| Summary: | Chili (<i>Capsicum annuum</i> L.) is highly susceptible to soilborne diseases, thereby presenting a significant threat that results in considerable yield losses in chili production. The exploration of genes conferring resistance and the underlying defense mechanisms presents a promising strategy for bolstering plant disease control. In this study, we selected two distinct cultivars, the disease-sensitive ‘Hailan 99’ and the disease-tolerant ‘Sanxiaqing’, to elucidate the molecular basis of their responses to soilborne disease intervention. We conducted a comprehensive analysis of root morphological characteristics and transcriptome profiles under stress conditions. Our findings revealed that, when subjected to soilborne disease intervention, these two cultivars exhibited contrasting root system characteristics and responses, reflecting diverse defense strategies. The disease-resistant cultivar demonstrated superior adaptability, possibly owing to its capacity for swift recognition of pathogen effectors, activation of defense responses, and effective containment of infection at localized sites, thus impeding disease progression. Noteworthy genes such as <i>T459_04053</i>, implicated in effector recognition; <i>MSTRG.26158</i>, <i>MSTRG.30886</i>, and <i>T459_22510</i>, associated with secondary metabolite biosynthesis; and <i>T459_05615</i>, partaking in the autophagy pathway, along with other differentially expressed genes linked to effector recognition, immune activation, and modulation of cell death processes, offer valuable insights into enhancing soilborne disease resistance in chili. Furthermore, these findings contribute to an enhanced understanding of the molecular mechanisms underlying soilborne disease resistance in diverse plant crops.
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