Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs

Wei Zhang; Mei Zhou; Linqing Liu; Shiguang Su; Lin Dong; Xinxin Meng; Xueting Li; Chonglong Wang

doi:10.3390/genes13112026

Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs

Genes (Basel). 2022 Nov 3;13(11):2026. doi: 10.3390/genes13112026.

Authors

Wei Zhang¹, Mei Zhou¹, Linqing Liu¹, Shiguang Su¹, Lin Dong¹, Xinxin Meng¹, Xueting Li¹, Chonglong Wang¹

Affiliation

¹ Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China.

Abstract

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.

Keywords: Asian wild boar; Wannan black pig; copy number variation (CNV); fixation index (FST); selection signatures; whole genome resequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
China
DNA Copy Number Variations* / genetics
Domestication*
Genome
Sequence Analysis, DNA
Swine / genetics

Grants and funding

This work was supported by the grants from Anhui Academy of Agricultural Sciences Key Laboratory Project (No.2021YL023), Anhui Province Financial Fund for Modern Seed Industry Project, Anhui Province Natural Science Foundation Youth Fund Project (2108085QC135); the Special Fund for Anhui Agricultural Research System (AHCYJSTX-05-12, AHCYJSTX-05-23); the Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering Young Talents Support Engineering Innovation Guidance Fund (XMT2022-09); 2021 Science and Technology Planning Project of Huangshan City; The university synergy innovation program of Anhui province, GXXT-2021-055.