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

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.

Fig 1. Distribution of CNVRs found in autosomes of porcine genome.

X axis indicates the 18 autosomes, Y axis the length of each chromosome, and the black frames the different chromosomes. The green bars (left border of each chromosome) represent copy number loss regions and the red bars (right border of each chromosome) represent copy number gain regions.

Fig 2. CNVs sharing intervals and basepairs among Western breeds.

In the Venn diagram, the top number indicates the count of shared CNVs, and the bottom number the CNV intervals and basepairs among three Western breeds. The table to the right of the diagram shows total CNV counts and length in each breed.

Fig 3. CN values predicted and observed near three gene loci.

The left pictures are CN values estimated from at least 5 individuals in different breeds using the qPCR method. X axis means different pig breeds (TC = Tongcheng; MS = Meishan; NJ = Neijiang; JH = Jinhua; PZ = Penzhou; LW = LargeWhite; DU = Duroc; LR = Landrace). Y axis means the CN values. The cycles indicate CN values for each individual. The right histograms describe the predicted and observed CN values in four Tongcheng pigs. CN gain in these four gene loci was predicted. (A) (B) and (C) The left pictures showed that CN was increased in most individuals in a large range for 2–12. Also, the same trend was observed for CN gain between predicted and observed events in three Tongcheng pigs according to the right histograms.

Fig 4. Heatmap analysis of CNV genes between Chinese and Western domestic pigs.

The heatmap boxes show the sliding and nonoverlapping windows, 1 Kb in (A) and (B) and 2 Kb in (C). CN values were plotted within these three regions and correspond to the different colors. On the top of the heatmap is the information of genes affected by CNVs. (A) A region of nearly 8 Kb (chr13: 158,547,001–158,554,500) in PVRL3 gene had higher CN (from 5 to 9 copies), especially in Chinese domestic pigs (15 individuals / 22 totals), which was not found in Western domestic pigs. The last exon of three transcripts and the fourth intron of one transcript of this gene were affected by this CNVR. (B) A 6 Kb region at chromosome 14 from 126,295,501 to 126,301,500 bp had a higher CN in Chinese domestic pigs, but not in Western pigs. In addition, no genes were overlapped within this region. (C) The heatmap of AATK and BAIAP2 genes indicated that CN gain was present in Western domestic pigs in this region, but not in Chinese domestic pigs (chr12: 1,496,701–1,546,473).