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Open Access Research article

Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array

Jiasen Liu12, Li Zhang1, Lingyang Xu1, Hangxing Ren3, Jian Lu1, Xiaoning Zhang1, Shifang Zhang1, Xinlei Zhou1, Caihong Wei1, Fuping Zhao1* and Lixin Du1*

Author Affiliations

1 National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, People’s Republic of China

2 Institute of Animal Science, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, Inner Mongolia Autonomous Region, 010031, People’s Republic of China

3 Chongqing Academy of Animal Sciences, Chongqing, 402460, People’s Republic of China

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BMC Genomics 2013, 14:229  doi:10.1186/1471-2164-14-229

Published: 8 April 2013

Abstract

Background

In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity.

Results

Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies.

Conclusions

In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.