Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs
文献类型： 外文期刊
作者： Zhang, Wei 1 ; Zhou, Mei 1 ; Liu, Linqing 1 ; Su, Shiguang 1 ; Dong, Lin 1 ; Meng, Xinxin 1 ; Li, Xueting 1 ; Wang, Chonglong 1 ;
作者机构： 1.Anhui Acad Agr Sci, Inst Anim Husb & Vet Med, Anhui Prov Key Lab Livestock & Poultry Prod Safet, Key Lab Pig Mol Quantitat Genet, Hefei 230031, Peoples R China
关键词： Wannan black pig; Asian wild boar; copy number variation (CNV); selection signatures; fixation index (F-ST); whole genome resequencing
期刊名称：GENES （ 影响因子：4.141； 五年影响因子：4.474 ）
ISSN：
年卷期： 2022 年 13 卷 11 期
页码：
收录情况： SCI
摘要： Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related (NDN, TMOD4, SFRP1, and SMYD3), reproduction related (GJA1, CYP26B1, WNT5A, SRD5A2, PTPN11, SPEF2, and CCNB1), residual feed intake (RFI) related (MAP3K5), and ear size related (WIF1). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig.
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