番茄材料PI 114490抗疮痂病T3小种相关基因的分离和功能分析
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摘要
由黄单胞杆菌属(Xanthomonas)引起的疮痂病已成为世界范围内番茄生产的毁灭性病害之一。番茄疮痂病病原菌的多样性以及抗药性给依赖于农药的化学防治带来巨大挑战,而利用抗性材料并揭示抗病机理被认为是防治该病长期有效的经济环保措施。番茄疮痂病抗性材料对病原菌的抗性反应可分为过敏反应抗性和田间抗性。目前针对番茄疮痂病的田间和过敏反应抗性遗传分析已做了较深入的研究,但是关于田间抗性反应所调控的差异表达谱还没有研究报道。
本论文利用cDNA-AFLP (cDNA-amplified fragment length polymorphism)技术分离田间抗性材料PI114490和感病材料OH88119受T3小种侵染第3、4和5d的差异表达基因。使用256对引物组合共获得71个差异表达基因,其中有60个基因在两材料接菌后3、4和5d持续上调表达,利用RT-PCR或qRT-PCR对18个上调表达基因的表达模式进行了确认,表明抗、感材料会激活部分相同的防御反应以应对T3小种的侵染。
利用RNA-seq技术对两份材料接种T3小种后6h和6d以及接水对照的数字表达谱进行了分析。6个样品平均得到7M的读段(reads),每个样品的clean read约匹配到21,526个基因,占番茄参考基因总数(34,727)的62%。利用维恩图和聚类分析对两材料接菌两个时间点的差异表达基因进行了交叉比较。总体而言,抗病材料PI114490在6h和6d的差异表达基因数目同比多于感病材料OH88119。接菌6h抗、感材料分别仅有78个和15个基因上调表达,功能注释表明可诱导的防御反应在接菌6h时可能还未被激活。抗、感材料接菌6d的差异表达数目同比多于6h,其中有326个差异基因在两材料中共同上调表达,这些基因可能参与了可诱导的基础防御反应。KEGG分析显示,涉及植物激素信号转导和植物-病原菌互作等防御反应相关途径中的基因在PI114490接菌6d上调表达的数目多于OH88119。而且与防御反应有关的NBS-LRR和、VRKY家族中的差异表达基因在抗病材料中也多于感病材料。比较并筛选cDNA-AFLP和RNA-seq两种技术获得的表达模式相同的差异基因,有14个基因在抗、感材料中都上调表达。cDNA-AFLP和RNA-seq的结果为了解番茄疮痂病田间抗性机理和分子标记辅助选择提供了大量有价值的差异表达基因。
面对大量的上调表达基因,利用病毒诱导的基因沉默技术(Virus-induced gene silencing, VIGS)筛选到一个编码U-box的基因-(?)KPUB24,该基因沉默植株接种T3小种后叶片表面的病斑数多于对照,利用农杆菌介导的瞬时表达技术显示该基因的过表达植株接种T3小种后叶片内病原菌数量少于对照,推测SlPUB24基因可能在番茄疮痂病田间抗性反应中起正调控的作用。洋葱表皮亚细胞定位显示该基因主要在细胞质中表达。为了进一步验证该基因的功能,构建番茄稳定遗传转化体系并将该基因的特异沉默载体S1PUB24-RNAi转入抗病材料PI114490,而过表达载体35S-S1PUB24转入感病材料OH88119,经PCR分子鉴定都已获得20株以上的To代阳性植株。
本论文所获得的差异表达谱信息和SlPUB24的功能对于番茄-疮痂病病原菌的互作机理以及番茄抗疮痂病遗传育种研究具有重要的理论意义和潜在的应用价值。
Bacterial spot caused by several Xanthomonas sp. is one of the most devastating diseases in tomato (Solanum lycopersicum L.). Due to the existence of multiple pathogen species and races, marginal efficacy of commonly applied chemicals, development of resistance to these chemicals in bacterial populations, and a lack of available disease resistance traits in commercial cultivars, control of the disease has not been effective once epidemics start. Exploiting host resistance gene(s) combined with important defense response genes for developing durable resistant cultivars is considered as an effective approach to manage the disease. The resistance response to bacterial spot can be divided into hypersensitive response and field resistance response. The genetics of hypersensitive resistance to X. perforans race T3has been intensively investigated, and regulatory genes during the infection of race T3have been identified through transcriptional profiling. However, no work on isolating regulatory genes for field resistance has been reported.
In this study, cDNA-amplified fragment length polymorphism technique was used to identify differentially expressed transcripts between resistant tomato accession PI114490and susceptible variety OH88119at3,4and5days post-inoculation of the pathogen. Using256selective primer combinations, a total of79differentially expressed transcript-derived fragments (TDFs) representing71genes were obtained. Of which,60were up-regulated at different levels in two tomato lines,4were down-regulated in both tomato lines,4were uniquely up-regulated and2were uniquely down-regulated in PI114490, and1was specific up-regulated in OH88119. The expression patterns of19representative TDFs were further confirmed by semi-quantitative and/or quantitative real time RT-PCR. These results suggested that the two tomato lines involve activation of partly similar defensive mechanism in response to race T3.
