title: Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine.
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.
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Ligang
authors.initials: L
authors.lastname: Wang
authors.affiliation: 1] Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China [2] Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Zhang
authors.affiliation: 1] Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China [2] Jilin Academy of Agricultural Sciences, Changchun 130033, China.
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: El Hamidi
authors.initials: el H
authors.lastname: Hay
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Yuebo
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Yan
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Kebin
authors.initials: K
authors.lastname: Zhao
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Longchao
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Lixian
authors.initials: L
authors.lastname: Wang
mesh_terms: D000818:Animals; D056915:DNA Copy Number Variations; D020224:Expressed Sequence Tags; D063427:Food Quality; D055106:Genome-Wide Association Study; D006239:Haplotypes; D008460:Meat; D009414:Nerve Growth Factors / Q000235:genetics; D000075388:Netrin-1; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D009414:Nerve Growth Factors; D025521:Tumor Suppressor Proteins; D000075388:Netrin-1