ArticleBMC genomics2014
Identification and functional characterization of copy number variations in diverse chicken breeds.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Genome-Wide Analysis of Copy Number Variation in Vietnamese Local Chickens.Animals : an open access journal from MDPI · 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
- Genome-Wide Detection of Copy Number Variations and Their Potential Association with Carcass and Meat Quality Traits in Pingliang Red Cattle.International journal of molecular sciences · 2024Article
- Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study.Veterinary sciences · 2024Article
- Genome-wide investigation to assess copy number variants in the Italian local chicken population.Journal of animal science and biotechnology · 2024Article
- 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
- Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken.BMC genomics · 2020Article
- Detection of CNV in the SH3RF2 gene and its effects on growth and carcass traits in chickens.BMC genetics · 2020Article
- First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data.BMC genomics · 2018Article
- 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
- Article
- Targeted capture enrichment and sequencing identifies extensive nucleotide variation in the turkey MHC-B.Immunogenetics · 2016Article
- Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek's disease.BMC genomics · 2015Article
- Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.Frontiers in genetics · 2015Article
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Authors and funding
9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe detection and functional characterization of genomic structural variations are important for understanding the landscape of genetic variation in the chicken. A recently recognized aspect of genomic structural variation, called copy number variation (CNV), is gaining interest in chicken genomic studies. The aim of the present study was to investigate the pattern and functional characterization of CNVs in five characteristic chicken breeds, which will be important for future studies associating phenotype with chicken genome architecture.
resultsUsing a commercial 385 K array-based comparative genomic hybridization (aCGH) genome array, we performed CNV discovery using 10 chicken samples from four local Chinese breeds and the French breed Houdan chicken. The female Anka broiler was used as a reference. A total of 281 copy number variation regions (CNVR) were identified, covering 12.8 Mb of polymorphic sequences or 1.07% of the entire chicken genome. The functional annotation of CNVRs indicated that these regions completely or partially overlapped with 231 genes and 1032 quantitative traits loci, suggesting these CNVs have important functions and might be promising resources for exploring differences among various breeds. In addition, we employed quantitative PCR (qPCR) to further validate several copy number variable genes, such as prolactin receptor, endothelin 3 (EDN3), suppressor of cytokine signaling 2, CD8a molecule, with important functions, and the results suggested that EDN3 might be a molecular marker for the selection of dark skin color in poultry production. Moreover, we also identified a new CNVR (chr24: 3484617-3512275), encoding the sortilin-related receptor gene, with copy number changes in only black-bone chicken.
conclusionsHere, we report a genome-wide analysis of the CNVs in five chicken breeds using aCGH. The association between EDN3 and melanoblast proliferation was further confirmed using qPCR. These results provide additional information for understanding genomic variation and related phenotypic characteristics.
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