RNA-seq was used to investigate transcript dynamics response to X. perforans race T3in the resistant line PI114490and susceptible line OH88119. A total of six samples were examined, which were mock-treatment and race T3post-inoculation at6h (6HPI) and6d (6DPI) for both two tomato lines. An average of7million reads was generated with approximately21,526mapped genes in each samples, accounting for approximately62%of reference tomato genes. The differentially expressed genes (DEGs) between two tomato lines and two time-points were compared through venn diagram and cluster analysis. Overall, the number of DEGs response to race T3was more in PI114490than that in OH88119at both two inoculation stages, and the number of DEGs at6DPI was significantly more than6HPI in both tomato lines. Only78and15genes were up-regulated at6HPI in PI114490and OH88119, respectively, while the down-regulated genes were numerically greater, demonstrating that the inducible defense response against race T3might have not been activated at6HPI. Accumulation expression levels of326co-up regulated genes in two tomato lines at6DPI were likely to involve in basal inducible defense response, while the specific and strongly induced genes at6DPI might be correlated with the absence of symptom in PI114490. KEGG enrichment analysis indicated the number of up-regulated genes which related to the process of defense response including plant hormone signal transduction and plant-pathogen interaction pathway were more in PI114490than that in OH88119at6DPI. The differentially expressed genes containing NBS-LRR domain, defense-related WRKY transcription factor were presented, which might take prominent roles in defense process. Comparing the cDNA-AFLP analysis and RNA-seq data discovered14common up-regulated genes. These data will provide a valuable resource for mechanism studies underlying X. perforans interaction with tomato plants.
Virus-induced gene silencing (VIGS) was used to validate the function of up-regulated genes. A gene encoding U-box protein, tentatively named SIPUB24, that may be related to the process of resistance was identified. SIPUB24VIGS-silenced plants showed numerically greater small black foliar lesions after inoculation with race T3than control plants. Using Agrobacterium-mediated transient expression assay to over-expressed SIPUB24in tomato leaves results in less race T3bacterial growth than control. So we speculated that SIPUB24gene might play a positive regulation role in tomato field-resistance to bacterial spot race T3. Subcellular localization showed the S1PUB24-eGFP fusion protein accumulated in the cytoplasm of transiently transformed onion epidermal. To further validate the function of SIPUB24, silencing vector of S1PUB24-RNAi and over-expression vector of35S-S1PUB24was transformated into tomato line PI114490and OH88119, respectively. Integration of S1PUB24-RNAi and35S-S1PUB24into tomato genome was confirmed by PCR, and at least twenty positive generation plants were obtained for disease evaluation.
The results of differentially expressed profiling and SIPUB24, obtained in this study, will help to uncover the mechanisms of tomato-X.perforans interaction, and have potential application value on tomato resistance breeding for bacterial spot.
本论文利用cDNA-AFLP (cDNA-amplified fragment length polymorphism)技术分离田间抗性材料PI114490和感病材料OH88119受T3小种侵染第3、4和5d的差异表达基因。使用256对引物组合共获得71个差异表达基因,其中有60个基因在两材料接菌后3、4和5d持续上调表达,利用RT-PCR或qRT-PCR对18个上调表达基因的表达模式进行了确认,表明抗、感材料会激活部分相同的防御反应以应对T3小种的侵染。
利用RNA-seq技术对两份材料接种T3小种后6h和6d以及接水对照的数字表达谱进行了分析。6个样品平均得到7M的读段(reads),每个样品的clean read约匹配到21,526个基因,占番茄参考基因总数(34,727)的62%。利用维恩图和聚类分析对两材料接菌两个时间点的差异表达基因进行了交叉比较。总体而言,抗病材料PI114490在6h和6d的差异表达基因数目同比多于感病材料OH88119。接菌6h抗、感材料分别仅有78个和15个基因上调表达,功能注释表明可诱导的防御反应在接菌6h时可能还未被激活。抗、感材料接菌6d的差异表达数目同比多于6h,其中有326个差异基因在两材料中共同上调表达,这些基因可能参与了可诱导的基础防御反应。KEGG分析显示,涉及植物激素信号转导和植物-病原菌互作等防御反应相关途径中的基因在PI114490接菌6d上调表达的数目多于OH88119。而且与防御反应有关的NBS-LRR和、VRKY家族中的差异表达基因在抗病材料中也多于感病材料。比较并筛选cDNA-AFLP和RNA-seq两种技术获得的表达模式相同的差异基因,有14个基因在抗、感材料中都上调表达。cDNA-AFLP和RNA-seq的结果为了解番茄疮痂病田间抗性机理和分子标记辅助选择提供了大量有价值的差异表达基因。
面对大量的上调表达基因,利用病毒诱导的基因沉默技术(Virus-induced gene silencing, VIGS)筛选到一个编码U-box的基因-(?)KPUB24,该基因沉默植株接种T3小种后叶片表面的病斑数多于对照,利用农杆菌介导的瞬时表达技术显示该基因的过表达植株接种T3小种后叶片内病原菌数量少于对照,推测SlPUB24基因可能在番茄疮痂病田间抗性反应中起正调控的作用。洋葱表皮亚细胞定位显示该基因主要在细胞质中表达。为了进一步验证该基因的功能,构建番茄稳定遗传转化体系并将该基因的特异沉默载体S1PUB24-RNAi转入抗病材料PI114490,而过表达载体35S-S1PUB24转入感病材料OH88119,经PCR分子鉴定都已获得20株以上的To代阳性植株。
本论文所获得的差异表达谱信息和SlPUB24的功能对于番茄-疮痂病病原菌的互作机理以及番茄抗疮痂病遗传育种研究具有重要的理论意义和潜在的应用价值。
