Wang Chengbin, Chen Hao, Wang Xiaopeng, Wu Zhongping, Liu Weiwei, Guo Yuanmei, Ren Jun, Ding Nengshui
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
Asian-Australas J Anim Sci. 2019 Dec 1;32(12):1809-1815. doi: 10.5713/ajas.18.0696. Epub 2019 Feb 7.
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.
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.
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.
The findings improve the catalog of pig CNVs and provide insights and novel molecular markers for further genetic analyses of Chinese indigenous pigs.
拷贝数变异（CNV）是动物遗传多样性的主要来源，是对单核苷酸多态性（SNP）的补充。本研究旨在基于高密度全基因组SNP标记对中国东乡花猪的CNV进行全面的基因组分析。
我们使用定制的包含140万个SNP的Affymetrix Axiom Pig1.4M基因芯片和PennCNV算法来鉴定中国东乡花猪常染色体上的猪CNV。然后，利用二代测序数据对检测到的CNV进行验证。接下来，对拷贝数变异区域（CNVR）中的基因内容进行功能分析。此外，我们将鉴定出的CNVR与先前报道的以及猪QTL数据库中的数量性状位点（QTL）进行了比较。
我们在17条常染色体上鉴定出871个推定的CNV，属于2221个CNVR。我们进一步剔除了仅在一个个体中检测到的CNVR，最终共得到166个CNVR。这166个CNVR的长度范围为2.89 kb至617.53 kb，平均值为93.65 kb，基因组覆盖度为15.55 Mb，占猪基因组的0.58%。二代测序数据证实了总共119个（71.69%）鉴定出的CNVR。此外，功能注释表明这些CNVR参与了多种分子功能。超过一半（56.63%）的CNVR（n = 94）在先前的研究中已有报道，而72个CNVR是首次报道。此外，发现162个（97.59%）CNVR与先前报道的影响378个表型性状的2765个QTL重叠。
这些发现完善了猪CNV的目录，并为中国地方猪种的进一步遗传分析提供了见解和新的分子标记。
