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Open Access Research article

A genome-wide detection of copy number variations using SNP genotyping arrays in swine

Jiying Wang12, Jicai Jiang1, Weixuan Fu1, Li Jiang1, Xiangdong Ding1, Jian-Feng Liu1* and Qin Zhang1*

Author affiliations

1 Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China

2 Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China

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Citation and License

BMC Genomics 2012, 13:273  doi:10.1186/1471-2164-13-273

Published: 22 June 2012

Abstract

Background

Copy Number Variations (CNVs) have been shown important in both normal phenotypic variability and disease susceptibility, and are increasingly accepted as another important source of genetic variation complementary to single nucleotide polymorphism (SNP). Comprehensive identification and cataloging of pig CNVs would be of benefit to the functional analyses of genome variation.

Results

In this study, we performed a genome-wide CNV detection based on the Porcine SNP60 genotyping data of 474 pigs from three pure breed populations (Yorkshire, Landrace and Songliao Black) and one Duroc × Erhualian crossbred population. A total of 382 CNV regions (CNVRs) across genome were identified, which cover 95.76Mb of the pig genome and correspond to 4.23% of the autosomal genome sequence. The length of these CNVRs ranged from 5.03 to 2,702.7kb with an average of 250.7kb, and the frequencies of them varied from 0.42 to 20.87%. These CNVRs contains 1468 annotated genes, which possess a great variety of molecular functions, making them a promising resource for exploring the genetic basis of phenotypic variation within and among breeds. To confirmation of these findings, 18 CNVRs representing different predicted status and frequencies were chosen for validation via quantitative real time PCR (qPCR). Accordingly, 12 (66.67%) of them was successfully confirmed.

Conclusions

Our results demonstrated that currently available Porcine SNP60 BeadChip can be used to capture CNVs efficiently. Our study firstly provides a comprehensive map of copy number variation in the pig genome, which would be of help for understanding the pig genome and provide preliminary foundation for investigating the association between various phenotypes and CNVs.

Keywords:
Copy number variations; Genetic variation; SNP arrays; Quantitative real time PCR; Pig