A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits

• Published in: PloS one Vol. 12; no. 5; p. e0177014
• Main Authors: Revilla, Manuel, Puig-Oliveras, Anna, Castelló, Anna, Crespo-Piazuelo, Daniel, Paludo, Ediane, Fernández, Ana I., Ballester, Maria, Folch, Josep M.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.05.2017; Public Library of Science (PLoS)
• Subjects: Animals; Association analysis; Biology and Life Sciences; Biomarkers; Biosynthesis; Chloride channels (calcium-gated); Composition; Copy number; Copy number variations; Data processing; DNA Copy Number Variations; DNA sequencing; Domestic animals; Economic importance; Enzymes; Fatty acid composition; Fatty acids; Fatty Acids - metabolism; Gene expression; Genes; Genetic diversity; Genetic variance; Genome; Genomes; Genomic analysis; Genomics; Growth; Hogs; Kinases; Livestock; Meat quality; Medicine and Health Sciences; Nucleotide sequence; Physiological aspects; Population studies; Real-Time Polymerase Chain Reaction; Research and Analysis Methods; Single-nucleotide polymorphism; Statistical analysis; Statistical methods; Swine; Swine - genetics; Swine - growth & development; Swine - metabolism; Triglycerides; Spain
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0177014

Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace backcross population and study their association with fatty acid composition and growth-related traits. A total of 1,279 CNVs, including duplications and deletions, were detected, ranging from 106 to 235 CNVs across samples, with an average of 183 CNVs per sample. Moreover, we detected 540 CNV regions (CNVRs) containing 245 genes. Functional annotation suggested that these genes possess a great variety of molecular functions and may play a role in production traits in commercial breeds. Some of the identified CNVRs contained relevant functional genes (e.g., CLCA4, CYP4X1, GPAT2, MOGAT2, PLA2G2A and PRKG1, among others). The variation in copy number of four of them (CLCA4, GPAT2, MOGAT2 and PRKG1) was validated in 150 BC1_LD (25% Iberian and 75% Landrace) animals by qPCR. Additionally, their contribution regarding backfat and intramuscular fatty acid composition and growth-related traits was analyzed. Statistically significant associations were obtained for CNVR112 (GPAT2) for the C18:2(n-6)/C18:3(n-3) ratio in backfat and carcass length, among others. Notably, GPATs are enzymes that catalyze the first step in the biosynthesis of both triglycerides and glycerophospholipids, suggesting that this CNVR may contribute to genetic variation in fatty acid composition and growth traits. These findings provide useful genomic information to facilitate the further identification of trait-related CNVRs affecting economically important traits in pigs.