Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars.
Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars.
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拷贝数变异（Copy number variation，CNV）已被广泛用于研究不同物种的进化。为了了解野猪和家猪的遗传进化与生产性状的关系，我们首次在24头安庆柳白猪和6头亚洲野猪中发现了不同的CNV。共鉴定出97,489个CNV，分为10,429个拷贝数变异区（CNVRs），占猪基因组的32.06%。1号染色体CNVRs最多，18号染色体最少。基于所有CNVRs的签名，使用VST 1%选择96个CNVRs，并且在所选区域中鉴定出65个基因。通过基因本体论和京都基因和基因组途径百科全书的富集，这些基因与性状区分组强烈相关，例如生长（CD 36）、繁殖（CIT、RLN）、解毒（CYP 3A 29）和脂肪酸代谢（CYP 3VL 6）。QTL重叠区与肉质性状、生长和免疫力相关，与CNV分析结果一致。我们的发现增加了对野猪和家猪之间进化的基因组结构变异的理解，并提供了新的分子生物标志物来指导育种和有效利用现有的遗传资源。
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.
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