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Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds
Author(s) -
Dong K.,
Pu Y.,
Yao N.,
Shu G.,
Liu X.,
He X.,
Zhao Q.,
Guan W.,
Ma Y.
Publication year - 2015
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12247
Subject(s) - biology , copy number variation , genotyping , genetics , quantitative trait locus , snp genotyping , snp array , genome , gene , structural variation , snp , human genome , single nucleotide polymorphism , computational biology , genotype
Summary We performed genome‐wide CNV detection based on SNP genotyping data of 96 Chinese‐native Tibetan, Dahe and Wuzhishan pigs. These pigs are particularly interesting because of their excellent adaptation to hypoxia or small body size, which facilitates the use of them as models of different human diseases in addition to valuable agricultural animals. A total of 105 CNV regions ( CNVR s) were identified, encompassing 16.71 Mb of the pig genome. Seven of 10 (70%) CNVR s selected randomly were validated by quantitative real‐time PCR . Comparison with previous studies revealed 25 (23.81%) novel CNVR s, indicating that CNV coverage of the pig genome is still incomplete and there exists large diversity between pig breeds. Functional analysis of genes located in these CNVR s confirmed the high representation of genes involved in sensory perception, neurological system processes and other basic metabolic processes. In addition, the majority of these CNVR s were detected to span reported pig QTL that affect various traits, which highlighted three biologically interesting genes with copy number changes ( i.e ., ANKRD 34B , FAM 110B and ABCG 1 ). These genes may have economic importance in pig breeding and are worth being further investigated. We also obtained some CNVR s harboring genes that had human orthologs involved in human diseases such as cardiovascular disease and Alzheimer's disease. The findings of this study are a significant extension of the coverage of CNVR s in the pig genome and provide valuable resources for follow‐up‐associated studies of CNV s in pig complex traits as well as important implications of human diseases.