Hormone priming and metabolic engineering of phytohormone crosstalk in rice under combined biotic and abiotic stresses: a multi-omics perspective for climate-resilient crop development

Systems-Level Integration of Stress Signaling, Multi-Omics, and Predictive Breeding for Abiotic Stress Tolerance in Brassica Crops

By connecting stress biology with translational breeding, this review provides a framework for developing climate-resilient Brassica cultivars by synthesizing recent progress in abiotic stress tolerance from physiological, genetic, epigenetic, and multi-omics perspectives.

A review of flavonoids at the crossroads of plant defense: integrating biotic and abiotic stress tolerance through AI- and CRISPR/Cas-guided metabolic reprogramming

Flavonoids are multifunctional phenylpropanoid-derived metabolites that occupy a central position in plant adaptation to environmental stress. Beyond their established roles in antioxidant protection, they contribute to defense against pathogens and herbivores, signaling processes, and physiological acclimation to adverse environmental conditions. Although flavonoid responses to individual biotic or abiotic stresses have been extensively investigated, considerably less attention has been given to how flavonoid-associated regulatory networks function when multiple stresses occur simultaneously. This gap is particularly important because crops in agricultural systems are routinely exposed to overlapping biotic and abiotic challenges that generate distinct physiological, transcriptional, and metabolic responses. This review synthesizes current knowledge of flavonoid biosynthesis, structure-activity relationships, and the regulatory mechanisms governing flavonoid accumulation under diverse stress conditions. Particular emphasis is placed on the reorganization of flavonoid-associated networks under combined stress, including signaling crosstalk, pathway competition, metabolic trade-offs, and flux allocation that collectively shape adaptive responses. This review further evaluates how artificial intelligence can support identification of regulatory targets and pathway bottlenecks, how integration with CRISPR/Cas technologies may facilitate more precise manipulation of flavonoid biosynthesis, and how iterative Design–Build–Test–Learn (DBTL) frameworks could improve predictive flavonoid engineering through continuous integration of computational prediction and experimental validation. By integrating advances in stress biology, computational prediction, genome engineering, and iterative DBTL frameworks, this review outlines a roadmap for predictive reprogramming of flavonoid networks under combined stress and the development of crops with improved resilience to increasingly complex environmental conditions.

Synthetic Rice Genome and Epigenetic Engineering: Emerging Strategies for Climate-Resilient Crops: Review Article

Rice (Oryza sativa) is among the most important staple food crops in the world, serving as a main source of food security for approximately one-half of the world's population. Nevertheless, its cultivation is becoming compromised due to climate change, as repeated drought and saline soils, along with erratic temperatures, pose heavy restrictions on its yield. Traditional breeding and genetic engineering have contributed to enhancing crop performance; however, they are still constrained by the complex stress-responsive networks and by the time taken to develop tolerant cultivars. In order to overcome these challenges, technologies on the horizon, synthetic genomics and epigenetic engineering, are becoming game-changers in crop science. Synthetic genomics permits the refactoring and partial reassembly of plant genomes, thereby allowing new gene circuits to be built in, synthetic chromosomes to be installed, and multiplex editing via CRISPR-mediated alterations to increase drought tolerance or salinity resistance or boost photosynthesis in rice. Concurrently, epigenetic changes such as DNA methylation and histone modification, as well as non-coding RNA-mediated regulation, can impose a more dynamic and reversible layer of control on gene expression by modulating stress responses while leaving the actual DNA sequence unaltered. Emerging evidence indicates that certain epigenetic marks are capable of being 'remembered' across generations and could influence long-term resilience to stress. This review emphasizes the use of synthetic genomics-based epigenetic regulation as a new horizon in climate-resilient rice improvement.

Crop Resilience to Combined Drought and Salinity Stress in Drylands: From Soil Processes to Genomic Solutions.

Drought and soil salinization increasingly co‑occur, threatening global food security, particularly in dryland farming systems where these stresses can interact additively, synergistically or antagonistically to reduce crop yields. This review critically distinguishes these interaction types and moves beyond single‑stress frameworks to provide a multiscale synthesis of plant responses, soil water-salt dynamics, root‑system plasticity, rhizosphere microbiome modulation, emerging breeding modelling and agronomic tools. This review provides a detailed overview of the multilevel damage from these co-occurring stresses, including osmotic shock, ionic toxicity and systemic oxidative damage, and examines plant strategies such as ion homoeostasis, osmotic adjustment and antioxidant responses. Beyond plant-centric views, the review explores epigenetic reprogramming for stress memory and the potential of rhizosphere microbiome engineering with plant growth-promoting rhizobacteria as a biological stress-alleviation strategy. It critically examines how high-throughput multiomics techniques, combined with innovative breeding methods, provide a transformative approach to decode complex tolerance traits and accelerate cultivar development. These techniques cover genomics, epigenomics, transcriptomics, proteomics and metabolomics, while the breeding methods include genomic selection and CRISPR-Cas gene editing. Despite progress, key challenges remain: validating combined stress resilience under field conditions, harnessing epigenetic inheritance and integrating microbial solutions into breeding pipelines. We propose a unified framework that merges mechanistic discovery, microbiome-assisted breeding, soil and water management and systems-level predictive modelling. This integrative approach is essential for developing climate-resilient crops to sustain dryland agriculture.

Epigenetic and metabolic regulation of drought stress memory in maize: from molecular mechanisms to field-applicable priming strategies

Maize ( Zea mays L.) is highly vulnerable to recurrent water deficits, particularly during vegetative-to-reproductive transition. Although physiological acclimation to drought is well documented, the capacity of maize to establish and transmit drought stress memory represents an underexplored frontier for climate-resilient agriculture. This review synthesizes the crop-specific epigenetic and metabolic mechanisms that govern drought priming and memory persistence in maize. We examine how initial osmotic stress triggers localized regulatory cascades, focusing on histone modifications (H3K4me2, H3K9ac, H3K27me3, and H3K36me3), DNA methylation dynamics, and transposable element regulation across the maize genome, where transposable elements comprise approximately 85% of the nuclear DNA. We detail the metabolic memory engram, which encompasses proline biosynthesis, carbon-nitrogen reallocation, and photosynthetic adjustments. Concurrently, we evaluate practical agronomic priming strategies—including hydropriming, osmopriming with CaCl 2 and PEG, chitosan priming, hormone priming (melatonin, SA, GA 3 ), and nanopriming—alongside emerging epigenetic biomarker screening platforms to identify drought-tolerant germplasms. By integrating molecular circuitry with field-applicable priming, this framework charts pathways for optimizing the memory yield equation. We explicitly identify critical knowledge gaps, including the limited direct measurements of proline biosynthetic enzyme kinetics (P5CS/P5CR) in primed versus unprimed maize and the largely uncharacterized phosphorylation states of PEPC under priming conditions, providing a roadmap for future research.

Crop Adaptation to Combined Abiotic Stresses: Mechanisms and Microbial Partners (Review)