Pan-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding

Crop production has been regarded as the major goal of agricultural activities, but the rapidly growing population and climate change have become more complex in the agricultural systems. Abiotic stress greatly affects crop productivity globally; developing more resilient crop varieties has become imperative. However, we can understand how plants tolerate abiotic stress better by using new methods that combine different scientific approaches like pan-genomics, pan-transcriptomics, pan-proteomics, pan-metabolomics, and pan-phenomics. Investigations using a pan-omics approach are necessary to consider the variation resulting from complex interactions among genes, proteins, metabolites, and regulatory networks within a species. A comparative study of core, dispensable, and unique components across different accessions assists in identifying novel genes, proteins, and metabolites responsible for stress tolerance. Moreover, databases and online repositories now enable the storage, analysis, and retrieval of data generated by high-throughput technologies. The combination provides guidelines for researchers to harness the potential of pan-omics in promoting sustainable agricultural practices. Therefore, the review focuses on recent trends in pan-omics for studying abiotic stress responses and their applications in crop improvement. It also highlights the application of artificial intelligence (AI) in data integration and monitoring crop environments.