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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.
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
May 2010,
Genome research,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
December 2012,
BMC genomics,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
April 2015,
G3 (Bethesda, Md.),
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
January 2013,
PloS one,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
January 2022,
Animals : an open access journal from MDPI,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
January 2014,
PloS one,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
August 2017,
Animal genetics,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
September 2021,
Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
June 2013,
BMC genomics,
Ruili Han, and
Pengkun Yang, and
Yadong Tian, and
Dandan Wang, and
Zengxuan Zhang, and
Lele Wang, and
Zhuanjian Li, and
Ruirui Jiang, and
Xiangtao Kang
August 2022,
Animals : an open access journal from MDPI,
