Transcriptomic Profiling of Tomato Leaves Identifies Novel Transcription Factors Responding to Dehydration Stress

Abstract

Drought is among the most challenging environmental restrictions to tomatoes (Solanum lycopersi-cum), which causes dehydration of the tissues and results in massive loss of yield. Breeding for dehydration-tolerant tomatoes is a pressing issue as a result of global climate change that leads to increased duration and frequency of droughts. However, the key genes involved in dehydration response and tolerance in tomato are not widely known, and genes that can be targeted for dehydration-tolerant tomato breeding remains to be discovered. Here, we compared phenotypes and transcriptomic profiles of tomato leaves between control and dehydration conditions. We show that dehydration decreased the relative water content of tomato leaves after 2 h of dehydration treatment; however, it promoted the malondialdehyde (MDA) content and ion leakage ratio after 4 h and 12 h of dehydration, respectively. Moreover, dehydration stress triggered oxidative stress as we detected significant increases in H2O2 and O2− levels. Simultaneously, dehydration enhanced the activities of antioxidant enzymes including peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), and phenylalanine ammonia-lyase (PAL). Genome-wide RNA sequencing of tomato leaves treated with or without dehydration (control) identified 8116 and 5670 differentially expressed genes (DEGs) after 2 h and 4 h of dehydration, respectively. These DEGs included genes involved in translation, photosynthesis, stress response, and cytoplasmic translation. We then focused specifically on DEGs annotated as transcription factors (TFs). RNA-seq analysis identified 742 TFs as DEGs by comparing samples dehydrated for 2 h with 0 h control, while among all the DEGs detected after 4 h of dehydration, only 499 of them were TFs. Furthermore, we performed real-time quantitative PCR analyses and validated expression patterns of 31 differentially expressed TFs of NAC, AP2/ERF, MYB, bHLH, bZIP, WRKY, and HB families. In addition, the transcriptomic data revealed that expression levels of six drought-responsive marker genes were upregulated by de-hydration treatment. Collectively, our findings not only provide a solid foundation for further functional characterization of dehydration-responsive TFs in tomatoes but may also benefit the improvement of dehydration/drought tolerance in tomatoes in the future.

Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the ‘Epirus’ Region of Greece upon Consecutive Drought Stress

“…The transcription factors of the R2R3-MYB subfamily constitute key regulators in the process of responding to drought and other abiotic factors and their function (either by up- or down-regulation of specific members in a spatiotemporal manner) is associated with conferring tolerance to plants by controlling the expression of downstream stress-responsive genes [ 67 ]. Numerous studies have correlated the overexpression or down-regulation of MYB superfamily members with enhanced drought tolerance, possibly by inducing stomatal closure, increasing antioxidant enzyme activity and reducing the accumulation of ROS species [ 68 , 69 , 70 , 71 , 72 , 73 , 74 ].…”

Transcriptome Analysis and Metabolic Profiling Reveal the Key Regulatory Pathways in Drought Stress Responses and Recovery in Tomatoes

“…High-throughput techniques for omics-based analyses may be combined to elucidate the mechanisms regulating complex plant traits, including drought stress resistance in tomatoes, which is controlled by diverse factors. Only a few studies have been conducted on tomato drought tolerance and recovery [34][35][36][37][38][39]. Consequently, differences in gene expression and metabolite contents between tomato cultivars and wild species are largely unknown.…”