Han Ruili, Yang Pengkun, Tian Yadong, Wang Dandan, Zhang Zengxuan, Wang Lele, Li Zhuanjian, Jiang Ruirui, Kang Xiangtao
College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resources, Zhengzhou, Henan 450002, China.
BMC Genomics. 2014 Oct 25;15(1):934. doi: 10.1186/1471-2164-15-934.
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.
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.
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.
基因组结构变异的检测和功能表征对于理解鸡的遗传变异格局非常重要。基因组结构变异中一个最近才被认识到的方面，即拷贝数变异（CNV），在鸡基因组研究中越来越受到关注。本研究的目的是调查五个特色鸡品种中CNV的模式和功能表征，这对于未来将表型与鸡基因组结构相关联的研究具有重要意义。
使用基于商业385K阵列的比较基因组杂交（aCGH）基因组阵列，我们对来自四个中国地方品种和法国胡丹鸡品种的10个鸡样本进行了CNV检测。以雌性安卡肉鸡作为参考。共鉴定出281个拷贝数变异区域（CNVR），覆盖12.8 Mb的多态性序列，占整个鸡基因组的1.07%。CNVR的功能注释表明，这些区域完全或部分与231个基因和1032个数量性状位点重叠，表明这些CNV具有重要功能，可能是探索不同品种间差异的有前途的资源。此外，我们采用定量PCR（qPCR）进一步验证了几个具有重要功能的拷贝数可变基因，如催乳素受体、内皮素3（EDN））、细胞因子信号转导抑制因子2、CD8a分子，结果表明EDN3可能是家禽生产中深色皮肤选择的分子标记。此外，我们还鉴定了一个新的CNVR（chr24: 3484617 - 3512275），其编码sortilin相关受体基因，且仅在乌鸡中存在拷贝数变化。
在此，我们报告了使用aCGH对五个鸡品种中CNV进行的全基因组分析。通过qPCR进一步证实了EDN3与黑素母细胞增殖之间的关联。这些结果为理解基因组变异和相关表型特征提供了更多信息。
