ArticleBMC genomics2014
Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 101 citations in OpenAlex.
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- Genome-Wide Analysis of Copy Number Variation in Vietnamese Local Chickens.Animals : an open access journal from MDPI · 2026Article
- Comprehensive Analysis of 122 Guinea Fowl Genomes Across Three Continents Delineates Their Domestication and Evolutionary Patterns with Special Reference to India.International journal of molecular sciences · 2026Article
- Genome-wide characterization of copy number variants and their functional relevance in indigenous draught cattle of South Asia.PloS one · 2026Article
- Copy Number Variation and SNP Affect Egg Production in Chickens by Regulating AP2M1 Expression to Inhibit GnRH Synthesis.Animals : an open access journal from MDPI · 2025Article
- Population genomic analysis identifies the complex structural variation at the fibromelanosis (FM) locus in chicken.Scientific reports · 2025Article
- Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments.BMC genomics · 2024Article
- Genome-Wide Scan for Copy Number Variations in Chinese Merino Sheep Based on Ovine High-Density 600K SNP Arrays.Animals : an open access journal from MDPI · 2024Article
- Genetic diversity, demographic history, and selective signatures of Silkie chicken.BMC genomics · 2024Article
- Genome-wide investigation to assess copy number variants in the Italian local chicken population.Journal of animal science and biotechnology · 2024Article
- Whole-genome sequencing revealed genetic diversity, structure and patterns of selection in Guizhou indigenous chickens.BMC genomics · 2023Article
- Effects of Genetic Variation of the Sorting Nexin 29 (Animals : an open access journal from MDPI · 2022Article
- Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks.Frontiers in cell and developmental biology · 2022Article
- Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions.Frontiers in genetics · 2022Article
- Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken.Frontiers in genetics · 2022Article
- CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.GigaScience · 2021Article
- Genome-wide scan for selective footprints and genes related to cold tolerance in Chantecler chickens.Zoological research · 2021Article
- Article
- Genome-wide detection of CNVs and their association with performance traits in broilers.BMC genomics · 2021Article
- 863 genomes reveal the origin and domestication of chicken.Cell research · 2020Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopy 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.
resultsA 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.
conclusionsOur 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.
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