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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.18.0696    [Accepted] Published online February 7, 2019.
Identification of copy number variations using high density whole-genome SNP markers in Chinese Dongxiang spotted pigs
Chengbin Wang1, Hao Chen1, Xiaopeng Wang1, Zhongping Wu1, Weiwei Liu1, Yuanmei Guo1, Jun Ren1, Nengshui Ding1,*
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045 Nanchang, China
Correspondence:  Nengshui Ding, Tel: +86-791-83813080, Fax: +86-791-83900189, Email: 13631698@qq.com
Received: 12 September 2018   • Revised: 9 November 2018   • Accepted: 8 January 2019
Abstract
Objective: Copy number variations (CNVs) are a major source of genetic diversity complementary to single nucleotide polymorphism (SNP) in animals. The aim of the study was to performed a comprehensive genomic analysis of CNVs based on high density whole-genome SNP markers in Chinese Dongxiang spotted pigs.

Methods

We used customized Affymetrix Axiom Pig1.4M array plates containing 1.4 million SNPs and the PennCNV algorithm to identify porcine CNVs on autosomes in Chinese Dongxiang spotted pigs. Then, the next generation sequence data was used to confirm the detected CNVs. Next, functional analysis was performed for gene contents in copy number variation regions (CNVRs). In addition, we compared the identified CNVRs with those reported ones and quantitative trait loci (QTL) in the pig QTL database.

Results

We identified 871 putative CNVs belonging to 2,221 CNVRs on 17 autosomes. We further discarded CNVRs that were detected only in one individual, leaving us 166 CNVRs in total. The 166 CNVRs ranged from 2.89 kb to 617.53 kb with a mean value of 93.65 kb and a genome coverage of 15.55 Mb, corresponding to 0.58% of the pig genome. A total of 119 (71.69%) of the identified CNVRs were confirmed by next generation sequence data. Moreover, functional annotation showed that these CNVRs are involved in a variety of molecular functions. More than half (56.63%) of the CNVRs (n = 94) have been reported in previous studies, while 72 CNVRs are reported for the first time. In addition, 162 (97.59%) CNVRs were found to overlap with 2,765 previously reported QTLs affecting 378 phenotypic traits.
Conclusion
The findings improve the catalog of pig CNVs and provide insights and novel molecular markers for further genetic analyses of Chinese indigenous pigs.
Keywords: CNV; Pig1.4M Array Plate; Next Generation Sequence; Complex Traits; Chinese Indigenous Pigs
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