State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
Anim Genet. 2012 Jun;43(3):282-9. doi: 10.1111/j.1365-2052.2011.02308.x. Epub 2012 Jan 4.
The discovery of copy number variation (CNV) in the genome has provided new insight into genomic polymorphism. Studies with chickens have identified a number of large CNV segments using a 385k comparative genomic hybridization (CGH) chip (mean length >140 kb). We present a detailed CNV map for local Chinese chicken breeds and commercial chicken lines using an Agilent 400k array CGH platform with custom-designed probes. We identified a total of 130 copy number variation regions (CNVRs; mean length = 25.70 kb). Of these, 104 (80.0%) were novel segments reported for the first time in chickens. Among the 104 novel CNVRs, 56 (53.8%) of the segments were non-coding sequences, 65 (62.5%) showed the gain of DNA and 40 (38.5%) showed the loss of DNA (one locus showed both loss and gain). Overlapping with the formal selective sweep data and the quantitative trait loci data, we identified four loci that might be considered to be high-confidence selective segments that arose during the domestication of chickens. Compared with the CNVRs reported previously, genes for the positive regulation of phospholipase A2 activity were discovered to be significantly over-represented in the novel CNVRs reported here by gene ontology analysis. Availability of our results should facilitate further research in the study of the genetic variability in chicken breeds.
基因组拷贝数变异 (CNV) 的发现为基因组多态性提供了新的认识。鸡的研究使用 385k 比较基因组杂交 (CGH) 芯片鉴定了许多大片段 CNV（平均长度 >140kb）。我们使用定制设计的 Agilent 400k 阵列 CGH 平台为本地中国鸡品种和商业鸡系提供了详细的 CNV 图谱。我们总共鉴定了 130 个拷贝数变异区（CNVRs；平均长度 = 25.70kb）。其中，104 个（80.0%）是首次在鸡中报道的新片段。在 104 个新的 CNVR 中，56 个（53.8%）是非编码序列，65 个（62.5%）显示 DNA 获得，40 个（38.5%）显示 DNA 丢失（一个位点显示获得和丢失）。与正式的选择清除数据和数量性状位点数据重叠，我们鉴定了四个可能被认为是鸡驯化过程中出现的高可信度选择片段的位点。与以前报道的 CNVR 相比，通过基因本体分析，发现这里报道的新 CNVR 中与磷脂酶 A2 活性的正调控相关的基因显著过表达。我们结果的可用性应该有助于进一步研究鸡品种的遗传变异性。
