Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

<div><p>Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.</p></div

Chromosome distribution of CNVRs in pigs.

<p>Chromosome distribution of CNVRs in pigs.</p

Genomic distribution of CNVRs in 18 pairs of autosomal chromosomes of pigs.

<p>The chromosomal locations of 348 CNVRs are indicated by lines. Y-axis values are chromosome names, and X-axis values are chromosome positions in Mb, which are proportional to the real size of swine genome sequence assembly (10.2). Round represents CNVRs identified only in Chinese indigenous breeds; triangle represents CNVRs identified only in western breeds; and quadrate represents those identified both in Chinese and western breeds.</p

QPCR validation of 8 identified CNVRs.

<p>The x-axis represents the animals and the y-axis shows the relative quantification value.</p

Sample size and CNVs number detected in nine breeds.

<p>Sample size and CNVs number detected in nine breeds.</p