Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

BMC Genomics

Ning Yang¹  Guiyun Xu¹  Yiyuan Yan¹  Jianfeng Liu¹  Lujiang Qu¹  Guoqiang Yi¹ 

[1]Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China

关键词: Chicken;    Genetic diversity;    aCGH;    Whole genome sequencing;    Copy number variation;   

Others  :  1127728
DOI  :  10.1186/1471-2164-15-962

 received in 2014-03-04, accepted in 2014-10-13,  发布年份 2014

【 摘 要 】

Background

Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing.

Results

A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson’s correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding.

Conclusions

Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.

【 授权许可】

   
2014 Yi et al.; licensee BioMed Central Ltd.

【 图 表 】

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