Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum.

Transcriptomic analysis in response to Botrytis cinerea infections under conrasting nitrate regime Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants. To better understand the molecular changes underlying the impact of nitrate availability on plant susceptibility to B. cinerea, we performed plant transcriptome profiling assays on mock-treated (3 biological replicates) and infected plants ( 3 biological replicates) grown under three N conditions, using GeneChip Tomato Genome Arrays (Affymetrix).

不同硝酸盐供应条件下灰葡萄孢（Botrytis cinerea）侵染的转录组学分析
氮（Nitrogen, N）是限制植物生长与作物产量的核心营养元素之一。现有大量研究证实，作为农业土壤中主要氮源的硝酸盐，其可用性变化会调控众多植物发育程序与生理过程，其中亦包含植物防御响应过程。诸多农学研究均表明，植物的氮营养状态会显著影响其应对不同病原菌侵染时的有效防御能力。然而，氮素调控植物病原菌易感性的分子机制，目前仍未得到充分阐释。
本研究证实，番茄（Solanum lycopersicum）对死体营养型真菌灰葡萄孢的防御响应会受到植物氮素可用性的调控：在硝酸盐限制条件下，番茄对该病原菌的易感性显著升高。对不同硝酸盐供应条件下番茄应对灰葡萄孢侵染的全基因表达谱分析显示，无论硝酸盐供应水平如何，真菌侵染均会显著影响植物的初级代谢过程。这一结果提示，不同氮素条件下植物对病原菌侵染易感性的差异，并非仅能通过代谢水平的改变来解释。
我们采用系统生物学研究策略，鉴定出了不同硝酸盐供应条件下植物应对真菌侵染的转录调控网络。值得注意的是，该网络中的枢纽基因（hub genes）均为已知参与乙烯与茉莉酸信号通路的关键转录因子。这一结果表明，这两类激素是番茄植株中整合硝酸盐信号与灰葡萄孢防御响应的核心调控节点。本研究结果为解析植物死体营养型防御响应与氮素营养状态之间潜在的信号串扰机制提供了全新的研究视角。
为了更深入地解析硝酸盐可用性影响植物对灰葡萄孢易感性背后的分子变化，我们使用基因芯片番茄基因组阵列（GeneChip Tomato Genome Arrays，Affymetrix），对在三种氮素培养条件下的空白对照（mock-treated）组（3个生物学重复）与病原菌侵染植株组（3个生物学重复）开展了转录组谱分析实验。