Allelic genome structural variations in maize detected by array comparative genome hybridization
Allelic genome structural variations in maize detected by array comparative genome hybridization
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DOI：
10.1007/s00122-009-1128-9
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发表时间：
2010-01-01
影响因子：
5.4
通讯作者：
Rafalski, Antoni
中科院分区：
文献类型：
--
作者：
Belo, Andre;Beatty, Mary K.;Rafalski, Antoni
DNA 多态性（例如影响大于 1 kb 的基因组片段的插入/删除和重复）被称为拷贝数变异 (CNV) 或结构变异 (SV)。最近通过使用阵列比较基因组杂交（aCGH）对动物和人类进行了研究，并发现它们与多种人类疾病有关。尽管已经描述了影响性状的个体结构变异，但尚未在基因组规模上研究它们在植物中的存在和表型效应。我们使用 aCGH 通过比较 13 个玉米自交系与 B73 的基因组来研究玉米中 CNV 的存在。通过分析近交体之间 60,472 个 60 聚体寡核苷酸探针相对于它们在参考基因组 (B73) 中的位置的杂交信号比率，我们能够识别出偏离相同拷贝数预期比率的探针簇。我们发现 CNV 分布在玉米基因组的所有染色体臂上。它们在不同种质亚群中出现的频率相当高，表明其起源古老。对几个 CNV 区域的验证显示插入/缺失和拷贝数差异。检测到的 CNV 的性质表明 CNV 可能对植物表型产生相当大的影响，包括疾病反应和杂种优势。
DNA polymorphisms such as insertion/deletions and duplications affecting genome segments larger than 1 kb are known as copy-number variations (CNVs) or structural variations (SVs). They have been recently studied in animals and humans by using array-comparative genome hybridization (aCGH), and have been associated with several human diseases. Their presence and phenotypic effects in plants have not been investigated on a genomic scale, although individual structural variations affecting traits have been described. We used aCGH to investigate the presence of CNVs in maize by comparing the genome of 13 maize inbred lines to B73. Analysis of hybridization signal ratios of 60,472 60-mer oligonucleotide probes between inbreds in relation to their location in the reference genome (B73) allowed us to identify clusters of probes that deviated from the ratio expected for equal copy-numbers. We found CNVs distributed along the maize genome in all chromosome arms. They occur with appreciable frequency in different germplasm subgroups, suggesting ancient origin. Validation of several CNV regions showed both insertion/deletions and copy-number differences. The nature of CNVs detected suggests CNVs might have a considerable impact on plant phenotypes, including disease response and heterosis.