College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230036, China.
Genes (Basel). 2023 Feb 12;14(2):472. doi: 10.3390/genes14020472.
Copy number variation (CNV) has been widely used to study the evolution of different species. We first discovered different CNVs in 24 Anqingliubai pigs and 6 Asian wild boars using next-generation sequencing at the whole-genome level with 10× depth to understand the relationship between genetic evolution and production traits in wild boars and domestic pigs. A total of 97,489 CNVs were identified and divided into 10,429 copy number variation regions (CNVRs), occupying 32.06% of the porcine genome. Chromosome 1 had the most CNVRs, and chromosome 18 had the least. Ninety-six CNVRs were selected using VST 1% based on the signatures of all CNVRs, and sixty-five genes were identified in the selected regions. These genes were strongly correlated with traits distinguishing groups by enrichment in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways, such as growth (CD36), reproduction (CIT, RLN), detoxification (CYP3A29), and fatty acid metabolism (ELOVL6). The QTL overlapping regions were associated with meat traits, growth, and immunity, which was consistent with CNV analysis. Our findings increase the understanding of evolved genome structural variations between wild boars and domestic pigs, and provide new molecular biomarkers to guide breeding and the efficient use of available genetic resources.
拷贝数变异（CNV）已被广泛用于研究不同物种的进化。我们首次使用 10×深度的全基因组下一代测序技术，在 24 头安庆六白猪和 6 头亚洲野猪中发现了不同的 CNV，以了解野猪和家猪的遗传进化与生产性状之间的关系。总共鉴定出 97489 个 CNV，并将其分为 10429 个拷贝数变异区（CNVR），占猪基因组的 32.06%。染色体 1 上的 CNVR 最多，染色体 18 上的 CNVR 最少。根据所有 CNVR 的特征，使用 VST 1%选择了 96 个 CNVR，并在选定区域中鉴定出 65 个基因。这些基因与区分组群的特征密切相关，如生长（CD36）、繁殖（CIT、RLN）、解毒（CYP3A29）和脂肪酸代谢（ELOVL6）。与肉质性状、生长和免疫相关的 QTL 重叠区域与 CNV 分析一致。我们的研究结果增加了对野猪和家猪之间进化基因组结构变异的理解，并提供了新的分子生物标志物，以指导繁殖和有效利用现有遗传资源。
