 0.94% of the porcine genome and overlapped 1,442 genes. The Gene ontology analysis identified that CNV genes were enriched for functions related to neurophysiological processing of environmental stimuli, including sensory perception, signal transduction, and olfactory receptor activity, as well as many functions related to organism development. Many of these genetic variants (SNP and CNV) are expected to alter protein production and likely contribute to phenotypic variation in economically important traits.