Abstract
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.
Highlights
The pig (Sus scrofa) is one of the most economically important livestock animals worldwide, and one of the main sources of animal meat for humans
The overall profile of these Copy number variations (CNVs) across the genome for each individual is detailed in S2 Table.All detected CNV segments were further merged into 540 unique CNV regions (CNVRs) (S3 Table) across all experimental animal genomes following the criteria that the union of overlapping CNVs across individuals is considered as a CNVR [1]
We have described a map of swine CNVRs based on whole genome sequence (WGS) data
Summary
The pig (Sus scrofa) is one of the most economically important livestock animals worldwide, and one of the main sources of animal meat for humans. Several studies on CNVs showed association with Mendelian diseases and complex genetic disorders, such as schizophrenia [4], cancer [5,6], and various congenital defects [7]. CNVs have been associated with several phenotypes such as coat color [8], backfat (BF) thickness [3] and meat quality [9], demonstrating that CNVs can be considered as promising biomarkers for some economically important traits in domestic animals. Pork quality is important to the meat-processing industry, a higher IMF content and a better FA profile, while maintaining a reduced amount of BF, is a main selection objective [11,12]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
