ArticleBMC genomics2013
Large scale variation in DNA copy number in chicken breeds.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Genome-Wide Analysis of Copy Number Variation in Vietnamese Local Chickens.Animals : an open access journal from MDPI · 2026Article
- Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds.BMC genomics · 2023Article
- Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations.BMC genomics · 2022Article
- Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken.Frontiers in genetics · 2022Article
- Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing.BMC genetics · 2020Article
- The Association of the Copy Number Variation of theAnimals : an open access journal from MDPI · 2020Article
- Accumulation of genetic variants associated with immunity in the selective breeding of broilers.BMC genetics · 2020Article
- A large interactive visual database of copy number variants discovered in taurine cattle.GigaScience · 2019Article
- A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence.Frontiers in genetics · 2019Article
- Copy number variation study in Japanese quail associated with stress related traits using whole genome re-sequencing data.PloS one · 2019Article
- Detection of copy number variations in brown and white layers based on genotyping panels with different densities.Genetics, selection, evolution : GSE · 2018Article
- Copy number variation in livestock: A mini review.Veterinary world · 2018Review
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- Characterization of Copy Number Variation's Potential Role in Marek's Disease.International journal of molecular sciences · 2017Article
- Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools.BMC genomics · 2016Article
- Dysfunction of the Voltage-Gated K+ Channel β2 Subunit in a Familial Case of Brugada Syndrome.Journal of the American Heart Association · 2016Article
- Targeted capture enrichment and sequencing identifies extensive nucleotide variation in the turkey MHC-B.Immunogenetics · 2016Article
- Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome.Frontiers in genetics · 2016Article
- Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek's disease.BMC genomics · 2015Article
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Authors and funding
8 authors.
Funding
Abstract
backgroundDetecting 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.
resultsWe 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.
conclusionsA 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.
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