Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome-wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.

中文翻译：

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使用 80 K SNP Beadchip 检测和分析猪基因组中的全基因组拷贝数变异

拷贝数变异 (CNV) 是人类或动物基因组遗传变异的重要来源，在表型多样性和疾病易感性中起着关键作用。在本研究中，我们使用 857 头大白猪的 SNP 基因分型数据对 CNV 检测进行了全基因组分析。PennCNV算法共检测到312个CNV区域（CNVR），覆盖猪基因组的57.76 Mb，对应基因组序列的2.36%。常染色体上 CNVR 的长度从 1.77 Kb 到 1.76 Mb 不等，平均为 185.11 Kb。其中，220 个与 1,092 个注释基因完全或部分重叠，丰富了各种生物过程。与先前报道的猪 CNVR 的比较揭示了 92 (29.49%) 种新型 CNVR。实验上，80% 随机选择的 CNVR 通过定量 PCR (qPCR) 进行验证。我们还进行了一些 CNVR 与生殖性状之间的关联分析，结果表明 CNVR61 和 CNVR283 与窝产仔数相关的潜在重要性。值得注意的是，位于 CNVR61 中的 GPER1 基因在繁殖中起着关键作用。我们的研究是对猪基因组中 CNV 图的重要补充，并为研究基因组变异与经济性状之间的关联提供了有价值的信息。