Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization
Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization
复制标题
DOI：
10.1111/age.12141
复制
发表时间：
2014-06-01
期刊：
影响因子：
2.4
通讯作者：
Zhou, H.
中科院分区：
文献类型：
--
作者：
Abernathy, J.;Li, X.;Zhou, H.
拷贝数变异是指染色体上沿着的区域具有一种类型的结构变异，如重复或缺失。拷贝数变异（CNVs）在许多重要性状以及遗传多样性中起作用。以前的分析鸡使用阵列比较基因组杂交或单核苷酸多态性芯片测定已进行了各种品种和遗传线，以发现CNV。在这项研究中，我们评估了来自两个高度近交（近交系数>99.99%）品系，Leghorn G-B2和Fayoumi M15.2的个体，以发现鸡中的新CNV。这些品系以前已经被研究过抗病性，据我们所知，这代表了Fayoumi品种中CNV的首次全球评估。使用Agilent鸡244 K比较基因组杂交阵列和定量PCR检查来自个体的基因组DNA。我们总共确定了273个CNVs，其中112个是新的，以前没有报道过。使用标准曲线方法的定量PCR验证了我们的阵列数据的子集。通过对CNV区域内基因的富集分析，我们观察到多个染色体、术语和途径显著富集，主要涉及主要组织相容性复合体和免疫应答。使用另一轮计算和统计分析与不同的生物信息学管道，我们确定了43个CNV作为高置信度区域，其中14个被发现是新的。我们进一步比较和对比两个近交系的个体，以发现在品系之间具有显著拷贝数差异的区域。总共有40个区域在线条之间有明显的缺失或重复。还进行了株系之间含有CNV的基因组区域的基因本体论分析。该株系间候选CNV列表将在这两个独特遗传株系的研究中有用，这两个独特遗传株系可能含有作为抗病性和其他重要性状的数量性状基因座基础的变异。通过在鸡中发现新的CNVs，这些数据也为进一步的遗传和功能基因组学研究提供了资源。
Copy number variation refers to regions along chromosomes that harbor a type of structural variation, such as duplications or deletions. Copy number variants (CNVs) play a role in many important traits as well as in genetic diversity. Previous analyses of chickens using array comparative genomic hybridizations or single-nucleotide polymorphism chip assays have been performed on various breeds and genetic lines to discover CNVs. In this study, we assessed individuals from two highly inbred (inbreeding coefficiency>99.99%) lines, Leghorn G-B2 and Fayoumi M15.2, to discover novel CNVs in chickens. These lines have been previously studied for disease resistance, and to our knowledge, this represents the first global assessment of CNVs in the Fayoumi breed. Genomic DNA from individuals was examined using the Agilent chicken 244K comparative genomic hybridization array and quantitative PCR. We identified a total of 273 CNVs overall, with 112 CNVs being novel and not previously reported. Quantitative PCR using the standard curve method validated a subset of our array data. Through enrichment analysis of genes within CNV regions, we observed multiple chromosomes, terms and pathways that were significantly enriched, largely dealing with the major histocompatibility complex and immune responsiveness. Using an additional round of computational and statistical analysis with a different bioinformatic pipeline, we identified 43 CNVs among these as high-confidence regions, 14 of which were found to be novel. We further compared and contrasted individuals of the two inbred lines to discover regions that have a significant difference in copy number between lines. A total of 40 regions had significant deletions or duplications between the lines. Gene Ontology analysis of genomic regions containing CNVs between lines also was performed. This between-line candidate CNV list will be useful in studies with these two unique genetic lines, which may harbor variations that underlie quantitative trait loci for disease resistance and other important traits. Through the global discovery of novel CNVs in chicken, these data also provide resources for further genetic and functional genomics studies.