Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray
Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray
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DOI：
10.1007/s10142-005-0010-3
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发表时间：
2006-04-01
影响因子：
2.9
通讯作者：
Ogihara, Yasunari
中科院分区：
文献类型：
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作者：
Kawaura, Kanako;Mochida, Keiichi;Ogihara, Yasunari
在本研究中，我们构建了一个22 k小麦寡聚DNA芯片。从日本小麦基因组学协会的数据库中收集了总共148，676个普通小麦的表达序列标签。这些被分组为34，064个重叠群，然后用于设计寡核苷酸DNA微阵列。在正义链的多步选择之后，选择21，939个60-mer寡聚DNA探针用于附着在微阵列载玻片上。利用该基因芯片研究了小麦对盐胁迫的转录响应。当用从盐处理的小麦芽和根中提取的RNA作为靶时，超过95%的探针给出了可重复的杂交信号。通过微阵列，我们确定了1，811个基因，其表达在盐的反应中变化超过2倍。这些包括已知介导对盐的反应的基因，以及未知的基因，通过层次聚类将它们分为12个主要组。这些基因的表达模式也证实了实时逆转录PCR。许多功能未知的基因与已知参与盐胁迫反应的基因聚集在一起。因此，结合基因本体论分析基因表达模式有助于确定未知基因的功能。此外，这些小麦基因的功能分析应该提供新的见解盐胁迫的反应。最后，这些结果表明，22 k oligo-DNA微阵列是一种可靠的方法来监测全球基因表达模式的小麦。
In this study, we constructed a 22k wheat oligo-DNA microarray. A total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan. These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray. Following a multistep selection of the sense strand, 21,939 60-mer oligo-DNA probes were selected for attachment on the microarray slide. This 22k oligo-DNA microarray was used to examine the transcriptional response of wheat to salt stress. More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots. With the microarray, we identified 1,811 genes whose expressions changed more than 2-fold in response to salt. These included genes known to mediate response to salt, as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering. These gene expression patterns were also confirmed by real-time reverse transcription-PCR. Many of the genes with unknown function were clustered together with genes known to be involved in response to salt stress. Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes. Also, functional analysis of these wheat genes should provide new insight into the response to salt stress. Finally, these results indicate that the 22k oligo-DNA microarray is a reliable method for monitoring global gene expression patterns in wheat.