Pardo-Hernandez, M. | bioRxiv Science

bioRxiv2024

Multi-Omics Exploration of ABA Involvement in Identifying Unique Molecular Markers for Single and Combined Stresses in tomato plants

Over the past decade, our research group has found that plant responses to combined abiotic stresses are unique and cannot be inferred from studying plants exposed to individual stresses. Adaptive mechanisms involve changes in gene expression, ion regulation, hormonal balance, and metabolite biosynthesis or degradation. Understanding how these mechanisms integrate from stress perception to biochemical and physiological adjustments is a major challenge in abiotic stress signaling studies. Today, vast amounts of -omics data (genomics, transcriptomics, proteomics, metabolomics, phenomics) are readily available. Additonally, each -omic level is regulated and influenced by the others, highlighting the complexity of plant metabolisms response to stress. Considering abscisic acid (ABA) as a key regulator in plant abiotic stress responses, in our study, ABA-deficient plants (flc) exposed to single or combined salinity and heat stresses were evaluated and different -omics analyses were conducted. Significant changes in biomass, photosynthesis, ions, transcripts, and metabolites occurred in mutant plants under single or combined stresses. Exogenous ABA application in flc mutants did not fully recover plant phenotypes or metabolic levels but induced cellular reprogramming with changes in specific markers. Multi-omics analysis aimed to identify ABA-dependent, ABA-independent, or stress-dependent markers in plant responses to single or combined stresses. We demonstrated that studying different -omics together identifies specific markers for each stress condition not detectable individually. Our findings provide insight into specific metabolic markers in plant responses to single and combined stresses, highlighting specific regulation of metabolic pathways, ion absorption, and physiological responses crucial for plant tolerance to climate change. HighlightThe integration of different -omics has enabled the identification of specific ABA-dependent or -independent markers for single or combined abiotic stresses. These markers were not initially detectable when studying the different -omics individually.

plant biology↗

bioRxiv2023

Specific ABA-independent tomato transcriptome reprogramming under abiotic stress combination

Crops often have to face several abiotic stresses simultaneously, and under these conditions, the plants 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 plants 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 plants 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.

plant biology↗