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

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

Wei Zhang  1 , Mei Zhou  1 , Linqing Liu  1 , Shiguang Su  1 , Lin Dong  1 , Xinxin Meng  1 , Xueting Li  1 , Chonglong Wang  1
Affiliations

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

Wei Zhang et al. Genes (Basel). .

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
(A)The Venn diagram of CNVs between WBP and AWB. (B) The allele frequencies of variants in the WBP (n = 45). (C) The allele frequencies of variants in the AWB (n = 19).
Figure 2
Figure 2
(A) Neighbor-joining tree constructed from CNV data in study population. (B) PCA plots for the first two PCs for all 64 individuals, PC1 and PC2 explain 13.77% and 6.87% of the total variations, respectively. (C) Structure analysis on all the AWB and WBP with K = 2.
Figure 3
Figure 3
Identification of the selected CNVs in WBP with Fst. The red line represents the top 1% threshold.
Figure 4
Figure 4
The function analysis of the selected genes, (A) GO analysis of the selected genes, red referring to biological process, green referring to cellular component and blue referring to molecular function. (B) KEGG analysis of the selected genes, the size of dot refers to the number genes related to pathway, and the red to blue indicate the significant p-value change.
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