Integrative multi-omics approaches for crop abiotic stress tolerance

Abstract Over the past decade, extensive research has advanced our understanding of plants' responses to abiotic stress, such as extreme temperatures, water scarcity, and metal toxicity. These stresses arise from human activities and urbanization that accelerate global warming and ultimately reduce crop yields. The use of agrochemicals further intensifies these stresses. In response, plants undergo a cascade of physiological changes, including the generation of reactive oxygen species (ROS), stomatal opening and closing, changes in cytosolic calcium ion concentrations, activation of potassium channels, metabolite production, and stress-responsive gene expression. To investigate these changes at molecular, cellular and morphological levels in plants, genomics, transcriptomics, epigenomics, and metabolomics approaches have been employed. Advances in plant genomics have identified key genes related to stress, quantitative trait loci (QTLs) and regulatory networks involved in stress perception, signal transduction, and adaptive responses. Epigenomic studies have revealed the dynamic regulation of gene expression through modifications such as DNA methylation, histone modifications, and small RNAs, which play crucial roles in fine-tuning stress-responsive gene expression and memory. Metabolomic profiling, validated by techniques such as liquid chromatography–mass spectrometry (LC–MS/MS), has identified metabolic pathways and molecular signatures associated with stress acclimation and resilience. We propose an integrative multi-omics approach, combined with CRISPR-based genome editing and high-throughput phenotyping, to accelerate the discovery of stress-resilient traits. This comprehensive strategy provides a powerful framework to unravel complex stress response networks and identify potential targets for genetic improvement of stress tolerance in crops. For example, CRISPR enables precise editing of stress-responsive genes, while phenotyping platforms allow rapid screening of multi-trait responses under field conditions. Ultimately, the synergistic application of plant genomics, epigenomics, and metabolomics is driving forward our understanding of plant stress biology. This integrated knowledge opens new avenues for sustainable agriculture in the face of climate change and environmental challenges.