Molecular orchestration of plant resilience: basis for precision breeding and biotic and abiotic stress tolerance

Abstract

Global agriculture is currently confronted with unprecedented pressures resulting from soil salinization and climate change, necessitating a transition from conventional breeding to a more rational, systems-based approach. This thesis investigates the molecular coordination of plant resilience through an integrative framework grounded in systems biology and omics technologies, focusing on both the oil palm (Elaeis guineensis) and the extremophile models Portulaca oleracea and Gliricidia sepium. By integrating phylogenomics, high-throughput sequencing, and the computational inference of Gene Regulatory Networks (GRNs), this research facilitates the identification of master regulators and functional gene targets involved in the response to complex environmental stressors. The first component of this work introduces EG-Net, an unprecedented regulatory blueprint designed to guide precision breeding in oil palm by mapping the intricate molecular interactions governing responses to lethal diseases and abiotic stresses. Complementing this applied tool, the study of the halophyte P. oleracea reveals a complex age- and tissue-dependent transcriptional reprogramming characterized by the dynamic regulation of aquaporins (AQPs), heat shock proteins (HSPs), and LEA/dehydrin proteins, which is governed by a core of 22 unique stress regulators that mediate the trade-off between growth and defense. Furthermore, the investigation of G. sepium deepens the adaptation phenotype wherein the phases of shock survival and physiological recovery are marked by hydraulic regulation, the coordinated adjustment of LEA and HSP proteins, the ectopic induction of the seed-specific aquaporin TIP3-1, and the modulation of specific hormonal signaling pathways. Collectively, these findings demonstrate that plant resilience is not a static attribute but a dynamic process dependent on the plasticity of the transcriptional architecture and precise temporal coordination. By moving beyond the identification of isolated candidate genes, this thesis establishes a robust conceptual foundation for future biotechnological interventions. The integration of these results reinforces a significant paradigm shift toward systems-based engineering, providing the genomic intelligence necessary to develop high-performance crops capable of maintaining productivity amidst the global expansion of marginal environments and the intensification of climatic instabilities.