Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis.
Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis.
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DOI：
10.1371/journal.pone.0049522
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Tran LS
中科院分区：
文献类型：
--
作者：
Le DT;Nishiyama R;Watanabe Y;Tanaka M;Seki M;Ham le H;Yamaguchi-Shinozaki K;Shinozaki K;Tran LS
大豆全基因组序列的可获得性使研究团体能够设计出用于大豆全基因组表达谱分析的66K Affymetrix大豆阵列基因芯片。在这项研究中，我们对大豆植株的叶片组织进行了微阵列分析，这些植株在营养生长后期V6和盛花期生殖阶段R2受到干旱胁迫。我们的数据分析表明，在大约66000个假定基因中，有46093个被高度可信地预测的大豆基因，其中41059个基因可被赋予已知功能。采用比值变化≥2且q值<0.05的标准，我们在受干旱胁迫的V6和R2叶片中分别鉴定出1458个和1818个上调基因以及1582个和1688个下调基因。这些数据集被分类为19个最丰富的生物学类别，且比例相似。在两个阶段中，上调基因和下调基因中分别仅有612个和463个基因重叠，这表明在植物发育的不同阶段，干旱响应的调控可能涉及保守和非保守的途径。利用我们的数据集以及干旱胁迫的拟南芥叶片数据集进行的比较表达分析揭示了调控干旱响应的保守和物种特异性机制的存在。许多上调基因编码调节蛋白，如转录因子（包括与拟南芥DREB、NAC、AREB和ZAT/STZ转录因子具有高度同源性的那些）、激酶和双组分系统成员，或者功能蛋白，例如晚期胚胎发生丰富蛋白、糖基转移酶、糖苷水解酶、防御素和乙二醛酶I家族蛋白。对GmNAC家族和激素相关基因类别的详细分析表明，许多GmNAC和激素相关基因在V6和/或R2叶片中的表达因干旱而改变。此外，许多光合作用相关基因的下调（这有助于干旱胁迫下的生长迟缓）可能作为植物生存的一种适应机制。这项研究已经鉴定出了优秀的干旱响应候选基因，以便进行深入表征以及未来开发改良的耐旱转基因大豆。
The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46093 soybean genes, which were predicted with high confidence among approximately 66000 putative genes, 41059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.
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DOI：
10.1093/dnares/dsq032
发表时间：
2011-02
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Le DT;Nishiyama R;Watanabe Y;Mochida K;Yamaguchi-Shinozaki K;Shinozaki K;Tran LS
通讯作者：
Tran LS
影响因子：
6.9
作者：
Choudhary SP;Oral HV;Bhardwaj R;Yu JQ;Tran LS
通讯作者：
Tran LS
DOI：
10.1093/dnares/dsp023
发表时间：
2009-12
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Mochida K;Yoshida T;Sakurai T;Yamaguchi-Shinozaki K;Shinozaki K;Tran LS
通讯作者：
Tran LS
影响因子：
4.9
作者：
Matsui, Akihiro;Ishida, Junko;Seki, Motoaki
通讯作者：
Seki, Motoaki
DOI：
10.1073/pnas.0604882103
发表时间：
2006-08-29
影响因子：
11.1
作者：
Hu, Honghong;Dai, Mingqiu;Xiong, Lizhong
通讯作者：
Xiong, Lizhong