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Copy number variants selected during pig domestication inferred from whole genome resequencing

文献类型： 外文期刊

作者： Zhang, Wei 1 ; Xu, Chengliang 1 ; Zhou, Mei 1 ; Liu, Linqing 1 ; Ni, Zelan 2 ; Su, Shiguang 1 ; Wang, Chonglong 1 ;

作者机构： 1.Anhui Acad Agr Sci, Inst Anim Husb & Vet Med, Anhui Prov Breeding Pig Genet Evaluat Ctr, Key Lab Pig Mol Quantitat Genet,Anhui Prov Key Lab, Hefei, Peoples R China

2.Anhui Prov Livestock & Poultry Genet Resources Con, Hefei, Peoples R China

关键词： Wanbei pig; Asian wild boar; copy number variation (CNV); selection signature; whole genome resequencing

期刊名称：FRONTIERS IN VETERINARY SCIENCE （ 影响因子：3.2； 五年影响因子：3.5 ）

ISSN：

年卷期： 2024 年 11 卷

页码：

收录情况： SCI

摘要： Over extended periods of natural and artificial selection, China has developed numerous exceptional pig breeds. Deciphering the germplasm characteristics of these breeds is crucial for their preservation and utilization. While many studies have employed single nucleotide polymorphism (SNP) analysis to investigate the local pig germplasm characteristics, copy number variation (CNV), another significant type of genetic variation, has been less explored in understanding pig resources. In this study, we examined the CNVs of 18 Wanbei pigs (WBP) using whole genome resequencing data with an average depth of 12.61. We identified a total of 8,783 CNVs (similar to 30.07 Mb, 1.20% of the pig genome) in WBP, including 8,427 deletions and 356 duplications. Utilizing fixation index (Fst), we determined that 164 CNVs were within the top 1% of the Fst value and defined as under selection. Functional enrichment analyses of the genes associated with these selected CNVs revealed genes linked to reproduction (SPATA6, CFAP43, CFTR, BPTF), growth and development (NR6A1, SMYD3, VIPR2), and immunity (PARD3, FYB2). This study enhances our understanding of the genomic characteristics of the Wanbei pig and offers a theoretical foundation for the future breeding of this breed.

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