European Journal of Sustainable Agroecosystems

Context: Climate change exacerbates abiotic and biotic stressors, which serve as the major hindrance in improving the productivity of crops around the globe. Recent improvements in genomic, proteomic, transcriptomic, metabolomic, epigenomic, and phenomic technologies support a huge amount of data concerning plant responses to environmental stresses; however, mono-omic studies fail to provide an adequate understanding of the complex processes of stress adaptation.

Aim: The aim of the paper was to summarize the literature on various integrative multi-omics approaches to studying the stresses for plants, discussing the strengths and weaknesses of the methods analyzed.

Methods: To obtain the information on the topic, the literature was searched using various tools, such as PubMed, Scopus, Google Scholar, and Web of Science databases, as well as other reports published between the years 2015 to 2026 containing keywords like "multi-omics," "crop stress adaptation," "transcriptomics," "metabolomics," "epigenomics," and "phenomics."

Important results: Evidence from our literature survey suggests that the combination of genomics, transcriptomics, proteomics, metabolomics, and epigenomics with high-throughput pheno-mics, and machine learning can significantly improve our understanding of the complex gene-to-phenotype mechanisms involved in drought, heat, salinity, and combined stress tolerance. Several multi-omics analyses show that transcriptional dynamics do not necessarily trans-late proportionally into proteomic or metabolic changes, which indicates that there are additional layers of post-transcriptional and epigenetic regulation. Currently, machine learning-based integration approaches and genomic selection techniques are becoming common in converting multi-omics information into breeding practicable molecular markers.

Remaining research deficiencies: The existing problems include a lack of standardiza-tion of the data integration pipelines, lack of examples of field relevant combined stress conditions, insufficient availability of multi-omics data for non-model and orphan crops, and lack of effective approaches for application of the identified biomarkers in breeding programs.

Final conclusion: Integrative omics is a powerful yet still developing tool in the study of crop stress; future success will strongly depend on the introduction of practical multi-omics protocols, expanding the infrastructure of phenomics, as well as proper interdisciplinary collaboration of molecular biology experts, bioinformaticians.