Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
BMC Genomics. 2012 Jun 22;13:273. doi: 10.1186/1471-2164-13-273.
Copy Number Variations (CNVs) have been shown important in both normal phenotypic variability and disease susceptibility, and are increasingly accepted as another important source of genetic variation complementary to single nucleotide polymorphism (SNP). Comprehensive identification and cataloging of pig CNVs would be of benefit to the functional analyses of genome variation.
In this study, we performed a genome-wide CNV detection based on the Porcine SNP60 genotyping data of 474 pigs from three pure breed populations (Yorkshire, Landrace and Songliao Black) and one Duroc × Erhualian crossbred population. A total of 382 CNV regions (CNVRs) across genome were identified, which cover 95.76Mb of the pig genome and correspond to 4.23% of the autosomal genome sequence. The length of these CNVRs ranged from 5.03 to 2,702.7kb with an average of 250.7kb, and the frequencies of them varied from 0.42 to 20.87%. These CNVRs contains 1468 annotated genes, which possess a great variety of molecular functions, making them a promising resource for exploring the genetic basis of phenotypic variation within and among breeds. To confirmation of these findings, 18 CNVRs representing different predicted status and frequencies were chosen for validation via quantitative real time PCR (qPCR). Accordingly, 12 (66.67%) of them was successfully confirmed.
Our results demonstrated that currently available Porcine SNP60 BeadChip can be used to capture CNVs efficiently. Our study firstly provides a comprehensive map of copy number variation in the pig genome, which would be of help for understanding the pig genome and provide preliminary foundation for investigating the association between various phenotypes and CNVs.
拷贝数变异 (CNVs) 已被证明在表型变异性和疾病易感性方面都很重要，并且越来越被认为是与单核苷酸多态性 (SNP) 互补的另一种重要遗传变异来源。全面鉴定和编目猪 CNVs 将有助于对基因组变异的功能分析。
在这项研究中，我们基于来自三个纯种种群（约克夏、长白和松辽黑）和一个杜洛克×二花脸杂交种群的 474 头猪的 Porcine SNP60 基因分型数据进行了全基因组 CNV 检测。总共鉴定了 382 个基因组范围内的 CNV 区域（CNVRs），这些区域覆盖了猪基因组的 95.76Mb，相当于常染色体基因组序列的 4.23%。这些 CNVRs 的长度从 5.03kb 到 2702.7kb 不等，平均长度为 250.7kb，频率从 0.42%到 20.87%不等。这些 CNVRs 包含 1468 个注释基因，具有多种分子功能，是探索品种内和品种间表型变异遗传基础的有前途的资源。为了验证这些发现，选择了 18 个具有不同预测状态和频率的 CNVR 进行定量实时 PCR (qPCR) 验证。相应地，其中 12 个（66.67%）得到了成功验证。
我们的结果表明，目前可用的 Porcine SNP60 BeadChip 可有效地捕获 CNVs。我们的研究首次提供了猪基因组中拷贝数变异的全面图谱，这将有助于理解猪基因组，并为研究各种表型与 CNVs 之间的关系提供初步基础。
