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. 2022 Jun 30:9:909039.
doi: 10.3389/fvets.2022.909039. eCollection 2022.

Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs

Chunlei Zhang  1 , Jing Zhao  1 , Yanli Guo  1 , Qinglei Xu  1 , Mingzheng Liu  1 , Meng Cheng  1 , Xiaohuan Chao  1 , Allan P Schinckel  2 , Bo Zhou  1
Affiliations

Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs

Chunlei Zhang et al. Front Vet Sci. .

Abstract

Copy number variation (CNV) has been considered to be an important source of genetic variation for important phenotypic traits of livestock. In this study, we performed whole-genome CNV detection on Suhuai (SH) (n = 23), Chinese Min Zhu (MZ) (n = 11), and Large White (LW) (n = 12) pigs based on next-generation sequencing data. The copy number variation regions (CNVRs) were annotated and analyzed, and 10,885, 10,836, and 10,917 CNVRs were detected in LW, MZ, and SH pigs, respectively. Some CNVRs have been randomly selected for verification of the variation type by real-time PCR. We found that SH and LW pigs are closely related, while MZ pigs are distantly related to the SH and LW pigs by CNVR-based genetic structure, PCA, VST, and QTL analyses. A total of 14 known genes annotated in CNVRs were unique for LW pigs. Among them, the cyclin T2 (CCNT2) is involved in cell proliferation and the cell cycle. The FA Complementation Group M (FANCM) is involved in defective DNA repair and reproductive cell development. Ten known genes annotated in 47 CNVRs were unique for MZ pigs. The genes included glycerol-3-phosphate acyltransferase 3 (GPAT3) is involved in fat synthesis and is essential to forming the glycerol triphosphate. Glutathione S-transferase mu 4 (GSTM4) gene plays an important role in detoxification. Eleven known genes annotated in 23 CNVRs were unique for SH pigs. Neuroligin 4 X-linked (NLGN4X) and Neuroligin 4 Y-linked (NLGN4Y) are involved with nerve disorders and nerve signal transmission. IgLON family member 5 (IGLON5) is related to autoimmunity and neural activities. The unique characteristics of LW, MZ, and SH pigs are related to these genes with CNV polymorphisms. These findings provide important information for the identification of candidate genes in the molecular breeding of pigs.

Keywords: crossbreeding; economic traits; evolution; genetic structure analysis; livestock.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The genome distribution of CNVRs and variation types of LW (A), MZ (B), and SH (C) pigs. The legend of “Low” to “High” indicates the gene density on the pig chromosomes. The yellow square represents the both type, the green circle represents the gain type, and the purple triangle represents the loss type.
Figure 2
Figure 2
(A) PCA plot of LW, MZ, and SH pigs. Red, green, and blue represent LW, MZ, and SH pigs, respectively. (B) Diagram of genetic structure analysis, the K value represents the number of the hypothetical ancestor. When the ancestral population number K = 2, there are obvious differences between LW and MZ pigs, while the information of SH pigs is covered by LW pigs, green and red represent LW and MZ pigs, respectively. When K = 3, the three pig breeds are well separated. Green, red, and blue represent LW, SH, and MZ pigs, respectively. (C) Evolutionary tree diagram of LW, SH, and MZ pigs. The location of SH pigs is closer to the root, moreover, the genetic distance between SH and LW pigs is less than SH and MZ pigs.
Figure 3
Figure 3
The VST values of all the copy number variation regions (CNVRs) in SH and LW (A) pigs, SH and MZ (B) pigs, LW and MZ (C) pigs. The average VST value of SH and LW pigs is just 0.111; but the average VST values are 0.234 and 0.265 in SH and MZ pigs and LW and MZ pigs, respectively.
Figure 4
Figure 4
(A) Venn diagram of the CNVRs in LW, SH, and MZ pigs. The known genes of LW (B), MZ (C), and SH (D) pigs in the group-specific CNVRs were analyzed in the KEGG pathway.
Figure 5
Figure 5
(A) The genome distribution of the group-specific QTLs in SH, MZ, and LW pigs. (B–D) are the group-specific QTLs in SH, LW, and MZ pigs.
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