利用基因芯片分析小麦春化过程中茎尖基因表达谱的研究
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摘要
春化作用对冬小麦(Triticum aestivum L.)的开花时间以及穗发育均有重要影响,研究小麦春化作用的分子机制对小麦的引种、栽培等生产环节具有重要的指导意义。本研究以小偃6号小麦为材料,利用基因芯片技术检测了春化不同时期茎尖的基因表达谱。以芯片数据为基础,分析了小麦中已知春化相关基因、MADS-box类基因以及组蛋白修饰和DNA甲基化相关基因在春化处理和未春化处理的茎尖和叶片中的表达模式。根据芯片中基因表达量的变化,筛选出部分候选基因并进行序列克隆,通过异源转化拟南芥初步鉴定其功能。
1.春化过程中小麦茎尖的基因表达谱分析
利用SAM(Significance Analysis of Microarrays)软件对芯片数据进行分析,在FDR (False Discovery Rate)< 0.1时,共有1201组探针信号具有显著差异。结合形态学的观察结果,我们筛选到在春化作用关键时期发生显著变化的探针233组,并对其进行了功能分类。春化过程中发生显著变化的基因主要有:蛋白激酶、蛋白氧化还原酶及氨基酸转移酶相关基因(上调24个,下调11个),基因表达调控的相关基因(其中上调19个,下调14个),部分逆境胁迫基因及膜结合蛋白基因。推测这些基因参与了小麦茎尖响应春化信号的过程。
2.已知小麦春化相关基因的表达模式
通过对芯片数据的挖掘,找到了已知小麦春化相关基因VRN1、VRN2和VRN3的探针,利用qRT-PCR技术检测了这些基因在春化和未春化处理的小麦茎尖及叶片中的表达水平。结果显示,春化处理后VRN1在茎尖和叶片中均被诱导表达,未春化处理的茎尖和叶片中该基因的表达量较低;VRN2在春化和未春化处理的茎尖中表达量均较低,而在未春化处理的叶片中的表达量较高;在春化和未春化处理的茎尖和叶片中都没有检测到VRN3的mRNA积累。我们的实验结果支持了VRN1是小麦中响应春化处理并影响茎尖发育命运的关键基因这一假说。
3. MADS-box类基因可能在小麦春化作用中起到了重要作用
通过对芯片数据的分析,发现部分MADS-box基因在春化处理过程中的表达变化显著,进一步检测了这些基因在春化处理和未春化处理的茎尖以及叶片中的表达模式。我们发现,TaMADS1和TaAGL32在茎尖中具有与VRN1相似的表达模式,春化处理能够诱导这两个基因的表达。根据其表达模式,我们推测TaMADS1和TaAGL32可能与VRN1、WFL共同作用,促进了小麦茎尖在春化过程中的成花转变。此外,春化处理能够抑制TaAGL1、TaAGL11、TaAGL13和TaAGL41在茎尖中的表达,说明这些基因的功能可能是抑制小麦茎尖的成花转变,而春化处理能够解除这种抑制。
4.组蛋白修饰和DNA甲基化相关基因可能参与了小麦春化作用的过程
我们检测了小麦中组蛋白修饰和DNA甲基化相关基因在春化处理和未春化处理的茎尖及叶片中的表达模式。结果显示,春化处理能够抑制TaVIL1、TaVIL2、TaHAT2、TaHDAC3、TaCMT3和TaMBD1在茎尖的表达,推测这些基因参与了小麦茎尖响应春化处理并进行成花转变过程中的基因表达调控。
5.过表达TaAP2推迟了拟南芥的开花时间
在发生显著变化的233组探针中,我们选取了6个转录因子基因进行克隆,并转化拟南芥,研究其对拟南芥开花时间的影响。研究发现,过表达TaAP2能够延迟拟南芥在长日照下的开花时间,而春化处理能够抑制这个基因在茎尖的表达,因此,我们认为这个基因的功能可能是抑制小麦茎尖的成花转变。
综上所述,本研究以基因芯片分析为切入点,筛选在春化过程中小麦茎尖表达显著变化的基因,并检测了部分基因在春化处理和未春化处理的茎尖及叶片中的表达模式。通过对其表达模式的分析,我们认为MADS-box类基因(VRN1、VRN2、TaMADS1、TaAGL32、VRT2、TaAGL1、TaAGL11、TaAGL13和TaAGL41等)在小麦茎尖响应春化处理并影响茎尖发育命运的过程中起到了关键作用,同时组蛋白修饰和DNA甲基化相关基因也参与了小麦春化过程中茎尖的基因表达调控。
Vernalization is an important physiological process for heading date and spike initiation of winter wheat (Triticum aestivum L.). To study the molecular basis of vernalization in wheat, total RNAs were isolated from shoot apex after treatment at 4°C for 0, 5, 10, 15, 20 days for Microarray hybridization. Based on the Microarray data, 1201 differently expressed sequences were identified (FDR<1%). We examined the expression pattern of different class genes in shoot apex and leaves with or without vernalization. The results were as follows:
1. Microarray data analysis
The SAM system software was used to analyze the Microarray data. When the FDR (False Discovery Rate) < 0.1, there were 1201 sets of probes passed the significant difference test. Eighty three percent ( 10/12) differently expressed sequences were confirmed by qRT-PCR. Two hundred thirty three sets of probes may be involved in the transcriptional control of genes expression in wheat shoot apex during vernalization. Classification of differently expressed genes by their functions shows that the genes involved in protein kinase, oxidordeuctase, transferase and transcriptional regulation play the important roles in the wheat vernalization process.
