title: Identification and functional characterization of copy number variations in diverse chicken breeds.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  Using 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.
  
  
  CONCLUSIONS
  Here, 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.
authors.forename: Ruili
authors.initials: R
authors.lastname: Han
authors.forename: Pengkun
authors.initials: P
authors.lastname: Yang
authors.forename: Yadong
authors.initials: Y
authors.lastname: Tian
authors.forename: Dandan
authors.initials: D
authors.lastname: Wang
authors.forename: Zengxuan
authors.initials: Z
authors.lastname: Zhang
authors.forename: Lele
authors.initials: L
authors.lastname: Wang
authors.forename: Zhuanjian
authors.initials: Z
authors.lastname: Li
authors.forename: Ruirui
authors.initials: R
authors.lastname: Jiang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resources, Zhengzhou, Henan 450002, China. xtkang2001@263.net.
authors.forename: Xiangtao
authors.initials: X
authors.lastname: Kang
mesh_terms: D000818:Animals; D002645:Chickens / Q000145:classification* / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D019334:Endothelin-3 / Q000235:genetics / Q000378:metabolism; D016678:Genome; D008297:Male; D010641:Phenotype; D040641:Quantitative Trait Loci
chemical_list: D019334:Endothelin-3