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




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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 C18:2n-6-C18:3n-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.



Author: Manuel Revilla , Anna Puig-Oliveras, Anna Castelló, Daniel Crespo-Piazuelo, Ediane Paludo, Ana I. Fernández, Maria Ballester, J

Source: http://plos.srce.hr/



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