Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine

Citations Over TimeTop 11% of 2015 papers

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.

Related Papers

• → Gene and pathway-based second-wave analysis of genome-wide association studies(2009)240 cited
• → Lessons and implications from association studies and post-GWAS analyses of cervical cancer(2014)59 cited
• → The first broad replication study of SNPs and a pilot genome‐wide association study for androgenetic alopecia in Asian populations(2022)12 cited
• → Genome-wide association studies in aging-related processes such as diabetes mellitus, atherosclerosis and cancer(2007)43 cited
• → GWAS summary-based pathway analysis correcting for the genetic confounding impact of environmental exposures(2017)4 cited