Wang Ligang, Liu Xin, Zhang Longchao, Yan Hua, Luo Weizhen, Liang Jing, Cheng Duxue, Chen Shaokang, Ma Xiaojun, Song Xin, Zhao Kebin, Wang Lixian
Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
PLoS One. 2013 Oct 1;8(10):e74879. doi: 10.1371/journal.pone.0074879. eCollection 2013.
Copy number variations (CNVs) are one of the main contributors to genetic diversity in animals and are broadly distributed in the genomes of swine. Investigating the performance and evolutionary impacts of pig CNVs requires comprehensive knowledge of their structure and function within and between breeds. In the current study, 4 different programs (i.e., GADA, PennCNV, QuantiSNP, and cnvPartition) were used to analyze Porcine SNP60 genotyping data of 585 pigs from one Large White × Minzhu intercross population to detect copy number variant regions (CNVRs). Overlapping CNVRs recalled by at least 2 programs were used to construct a powerful and comprehensive CNVR map, which contained 249 CNVRs (i.e., 70 gains, 43 losses, and 136 gains/losses) and covered 26.22% of the regions in the swine genome. Ten CNVRs, representing different predicted statuses, were selected for validation via quantitative real-time PCR (QPCR); 9/10 CNVRs (i.e., 90%) were validated. When being traced back to the F0 generation, 58 events were identified in only Minzhu F0 parents and 2 events were identified in only Large White F0 parents. A series of CNVR function analyses were performed. Some of the CNVRs functions were predicted, and several interesting CNVRs for meat quality traits and hematological parameters were obtained. A comprehensive and lower false rate genome-wide CNV map was constructed for Large White and Minzhu pig genomes in this study. Our results may provide an important basis for determining the relationship between CNVRs and important qualitative and quantitative traits. In addition, it can help to further understand genetic processes in pigs.
拷贝数变异（CNV）是动物遗传多样性的主要贡献因素之一，广泛分布于猪的基因组中。研究猪CNV的性能和进化影响需要全面了解其在品种内和品种间的结构和功能。在本研究中，使用4种不同的程序（即GADA、PennCNV、QuantiSNP和cnvPartition）分析了一个大白猪×民猪杂交群体中585头猪的Porcine SNP60基因分型数据，以检测拷贝数变异区域（CNVR）。至少由2个程序召回的重叠CNVR用于构建一个强大而全面的CNVR图谱，该图谱包含249个CNVR（即70个增加、43个缺失和136个增减），覆盖了猪基因组中26.22%的区域。选择了代表不同预测状态的10个CNVR通过定量实时PCR（QPCR）进行验证；10个CNVR中有9个（即90%）得到了验证。追溯到F0代时，仅在民猪F0亲本中鉴定出58个事件，仅在大白猪F0亲本中鉴定出2个事件。进行了一系列CNVR功能分析。预测了一些CNVR的功能，并获得了几个与肉质性状和血液学参数相关的有趣CNVR。本研究为大白猪和民猪基因组构建了一个全面且错误率较低的全基因组CNV图谱。我们 的结果可能为确定CNVR与重要质量和数量性状之间的关系提供重要依据。此外，它有助于进一步了解猪的遗传过程。
