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

文献类型： 外文期刊

第一作者： Zhang, Wei

作者： Zhang, Wei;Zhou, Mei;Liu, Linqing;Li, Xiaoyu;Su, Shiguang;Wang, Chonglong;Jiang, Yao;Ni, Zelan

作者机构：

关键词： Wannan spotted pig; Asian wild boar; copy number variation; selection signatures; whole genome resequencing

期刊名称：ANIMALS （ 影响因子：3.0； 五年影响因子：3.2 ）

ISSN： 2076-2615

年卷期： 2024 年 14 卷 10 期

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收录情况： SCI

摘要： Simple Summary The aim of this study was to detect the copy number variations in 25 Wannan spotted pigs and 10 Asian wild boars with whole genome sequencing data. The selection signatures of Wannan spotted pigs compared to those of Asian wild boars were calculated with fixation index (Fst). A total of 195 selected CNVs were under selected, harboring 80 genes. The selected genes were associated with reproduction, fatty acid composition, immune system, ear size, and feed efficiency. This study provides a new insight for understanding the characteristics of Wannan spotted pigs based on copy number variations.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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