Abstract
Pork quality is important both to the meat processing industry and consumers’ purchasing attitude. Copy number variation (CNV) is a burgeoning kind of variants that may influence meat quality. In this study, a genome-wide association study (GWAS) was performed between CNVs and meat quality traits in swine. After false discovery rate (FDR) correction, a total of 8 CNVs on 6 chromosomes were identified to be significantly associated with at least one meat quality trait. All of the 8 CNVs were verified by next generation sequencing and six of them were verified by qPCR. Only the haplotype block containing CNV12 is adjacent to significant SNPs associated with meat quality, suggesting the effects of those CNVs were not likely captured by tag SNPs. The DNA dosage and EST expression of CNV12, which overlap with an obesity related gene Netrin-1 (Ntn1), were consistent with Ntn1 RNA expression, suggesting the CNV12 might be involved in the expression regulation of Ntn1 and finally influence meat quality. We concluded that CNVs may contribute to the genetic variations of meat quality beyond SNPs, and several candidate CNVs were worth further exploration.
Highlights
Significant SNPs associated with meat quality traits, these SNPs explain a small portion of the genetic variance[2,4]
We identified a total of 8 Copy number variations (CNVs) that were significantly associated with at least one trait using a linear regression model (Fig. 1 & S1 and Table 2)
Our results revealed a relatively lower CNV tagging rate comparing to cattle study[13], this finding may be due to the limited sample size for common CNVs detection in CNV analysis
Summary
Significant SNPs associated with meat quality traits, these SNPs explain a small portion of the genetic variance[2,4]. Alternative variances, which could explain the “missing heritability” of meat quality traits, were urgently needed[14]. The intercross of Min × Large-white is a good model to analyze the genetics of meat quality[2]. The objective of this work was to perform systematic CNV association analysis with meat quality traits using the Porcine SNP60 Genotyping BeadChip (Illumina, San Diego, CA, USA), analyze the joint or independent effects of CNVs and SNPs, and provide some helpful information to identify genetic markers that may be suitable for inclusion in genetic improvement program
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