Climate change is intensifying drought, salinity, heat, chilling, flooding, and heavy-metal stresses across major fruit-producing regions, threatening yield stability and fruit quality in economically vital, perennial crops such as apple, grapevine, citrus, banana, strawberry, and peach. Because these species are long-lived, highly heterozygous, and polyploid, conventional breeding for climate resilience remains slow and often inadequate, necessitating molecular strategies informed by systems-level understanding. This review synthesizes recent advances in multi-omics research spanning genomics, transcriptomics, proteomics, metabolomics, epigenomics, ionomics, and phenomics that have collectively decoded the regulatory architecture underlying abiotic stress perception, signaling, and tolerance in fruit crops. Hormonal networks, particularly abscisic acid (ABA) crosstalk with jasmonate, salicylic acid, ethylene, and brassinosteroids, emerge as central integrators of stress responses, coordinating stomatal regulation, osmolyte accumulation, antioxidant defense, and secondary metabolite biosynthesis. Genomic and pangenomic approaches have identified stress-associated loci and cultivar-specific structural variants, while transcriptomic and proteomic studies reveal transcription factor networks (MdERF38–MdMYB1, MaMYB4–MaHDA2, VvDREB1, CsNAC29) and post-translational regulatory switches governing tolerance mechanisms across drought, cold, salinity, and flooding stress. Metabolomic and ionomic profiling link biochemical reprogramming to fruit quality traits, whereas epigenomic mechanisms including DNA methylation, histone modifications, and small RNA regulation provide a chromatin-level layer mediating stress memory across growing seasons. Integration of these omics layers through systems biology, machine learning, and high-throughput phenomics is enabling functional validation via CRISPR-Cas9 and marker-assisted selection, translating correlative associations into causally validated breeding targets. Despite this progress, challenges including batch effects, tissue heterogeneity, and methodological inconsistencies in data integration continue to constrain translational applications. This highlights convergent regulatory hubs across stress types and species, underscoring multi-omics-guided precision breeding as the most promising pathway toward developing climate-resilient, high-quality fruit crop cultivars for sustainable global production.
Rising atmospheric CO2 is altering carbon–nitrogen interactions in C3 crops, with tomato (Solanum lycopersicum L.) showing enhanced carbon assimilation but frequently reduced nitrogen acquisition and assimilation. Nitrate reductase (NR), the rate-limiting enzyme in nitrate reduction, plays a central role by integrating nitrate assimilation with carbon metabolism and nitric oxide (NO) signaling. This review summarizes current knowledge of NR regulation in tomato under elevated CO2 (eCO2), focusing on post-translational mechanisms and their contribution to photosynthetic acclimation. Elevated CO2 modulates NR activity through interconnected changes in photorespiration, carbohydrate-mediated feedback, redox regulation, source–sink dynamics, and nitrogen availability. While eCO2 generally suppresses leaf nitrate assimilation by reducing photorespiratory support, root-zone CO2 enrichment can transiently stimulate root NR activity, highlighting tissue-specific regulation. Multi-omics studies further demonstrate extensive metabolic and molecular reprogramming affecting carbon skeleton supply, amino acid biosynthesis, and nitrogen assimilation. In addition, NR-dependent NO production links nitrogen metabolism with stomatal regulation through ABA-independent H2O2–NO signaling. Despite these advances, the roles of NR phosphorylation, 14-3-3 protein interactions, and redox-mediated regulation under eCO2 remain poorly understood. Overall, NR functions as a key metabolic and signaling hub coordinating carbon and nitrogen metabolism under future climate conditions. Understanding these regulatory mechanisms will facilitate strategies to improve nitrogen-use efficiency, sustain photosynthesis, and enhance tomato productivity under elevated atmospheric CO2 while identifying priorities for future physiological, molecular, and multi-omics research.
Wheat is one of the world’s most important cereal crops, providing essential calories and nutrients for billions of people and playing a vital role in global food security. Its productivity is increasingly threatened by abiotic stresses, including salinity, drought, heavy metal toxicity, temperature extremes, nutrient deficiencies, and emerging environmental contaminants such as nanoplastics. These stresses disrupt plant growth and development by inducing oxidative damage, impairing photosynthesis, disturbing nutrient and water homeostasis, and altering protein synthesis and cellular metabolism. Wheat plants respond through coordinated physiological, biochemical, and molecular mechanisms involving antioxidant defenses, osmotic adjustment, phytohormone signaling, and stress-responsive gene regulation. Recent advances in molecular breeding, including genome-wide association studies (GWAS), genomic selection, multi-omics approaches, and CRISPR/Cas-based genome editing, have accelerated the discovery of stress-responsive genes and quantitative trait loci (QTLs) for improving abiotic stress tolerance in wheat. Unlike previous reviews that examine physiological and molecular aspects separately, this review addresses the lack of an integrated synthesis connecting physiological traits, molecular mechanisms, and breeding strategies for multiple abiotic stresses in wheat. It further highlights emerging breeding technologies and climate-smart approaches, including genomic selection and CRISPR/Cas-based genome editing, to develop high-yielding, stress-resilient wheat cultivars that support sustainable wheat production under changing environmental conditions.
