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

<div><p>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., <i>CLCA4</i>, <i>CYP4X1</i>, <i>GPAT2</i>, <i>MOGAT2</i>, <i>PLA2G2A</i> and <i>PRKG1</i>, among others). The variation in copy number of four of them (<i>CLCA4</i>, <i>GPAT2</i>, <i>MOGAT2</i> and <i>PRKG1</i>) 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 (<i>GPAT2</i>) 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.</p></div

Additive effect and p-value of the SNPs representing the top trio of transcription factors.

<p>Additive effect and p-value of the SNPs representing the top trio of transcription factors.</p

Co-association networks based on the AWM approach.

<p><b>A</b>) Full network formed by 1,747 nodes, representing genes and SNPs, and a total of 316,166 edges, accounting for the interactions among them. <b>B</b>) Network formed by 513 nodes and 639 edges representing genes and interactions among the top trio of transcription factors. Colours corresponded to different functions according to the legend.</p

Phenotypic traits registered in the BC1_LD (F1× Landrace) and in the BC (F2× Landrace) and F3 generations of the Iberian × Landrace cross.

<p>Phenotypic traits registered in the BC1_LD (F1× Landrace) and in the BC (F2× Landrace) and F3 generations of the Iberian × Landrace cross.</p