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. 2023 Apr 23;10(5):307.
doi: 10.3390/vetsci10050307.

Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation

Xinmiao He  1 , Ming Tian  1 , Wentao Wang  1 , Yanzhong Feng  1 , Zhongqiu Li  1 , Jiahui Wang  2 , Yan Song  2 , Jinfeng Zhang  3 , Di Liu  1
Affiliations

Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation

Xinmiao He et al. Vet Sci. .

Abstract

The Min pig is a famous native pig breed in northeast China, which has the special genetic character of villi hair growth in cold seasons. At present, little research has focused on the genetic mechanism of villi hair growth in Min pigs. Copy number variations (CNVs) are a type of variant that may influence many traits. In this study, we first investigated the phenotype of Large White × Min pigs' F2 pig villi hair in detail and then performed a CNV-based genome-wide association study (GWAS) between CNVs and pig villi hair appearance. Finally, a total number of 15 significant CNVRs were found to be associated with Min pig villi hair. The most significant CNVR was located on chromosome 1. Nearest gene annotation analysis indicated that the pig villi hair traits may be associated with the biological process of the G-protein-coupled receptor signaling pathway. QTL overlapping analysis found that among the CNVRs, 14 CNVRs could be co-located with known QTLs. Some genes such as MCHR2, LTBP2, and GFRA2 may be candidate genes for pig villi traits and are worth further study. Our study may provide a basic reference for the selection and breeding of cold-resistant pigs and outdoor breeding.

Keywords: Min pig; copy number variation; genome-wide association study; villi hair follicle.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
The genomic distribution of pig CNV regions (CNVRs). Different colors of the line within the chromosome indicate different number of CNVRs in the 1 Mb size region.
Figure 2
Figure 2
Manhattan plot of associated CNVs for villi hair appearance trait. The blue line indicates chromosome significant threshold, and the red line indicates the genome-wide significance threshold. Different colored dots indicate different chromosomes.
Figure 3
Figure 3
Relative expression of selected CNVRs (A) Relative expression of normal and deletion (Del) type of CNV13; (B) Relative expression of normal and duplicated (Dup) type of CNV667; (C) Relative expression of normal and Dup type of CNV540; (D) Relative expression of normal and deletion (Del) type of CNV64. A * represents significant difference (p < 0.05).
Figure 4
Figure 4
Enrichment of significant CNVRs’ nearest genes. (A) Top 20 GO enrichment terms of biological process for CNVRs nearby genes. (B) Top 20 KEGG Pathways of CNVRs nearby genes.
Figure 5
Figure 5
The intersection of the 4 most significant CNVRs with swine QTL data. The first column was the name of CNVRs, the second column was the name of chromosome, the third column was name of QTLs.
See this image and copyright information in PMC

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