Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2013
Publication Date: 6/13/2013
Publication URL: http://handle.nal.usda.gov/10113/57434
Citation: Crooijmans, R.P., Fife, M.S., Fitzgerald, T.W., Strickland, S., Cheng, H.H., Kaiser, P., Redon, R., Groenen, M.A. 2013. Large scale variation in DNA copy number in chicken breeds. Biomed Central (BMC) Genomics. 2013(14):398. Available: http://www.biomedcentral.com/1471-2164/14/398. Interpretive Summary: Understanding the underlying basis for variation in agronomic traits such as growth, reproduction, disease resistance, etc. is a scientific major goal. In poultry, this knowledge can be harnessed to improve animal breeding and welfare. In this paper, we catalog one type of structural variation in the chicken genome known as copy number variation (CNV). In brief, these are large duplications or losses in individual birds. More importantly, many of the regions with CNVs contain genes indicating the importance of this type of genetic variation. This report provides a strong foundation for future experimentation, which may ultimately help provide genetic markers to rapidly select for superior animals.
Technical Abstract: Background 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. Results 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. Conclusions 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.