Genome-wide Patterns of Copy Number Variation in the Diversified Chicken Genomes Using Next-generation Sequencing

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2014 Nov 8

PMID 25378104

Citations 40

Authors

Guoqiang Yi

Lujiang Qu

Jianfeng Liu

Yiyuan Yan

Guiyun Xu

Ning Yang

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

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References

Wang X, Nahashon S, Feaster T, Bohannon-Stewart A, Adefope N . An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics. 2010; 11:351. PMC: 2996973. DOI: 10.1186/1471-2164-11-351. View

Greenwold M, Sawyer R . Genomic organization and molecular phylogenies of the beta (beta) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution. BMC Evol Biol. 2010; 10:148. PMC: 2894828. DOI: 10.1186/1471-2148-10-148. View

Peltonen L, Altshuler D, de Bakker P, Deloukas P, Gabriel S, Gwilliam R . Integrating common and rare genetic variation in diverse human populations. Nature. 2010; 467(7311):52-8. PMC: 3173859. DOI: 10.1038/nature09298. View

Sudmant P, Kitzman J, Antonacci F, Alkan C, Malig M, Tsalenko A . Diversity of human copy number variation and multicopy genes. Science. 2010; 330(6004):641-6. PMC: 3020103. DOI: 10.1126/science.1197005. View

Campbell C, Sampas N, Tsalenko A, Sudmant P, Kidd J, Malig M . Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet. 2011; 88(3):317-32. PMC: 3059424. DOI: 10.1016/j.ajhg.2011.02.004. View

Abyzov A, Urban A, Snyder M, Gerstein M . CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011; 21(6):974-84. PMC: 3106330. DOI: 10.1101/gr.114876.110. View

Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T . Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol. 2011; 29(6):512-20. PMC: 3270583. DOI: 10.1038/nbt.1852. View

Yalcin B, Wong K, Agam A, Goodson M, Keane T, Gan X . Sequence-based characterization of structural variation in the mouse genome. Nature. 2011; 477(7364):326-9. PMC: 3428933. DOI: 10.1038/nature10432. View

Gokcumen O, Babb P, Iskow R, Zhu Q, Shi X, Mills R . Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection. Genome Biol. 2011; 12(5):R52. PMC: 3219974. DOI: 10.1186/gb-2011-12-5-r52. View

10.

Hincke M, Nys Y, Gautron J, Mann K, Rodriguez-Navarro A, McKee M . The eggshell: structure, composition and mineralization. Front Biosci (Landmark Ed). 2011; 17(4):1266-80. DOI: 10.2741/3985. View

11.

Dorshorst B, Molin A, Rubin C, Johansson A, Stromstedt L, Pham M . A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genet. 2012; 7(12):e1002412. PMC: 3245302. DOI: 10.1371/journal.pgen.1002412. View

12.

Patel R, Jain M . NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012; 7(2):e30619. PMC: 3270013. DOI: 10.1371/journal.pone.0030619. View

13.

Bickhart D, Hou Y, Schroeder S, Alkan C, Cardone M, Matukumalli L . Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 2012; 22(4):778-90. PMC: 3317159. DOI: 10.1101/gr.133967.111. View

14.

Wang Y, Gu X, Feng C, Song C, Hu X, Li N . A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method. Anim Genet. 2012; 43(3):282-9. DOI: 10.1111/j.1365-2052.2011.02308.x. View

15.

Wang J, Jiang J, Fu W, Jiang L, Ding X, Liu J . A genome-wide detection of copy number variations using SNP genotyping arrays in swine. BMC Genomics. 2012; 13:273. PMC: 3464621. DOI: 10.1186/1471-2164-13-273. View

16.

Clop A, Vidal O, Amills M . Copy number variation in the genomes of domestic animals. Anim Genet. 2012; 43(5):503-17. DOI: 10.1111/j.1365-2052.2012.02317.x. View

17.

Teo S, Pawitan Y, Ku C, Chia K, Salim A . Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics. 2012; 28(21):2711-8. DOI: 10.1093/bioinformatics/bts535. View

18.

Liu G, Bickhart D . Copy number variation in the cattle genome. Funct Integr Genomics. 2012; 12(4):609-24. DOI: 10.1007/s10142-012-0289-9. View

19.

Hu Z, Park C, Wu X, Reecy J . Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res. 2012; 41(Database issue):D871-9. PMC: 3531174. DOI: 10.1093/nar/gks1150. View

20.

Szatkiewicz J, Wang W, Sullivan P, Wang W, Sun W . Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation. Nucleic Acids Res. 2013; 41(3):1519-32. PMC: 3561969. DOI: 10.1093/nar/gks1363. View