Large scale variation in DNA copy number in chicken breeds. - Inserm - Institut national de la santé et de la recherche médicale Access content directly
Journal Articles BMC Genomics Year : 2013

Large scale variation in DNA copy number in chicken breeds.

Mark Fife
  • Function : Author
  • PersonId : 946061
Tomas Fitzgerald
  • Function : Author
  • PersonId : 904535
Shurnevia Strickland
  • Function : Author
  • PersonId : 946062
Hans Cheng
  • Function : Author
  • PersonId : 946063
Pete Kaiser
  • Function : Author
  • PersonId : 946064
Martien Groenen
  • Function : Author
  • PersonId : 946066


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.
Fichier principal
Vignette du fichier
1471-2164-14-398.pdf (887.64 Ko) Télécharger le fichier
1471-2164-14-398-S1.XLSX (426.48 Ko) Télécharger le fichier
1471-2164-14-398-S2.XLSX (69.04 Ko) Télécharger le fichier
1471-2164-14-398-S3.DOCX (14.73 Ko) Télécharger le fichier
1471-2164-14-398-S4.XLSX (16.21 Ko) Télécharger le fichier
1471-2164-14-398-S5.XLS (399 Ko) Télécharger le fichier
1471-2164-14-398.xml (72.18 Ko) Télécharger le fichier
Origin : Publisher files allowed on an open archive
Format : Other
Format : Other
Format : Other
Format : Other
Format : Other
Format : Other

Dates and versions

inserm-00868020 , version 1 (01-10-2013)



Richard Crooijmans, Mark Fife, Tomas Fitzgerald, Shurnevia Strickland, Hans Cheng, et al.. Large scale variation in DNA copy number in chicken breeds.. BMC Genomics, 2013, 14 (1), pp.398. ⟨10.1186/1471-2164-14-398⟩. ⟨inserm-00868020⟩
160 View
423 Download



Gmail Facebook Twitter LinkedIn More