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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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-934) contains supplementary material, which is available to authorized users.
Highlights
The detection and functional characterization of genomic structural variations are important for understanding the landscape of genetic variation in the chicken
After eliminating probes with uncertain chromosomal loci, we identified 446 non-redundant copy number variation (CNV) for the chicken autosome GGA1-28 and the Z sex chromosome
Among the four copy number variation regions (CNVR) selected for validation through quantitative PCR (qPCR), all four variations exhibited the expected copy number differences
Summary
The detection and functional characterization of genomic structural variations are important for understanding the landscape of genetic variation in the chicken. 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. There is a large genetic distance between Chinese and European chicken populations, which facilitates the detection of fruitful breed-specific CNVs. compared with humans and other model organisms, there is limited research on the extent and impact of CNVs in the chicken genome. The CNVs detected are complementary to the CNV map in the chicken genome, and this information will be important for future studies associating phenotype with genome architecture
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