Specific ABA-independent tomato transcriptome reprogramming under abiotic stress combination

Abstract

SUMMARYCrops often have to face several abiotic stresses simultaneously, and under these conditions, the plant’s response significantly differs from that observed under a single stress. Nevertheless, most of the molecular markers identified for increasing plant stress tolerance have been characterized under single abiotic stresses, explaining their unexpected results when they are tested under real field conditions. One important regulator of the plant’s responses to abiotic stresses is ABA. The ABA signaling system engages many stress-responsive genes, however, many others do not respond to ABA treatments. Thus, the ABA-independent pathway, which is still largely unknown, involve multiple signaling pathways and important molecular components necessary for the plant’s adaptation to climate change.In the present study, tomato ABA-deficient mutants (flacca, flc) were subjected to salinity, heat, or their combination. A deep RNA-seq analysis revealed that the combination of salinity and heat induced an important reprogramming of the tomato transcriptome, and from the 685 genes that were specifically regulated under this combination in our flc mutants, 463 genes were regulated by ABA-independent systems. Among these genes, we identified 6 transcription factors (TFs) belonging to the R2R3MYB family that were significantly upregulated. A protein-protein interaction network showed that the TFs SlMYB50 and SlMYB86 were directly involved in the upregulation of the flavonol biosynthetic pathway-related genes. This is the first time that some important ABA-independent TFs involved in the specific plant response to abiotic stress combination have been identified. Considering that ABA levels dramatically change in response to environmental factors, the study of ABA-independent genes that are specifically regulated under stress combination may provide a marvelous tool for increasing plant resilience to climate change.SIGNIFICANCE STATEMENTThis study in tomato Wt and ABA-deficient mutant plants reveals a specific and unique ABA-independent transcriptome reprogramming under abiotic stress combination, with the identification of some key TFs that were induced under these specific conditions. Taking into account that ABA levels dramatically change in all crops in response to environmental factors, the study of ABA-independent genes that are specifically regulated under stress combination may provide a marvelous tool for increasing plant resilience to climate change.