2. Expression patterns of the genes involved in vernalization.
The Microarray data displayed the primary expression patterns of the genes involved in vernalization. We further used qRT-PCR method to examine the expression patterns of these genes in shoot apex and leaves with or without vernalization treatment. The qRT-PCR results showed that the expression of VRN1 was induced in the shoot apex and leaves with vernalization treatment; but VRN1 was not expressed in the shoot apex or leaves without vernalization. VRN2 was not expressed in the shoot apices with or without vernalization; whereas VRN2 was expressed in leaves, and the vernalization treatment just represses its expression level slightly. Expression of VRN3 was not detected in both shoot apices and leaves with or without vernalization. The results supported the hypothesis that activation of VRN1 mediates the low-temperature flowering response in wheat.
3. MADS-box genes may play the important roles in wheat vernalization
Since many MADS-box genes involved in the flowering control and floral development in plants, we examined the expression patterns of wheat MADS-box genes in shoot apex and leaves with or without vernalization treatment. Among them, six genes were chosen for further expression analysis. TaMADS1 and TaAGL32 displayed a similar expression pattern with VRN1 in shoot apices during vernalization or not, but they were not expressed in the leaves. Based on their expression patterns, we proposed that TaMADS1 and TaAGL32 may function together with VRN1 and WFL. TaAGL1, TaAGL11, TaAGL13 and TaAGL41 showed the reduced expression levels in shoot apices with vernalization treatment; but low expression level was detected in leaves during vernalization or not. It was suggested that they may belongs to the repressors of flowering in shoot apices.
4. Histone modification and DNA methylation may be involved in the process of wheat vernalization
During vernalization, the levels of Histone modification and DNA methylation had been determined. Based on the microarray data, we examined the expression patterns of some genes including TaVIL1, TaVIL3, TaHAT2, TaHDAC3, TaCMT3 and TaMBD1, and these genes demonstrated the reduced expression patterns. By analysis of the expression levels of those genes in shoot apex with vernalization and without vernalization, we found that low temperature could repress the expression leves of these genes. Thus, it was proposed that these genes may participate in the regulation of gene expression during vernalization in wheat.
5. The flowering time was delayed by overexpression of TaAP2 in Arabidopsis
Finally, we isolate six transcription factor genes from these 233 sequences. Late flowering phenotype occurred in overexpressed TaAP2 plants under long day conditions. Related to the deduced expression pattern of TaAP2 in vernalized shoot apex, we proposed that TaAP2 may be a repressor of wheat flowering.
1.春化过程中小麦茎尖的基因表达谱分析
利用SAM(Significance Analysis of Microarrays)软件对芯片数据进行分析,在FDR (False Discovery Rate)< 0.1时,共有1201组探针信号具有显著差异。结合形态学的观察结果,我们筛选到在春化作用关键时期发生显著变化的探针233组,并对其进行了功能分类。春化过程中发生显著变化的基因主要有:蛋白激酶、蛋白氧化还原酶及氨基酸转移酶相关基因(上调24个,下调11个),基因表达调控的相关基因(其中上调19个,下调14个),部分逆境胁迫基因及膜结合蛋白基因。推测这些基因参与了小麦茎尖响应春化信号的过程。
2.已知小麦春化相关基因的表达模式
通过对芯片数据的挖掘,找到了已知小麦春化相关基因VRN1、VRN2和VRN3的探针,利用qRT-PCR技术检测了这些基因在春化和未春化处理的小麦茎尖及叶片中的表达水平。结果显示,春化处理后VRN1在茎尖和叶片中均被诱导表达,未春化处理的茎尖和叶片中该基因的表达量较低;VRN2在春化和未春化处理的茎尖中表达量均较低,而在未春化处理的叶片中的表达量较高;在春化和未春化处理的茎尖和叶片中都没有检测到VRN3的mRNA积累。我们的实验结果支持了VRN1是小麦中响应春化处理并影响茎尖发育命运的关键基因这一假说。
3. MADS-box类基因可能在小麦春化作用中起到了重要作用
通过对芯片数据的分析,发现部分MADS-box基因在春化处理过程中的表达变化显著,进一步检测了这些基因在春化处理和未春化处理的茎尖以及叶片中的表达模式。我们发现,TaMADS1和TaAGL32在茎尖中具有与VRN1相似的表达模式,春化处理能够诱导这两个基因的表达。根据其表达模式,我们推测TaMADS1和TaAGL32可能与VRN1、WFL共同作用,促进了小麦茎尖在春化过程中的成花转变。此外,春化处理能够抑制TaAGL1、TaAGL11、TaAGL13和TaAGL41在茎尖中的表达,说明这些基因的功能可能是抑制小麦茎尖的成花转变,而春化处理能够解除这种抑制。
4.组蛋白修饰和DNA甲基化相关基因可能参与了小麦春化作用的过程
我们检测了小麦中组蛋白修饰和DNA甲基化相关基因在春化处理和未春化处理的茎尖及叶片中的表达模式。结果显示,春化处理能够抑制TaVIL1、TaVIL2、TaHAT2、TaHDAC3、TaCMT3和TaMBD1在茎尖的表达,推测这些基因参与了小麦茎尖响应春化处理并进行成花转变过程中的基因表达调控。
5.过表达TaAP2推迟了拟南芥的开花时间
在发生显著变化的233组探针中,我们选取了6个转录因子基因进行克隆,并转化拟南芥,研究其对拟南芥开花时间的影响。研究发现,过表达TaAP2能够延迟拟南芥在长日照下的开花时间,而春化处理能够抑制这个基因在茎尖的表达,因此,我们认为这个基因的功能可能是抑制小麦茎尖的成花转变。
综上所述,本研究以基因芯片分析为切入点,筛选在春化过程中小麦茎尖表达显著变化的基因,并检测了部分基因在春化处理和未春化处理的茎尖及叶片中的表达模式。通过对其表达模式的分析,我们认为MADS-box类基因(VRN1、VRN2、TaMADS1、TaAGL32、VRT2、TaAGL1、TaAGL11、TaAGL13和TaAGL41等)在小麦茎尖响应春化处理并影响茎尖发育命运的过程中起到了关键作用,同时组蛋白修饰和DNA甲基化相关基因也参与了小麦春化过程中茎尖的基因表达调控。
