IMPROVEMENT OF TOMATO COLD TOLERANCE BY DISCOVERING AND ALTERING CONSERVED TRANSCRIPTIONAL REGULATORS

Most studies on molecular aspects of cold tolerance in plants have focused on Arabidopsis, a temperate species well adapted to cold environments. However, many vital global vegetable crops are tropical species (e.g., Tomato), and there is a lack of understanding of their cold tolerance mechanisms. Even mild cold stress, such as chilling (<10°C), can lead to adverse effects in tomato, including chlorosis, reduced leaf expansion, and necrosis. These differential consequences of cold stress between temperate and tropical plants are poorly understood. To address this knowledge gap, I compared the cold-responsive genes between Arabidopsis and tomato. Identified conserved early response genes, especially Transcription Factors (TFs), and validated their roles in tomato cold response. By identifying conserved mechanisms, I aimed to enhance tomato cold tolerance through targeted manipulation of regulatory genes. I hypothesized that a TF that consistently responds to cold in both species is an essential regulator of cold tolerance mechanisms, and altering the expression of such TF(s) will improve tomato cold tolerance. In this project, I employed a combination of computational approaches, such as regulatory network inference and molecular techniques like gene editing, to predict and validate the critical TFs that regulate cold response. I identified ~20 TFs that consistently respond to cold in Arabidopsis and tomato. Then, I generated tomato mutant lines using CRISPR/Cas9 and experimentally validated their phenotype using the knockout mutant plants. RNA-Seq was performed using the three cbfs and five additional early cold-responsive TFs mutant lines, and the results are discussed separately in chapters 3 and 4. We concluded that CBFs play a modest role in tomato cold response but a broader role in plant physiology under ambient conditions. Moreover, the regulation of tomato cold response is mediated by a complex network with multiple hubs with overlapping roles. This research enhanced our understanding of plant cold stress response and offered candidate genes/loci for improving the resilience of tropical crops to low temperatures, thereby mitigating yield losses and extending their geographical distribution and growing seasons.