Large scale variation in DNA copy number in chicken breeds.
Large scale variation in DNA copy number in chicken breeds.
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DOI：
10.1186/1471-2164-14-398
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发表时间：
2013-06-13
期刊：
影响因子：
4.4
通讯作者：
Groenen MA
中科院分区：
文献类型：
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作者：
Crooijmans RP;Fife MS;Fitzgerald TW;Strickland S;Cheng HH;Kaiser P;Redon R;Groenen MA
检测遗传变异是阐明表型多样性的分子机制的关键一步。直到最近，这种检测主要集中在单核苷酸多态(SNPs)上，因为筛选完整基因组很容易。另一种类型的变异，拷贝数变异(CNV)，正在成为许多物种表型变异的重要贡献者。在这里，我们描述了一项利用阵列比较基因组杂交(ACGH)在多种鸡种中进行的全基因组CNV研究。我们识别了3,154个CNV，分为1,556个CNV区域(CNVR)。30%的CNV是在至少2个人中检测到的。CNV的平均大小为46.3kb，其中最大的CNV位于GGAZ，为4.3Mb。相对于红色丛林鸡的参考基因组，大约75%的CNV是拷贝数丢失。本研究中CNVRs的基因组覆盖率为60Mb，几乎占鸡基因组的5.4%。尤其是大的基因家族，如角蛋白基因家族和MHC，表现出广泛的CNV。一组相对较大的CNV是线特异性的，其中几个先前被证明与一些表型变异的致病突变有关。在鸡中检测到的种间CNV落入CNVRs的可能性与物种之间的进化距离有关。我们的结果为研究这种表型多样性物种的遗传和表型变异提供了有价值的资源。
Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species.
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影响因子：
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通讯作者：
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通讯作者：
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影响因子：
64.8
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