Open Access Highly Accessed Research article

Large scale variation in DNA copy number in chicken breeds

Richard PMA Crooijmans1*, Mark S Fife2, Tomas W Fitzgerald3, Shurnevia Strickland5, Hans H Cheng6, Pete Kaiser7, Richard Redon34 and Martien AM Groenen1

Author Affiliations

1 Animal Breeding and Genomics Centre, Wageningen University, P.O. box 338, Wageningen 6700 AH, The Netherlands

2 Genetics and Genomics group, Compton Laboratory, The Pirbright Institute, Compton, Berkshire RG20 7NN, UK

3 Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK

4 L'institut du thorax, UMR Inserm 1087 CNRS 6291, University of Nantes, 8 quai Moncousu, BP 70721, Nantes, Cedex 1 44007, France

5 Department of Animal & Food Sciences, University of Delaware, Newark, DE 19717, USA

6 Avian Disease and Oncology Laboratory, 4279 E Mount Hope Road, East Lansing, MI 48823-5338, USA

7 The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK

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BMC Genomics 2013, 14:398  doi:10.1186/1471-2164-14-398

Published: 13 June 2013



Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds.


We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV.


A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species.

Copy number variation; Chicken; aCGH; Line-specific CNVs; Inter-specific CNVs; Genes