Breeding for resistance is the most effective tool for controlling the corky root disease of tomato caused by Pyrenochaeta lycopersici. A comparative RNA-Seq-based transcriptomic analysis was conducted at 96 hpi (hours post infection) on two tomato cultivars: resistant Mogeor and its genetic background, and susceptible Moneymaker to investigate the differences in their transcriptomic response and identify the molecular bases of this plant-pathogen interaction. The number of differentially expressed genes (DEGs) identified was much higher in the susceptible than in the resistant genotype; however, the proportion of upregulated genes was higher in Mogeor (70.81%) than in Moneymaker (52.95%). Gene Ontology (GO) analysis enabled identification of 24 terms shared by the two cultivars that were consistent with responses to external stimulus, such as fungal infection. On the other hand, as many as 54 GO were enriched solely in Moneymaker, including terms related to defense response and cell wall metabolism. Our results could support the previous observations in other pathosystems, that susceptibility and resistance have overlapping signaling pathways and responses, suggesting that the P. lycopersici resistance gene pyl might be a recessive allele at a susceptibility locus, for which different candidate genes were identified based on the differences in induction or expression levels, observed between the resistant and susceptible genotype. MapMan analysis highlighted a complex hormone and transcription factors interplay where SA- and JA-induced pathways are modulated in a similar way in both genotypes and thus take part in a common response while the ethylene signaling pathways, induced mainly in susceptible Moneymaker, seem putatively contribute to its susceptibility.

中文翻译：

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在抗性番茄品种Mogeor及其背景基因型易感Moneymaker中，对Pyrenochaeta lycopersici响应的比较转录组分析。

抗性育种是控制番茄斑节菜引起的根腐病最有效的工具。在96 hpi（感染后数小时）对两个番茄品种进行了基于RNA-Seq的比较转录组分析：两个抗性Mogeor及其遗传背景，以及易受害的Moneymaker，以研究其转录组反应的差异并鉴定该植物的分子基础-病原体相互作用。在易感人群中鉴定出的差异表达基因（DEG）数量比在耐药基因型中高得多。然而，Mogeor（70.81％）中的上调基因比例高于Moneymaker（52.95％）。基因本体论（GO）分析能够识别两个品种共享的24个术语，这些术语与对外部刺激（例如真菌感染）的反应一致。另一方面，多达54个GO仅在Moneymaker中进行了充实，包括与防御反应和细胞壁代谢有关的术语。我们的结果可以支持以前在其他病理系统中的观察，即易感性和耐药性具有重叠的信号传导途径和反应，表明lycopersici抗性基因pyl可能是易感性位点的隐性等位基因，基于在抗性和易感基因型之间观察到的诱导或表达水平差异，可以鉴定出不同的候选基因。MapMan分析强调了复杂的激素和转录因子之间的相互作用，其中SA和JA诱导的途径在两种基因型中都以相似的方式进行调节，因此参与了共同的反应，而主要在易感的Moneymaker中诱导的乙烯信号传导途径似乎是推定的其敏感性。