Bacterial spot caused by several Xanthomonas sp. is one of the most devastating diseases in tomato (Solanum lycopersicum L.). Due to the existence of multiple pathogen species and races, marginal efficacy of commonly applied chemicals, development of resistance to these chemicals in bacterial populations, and a lack of available disease resistance traits in commercial cultivars, control of the disease has not been effective once epidemics start. Exploiting host resistance gene(s) combined with important defense response genes for developing durable resistant cultivars is considered as an effective approach to manage the disease. The resistance response to bacterial spot can be divided into hypersensitive response and field resistance response. The genetics of hypersensitive resistance to X. perforans race T3has been intensively investigated, and regulatory genes during the infection of race T3have been identified through transcriptional profiling. However, no work on isolating regulatory genes for field resistance has been reported.
In this study, cDNA-amplified fragment length polymorphism technique was used to identify differentially expressed transcripts between resistant tomato accession PI114490and susceptible variety OH88119at3,4and5days post-inoculation of the pathogen. Using256selective primer combinations, a total of79differentially expressed transcript-derived fragments (TDFs) representing71genes were obtained. Of which,60were up-regulated at different levels in two tomato lines,4were down-regulated in both tomato lines,4were uniquely up-regulated and2were uniquely down-regulated in PI114490, and1was specific up-regulated in OH88119. The expression patterns of19representative TDFs were further confirmed by semi-quantitative and/or quantitative real time RT-PCR. These results suggested that the two tomato lines involve activation of partly similar defensive mechanism in response to race T3.
RNA-seq was used to investigate transcript dynamics response to X. perforans race T3in the resistant line PI114490and susceptible line OH88119. A total of six samples were examined, which were mock-treatment and race T3post-inoculation at6h (6HPI) and6d (6DPI) for both two tomato lines. An average of7million reads was generated with approximately21,526mapped genes in each samples, accounting for approximately62%of reference tomato genes. The differentially expressed genes (DEGs) between two tomato lines and two time-points were compared through venn diagram and cluster analysis. Overall, the number of DEGs response to race T3was more in PI114490than that in OH88119at both two inoculation stages, and the number of DEGs at6DPI was significantly more than6HPI in both tomato lines. Only78and15genes were up-regulated at6HPI in PI114490and OH88119, respectively, while the down-regulated genes were numerically greater, demonstrating that the inducible defense response against race T3might have not been activated at6HPI. Accumulation expression levels of326co-up regulated genes in two tomato lines at6DPI were likely to involve in basal inducible defense response, while the specific and strongly induced genes at6DPI might be correlated with the absence of symptom in PI114490. KEGG enrichment analysis indicated the number of up-regulated genes which related to the process of defense response including plant hormone signal transduction and plant-pathogen interaction pathway were more in PI114490than that in OH88119at6DPI. The differentially expressed genes containing NBS-LRR domain, defense-related WRKY transcription factor were presented, which might take prominent roles in defense process. Comparing the cDNA-AFLP analysis and RNA-seq data discovered14common up-regulated genes. These data will provide a valuable resource for mechanism studies underlying X. perforans interaction with tomato plants.
Virus-induced gene silencing (VIGS) was used to validate the function of up-regulated genes. A gene encoding U-box protein, tentatively named SIPUB24, that may be related to the process of resistance was identified. SIPUB24VIGS-silenced plants showed numerically greater small black foliar lesions after inoculation with race T3than control plants. Using Agrobacterium-mediated transient expression assay to over-expressed SIPUB24in tomato leaves results in less race T3bacterial growth than control. So we speculated that SIPUB24gene might play a positive regulation role in tomato field-resistance to bacterial spot race T3. Subcellular localization showed the S1PUB24-eGFP fusion protein accumulated in the cytoplasm of transiently transformed onion epidermal. To further validate the function of SIPUB24, silencing vector of S1PUB24-RNAi and over-expression vector of35S-S1PUB24was transformated into tomato line PI114490and OH88119, respectively. Integration of S1PUB24-RNAi and35S-S1PUB24into tomato genome was confirmed by PCR, and at least twenty positive generation plants were obtained for disease evaluation.
The results of differentially expressed profiling and SIPUB24, obtained in this study, will help to uncover the mechanisms of tomato-X.perforans interaction, and have potential application value on tomato resistance breeding for bacterial spot.
引文
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