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Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

Animals : an open access journal from MDPI(2024)

Anhui Acad Agr Sci

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Abstract
Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.
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Key words
Wannan spotted pig,Asian wild boar,copy number variation,selection signatures,whole genome resequencing
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要点】:本研究通过全基因组测序技术对25头皖南花猪(Wannan Spotted Pigs,WSPs)进行拷贝数变异(CNV)检测,并与10头亚洲野猪进行对比,揭示了WSPs的CNV特征及选择信号,为猪的遗传特性研究提供了新见解。

方法】:利用全基因组测序数据,通过CNV检测和Fst指数分析,识别WSPs的CNV和选择信号。

实验】:对25头WSPs进行全基因组测序,共检测到14,161个CNVs,占猪基因组的0.72%。通过Fst指数分析,选出195个CNV具有最高的1% Fst值,并在这些CNV区域中鉴定出80个基因。通过GO和KEGG功能分析,发现这些基因与繁殖、脂肪酸组成、免疫系统、耳朵大小和饲料效率等关键性状相关。