Vernalization is an important physiological process for heading date and spike initiation of winter wheat (Triticum aestivum L.). To study the molecular basis of vernalization in wheat, total RNAs were isolated from shoot apex after treatment at 4°C for 0, 5, 10, 15, 20 days for Microarray hybridization. Based on the Microarray data, 1201 differently expressed sequences were identified (FDR<1%). We examined the expression pattern of different class genes in shoot apex and leaves with or without vernalization. The results were as follows:
1. Microarray data analysis
The SAM system software was used to analyze the Microarray data. When the FDR (False Discovery Rate) < 0.1, there were 1201 sets of probes passed the significant difference test. Eighty three percent ( 10/12) differently expressed sequences were confirmed by qRT-PCR. Two hundred thirty three sets of probes may be involved in the transcriptional control of genes expression in wheat shoot apex during vernalization. Classification of differently expressed genes by their functions shows that the genes involved in protein kinase, oxidordeuctase, transferase and transcriptional regulation play the important roles in the wheat vernalization process.
2. Expression patterns of the genes involved in vernalization.
The Microarray data displayed the primary expression patterns of the genes involved in vernalization. We further used qRT-PCR method to examine the expression patterns of these genes in shoot apex and leaves with or without vernalization treatment. The qRT-PCR results showed that the expression of VRN1 was induced in the shoot apex and leaves with vernalization treatment; but VRN1 was not expressed in the shoot apex or leaves without vernalization. VRN2 was not expressed in the shoot apices with or without vernalization; whereas VRN2 was expressed in leaves, and the vernalization treatment just represses its expression level slightly. Expression of VRN3 was not detected in both shoot apices and leaves with or without vernalization. The results supported the hypothesis that activation of VRN1 mediates the low-temperature flowering response in wheat.
3. MADS-box genes may play the important roles in wheat vernalization
Since many MADS-box genes involved in the flowering control and floral development in plants, we examined the expression patterns of wheat MADS-box genes in shoot apex and leaves with or without vernalization treatment. Among them, six genes were chosen for further expression analysis. TaMADS1 and TaAGL32 displayed a similar expression pattern with VRN1 in shoot apices during vernalization or not, but they were not expressed in the leaves. Based on their expression patterns, we proposed that TaMADS1 and TaAGL32 may function together with VRN1 and WFL. TaAGL1, TaAGL11, TaAGL13 and TaAGL41 showed the reduced expression levels in shoot apices with vernalization treatment; but low expression level was detected in leaves during vernalization or not. It was suggested that they may belongs to the repressors of flowering in shoot apices.
4. Histone modification and DNA methylation may be involved in the process of wheat vernalization
During vernalization, the levels of Histone modification and DNA methylation had been determined. Based on the microarray data, we examined the expression patterns of some genes including TaVIL1, TaVIL3, TaHAT2, TaHDAC3, TaCMT3 and TaMBD1, and these genes demonstrated the reduced expression patterns. By analysis of the expression levels of those genes in shoot apex with vernalization and without vernalization, we found that low temperature could repress the expression leves of these genes. Thus, it was proposed that these genes may participate in the regulation of gene expression during vernalization in wheat.
5. The flowering time was delayed by overexpression of TaAP2 in Arabidopsis
Finally, we isolate six transcription factor genes from these 233 sequences. Late flowering phenotype occurred in overexpressed TaAP2 plants under long day conditions. Related to the deduced expression pattern of TaAP2 in vernalized shoot apex, we proposed that TaAP2 may be a repressor of wheat flowering.
引文
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