Multiomics-based insights into tomato adaptation to multifactorial stress combination

Multifactorial stress combination (MFSC) represents a major threat to crop productivity under climate change scenarios. While the physiological effects of MFSC have been studied, its impact on gene expression and primary metabolism remains poorly understood in tomato plants. In this study, we performed an integrative transcriptomic and metabolomic analysis of tomato (Solanum lycopersicum) plants exposed to combinations of up to six low-intensity abiotic stresses. RNA-seq analysis revealed a stress complexity-dependent increase in differentially expressed genes (DEGs), including 258 core transcripts and 155 transcription factors uniquely regulated under 4-, 5-, and 6-stress conditions. Heat-specific analysis identified 103 uniquely regulated transcripts, including two key transcription factors (Zinc Finger TF32 and a B3-domain family protein) suggested as central regulators of different combinations involving heat stress. Our findings define a conserved, stress-complexity-dependent molecular architecture in tomato and identify candidate markers for improving crop resilience under MFSC. Overall design: The experimental design to study wild-type tomato (Moneymaker) responses to MFSC included the following stresses: Nitrogen deficiency (N-), heat stress (HS), salinity (S), high light (HL), heavy metal as cadmium treatment (Cd), and the herbicide paraquat (PQ) were applied up to a combination of all six factors. HL, HS, S and PQ were combined in all their possible combinations of 2-, 3- and 4-factors and Cd and N- were added to 4-factor combination to generate 2 different groups of 5-factor stresses, and all of them simultaneously generate the 6-MFSC. N deficiency was applied by watering plants with a half strength Hoagland solution with 10% of N (Ca(NO3)2) content one week after transplanting the plants. One week after the starting of the N-deficiency stress, plants with and without N deficiency were watered with half strength Hoagland solution containing each stressor(s): S (75 mM NaCl), PQ (1 µM PQ), Cd (10 µM CdSO4), S+PQ (75 mM NaCl + 1 µM PQ), S+PQ+N- (75 mM NaCl + 1 µM PQ + 10% N), S+PQ+Cd (75 mM NaCl + 1 µM PQ + 10 µM CdSO4) and S+PQ+Cd+N- (75 mM NaCl + 1 µM PQ + 10 µM CdSO4 + 10% N). Following 15 days of stress treatments, a group of CT plants and a group of plants subjected to each of the individual and combined stresses were transferred to growth chambers and were subjected to HL (700 µmol m-2s-1) and/or HS (37ºC). The tissue sampled from tomato plants were young leaves. All experiments were repeated three times with at least 8 plants per stress treatment.