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

Copy number variation (CNV) refers to large insertions, deletions and duplications in 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 CNVs detection. Evidence has shown that CNVs occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and expression. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and western domestic pigs.

Based on 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 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 between Chinese and Western pigs.

In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered 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.