Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs.

Hongyang Wang,Jennifer J Michal,Yu Zhang,Jing Liu,Zhihua Jiang,Yanan Wang,Chao Wang,Bang Liu,Xuewen Xu,Kui Yang,Jian-Feng Liu

doi:10.1371/journal.pone.0131522

Abstract

Copy number variations (CNVs) refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs) were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs’ independent domestication, and facilitate further functional studies of CNV-associated genes.

Highlights

Genomic structural variations due to large insertions, deletions, inversions and translocations are called copy number variations (CNVs)
In humans a set of CNVs was present in 189 subjects diagnosed with major depressive disorder who previously attempted suicide compared to 1,073 subjects with major depressive disorder but never attempted suicide [18], while Liu et al [19] found that a deletion at 2p24.3 was significantly associated with prostate cancer risk in 498 aggressive prostate cancer cases using affymetrix Single nucleotide polymorphism (SNP) arrays
Loss variations accounted for 75% (2,364 loss/3,131 total) of CNVs, indicating that these variations may be related to the deletion of chromosome regions

Summary

Introduction

Genomic structural variations due to large insertions, deletions, inversions and translocations are called copy number variations (CNVs). Four types of duplications at the KIT locus were exclusively present in the dominant white allele, which caused white or white-spotted coat colours in pigs [22]. Another KIT gene related study performed a database of 50K SNP genotypes from 4,500 cattle revealed that colour sidedness was determined by translocation events between chromosomes 6 and 29 [23]. Disruption of the CCDC108 gene by structural rearrangement causes a sperm motility defect in male chickens homozygous for rose-comb phenotype, while a CNV in intron 1 of SOX5 causes the pea-comb phenotype in chickens [16, 26]

Methods

Results

Conclusion