All roads lead to Rome: integrated physiological and transcriptomic analysis of cacao drought response reveals different ways to achieve tolerance in two hybrid clones

Introduction: Global warming poses significant challenges to agriculture through increased extreme weather events, such as the water deficit, affecting the establishment and yield of crops like cacao and all its value chain. Understanding the complex drought response mechanisms in cacao through integrated methodologies is crucial for developing strategies to enhance crop resilience to this stress. Methods: Here, we evaluated the response to a 52 days-long water deficit stress of three commercial cacao hybrid clones: EET8, ICS60 and TSH565 combining growth and physiological parameters with transcriptomic profiles. Results: TSH565 and EET8 clones exhibited the highest drought-stress tolerance through different strategies, being able to cope with stress and to better recovery after rewatering. TSH565 showed stomatal limitation but maintained unimpaired photosynthesis under drought. This clone also displayed water use efficiency and relative water content levels comparable to the watered control group, and its total dry weight exceeded that of EET8 and ICS60 under stress. Transcriptomic profiling of TSH565 indicated upregulation of genes encoding aquaporins, PSII proteins, proteins of the antioxidant system and several enzymes participating in the synthesis of osmo-protective secondary metabolites, seemingly contributing to its tolerance. In contrast, EET8 experienced both stomatal limitation and impaired photosynthetic machinery upon the same stress. Its higher stomatal conductance led to a concomitant increased water loss with a significant decrease in leaf water potential. Transcriptomic profiling revealed the activation of numerous biological processes and metabolic pathways, including key hub transcription factors probably responsible for inducing several downstream effector genes, ultimately driving to its stress tolerance. The induction of genes related to acclimation to low water potential and photoprotection was vital for the survival of this clone. Discussion: Despite these differences, ABA metabolism and signaling pathways played a significant role in the drought stress tolerance of both clones. Osmoprotection, osmotic adjustment, and antioxidant response appear to be part of the core strategy of T. cacao’s tolerance to water deficit stress. This research provides valuable insights into the distinct molecular mechanisms underlying drought-stress tolerance in cacao plants. Specifically, it identifies stress-tolerance candidate genes of breeding value, as well as for T. cacao germplasm characterization, conservation and selection.