Multi-omics approaches for advancing edible fungi: from genomics-enabled strain development to metabolomics-guided postharvest preservation

Abstract

Edible fungi are globally significant sources of food and bioactive compounds, but realizing their full potential is constrained by challenges in cultivation and postharvest preservation. This review comprehensively examines the transformative impact of omics technologies (genomics, transcriptomics, proteomics, and metabolomics) on advancing the edible fungi industry. It explores how genomic insights are enabling the development of improved fungal strains, with an emphasis on functional and comparative genomics for identifying genes related to desirable traits such as enhanced bioactive compound production and disease resistance. The integration of transcriptomic, proteomic, and metabolomic data is detailed, demonstrating how multi-omics approaches elucidate complex regulatory networks controlling fungal development, metabolism, and stress responses. A major focus is given on how understanding fungal-microbial interactions, both beneficial and detrimental, can lead to optimized cultivation strategies. The review also discusses how an omics-driven understanding of postharvest physiology, particularly metabolomics identifying key spoilage biomarkers like specific volatile organic compounds or enzyme activity changes, is informing the development of targeted preservation techniques, including physical, chemical, and biological methods to reduce quality loss. By addressing current limitations, identifying research gaps, and outlining future directions, this review highlights the critical role of systems biology approaches in driving innovation for enhanced food security and sustainability within the edible fungi industry. Ultimately, the consistent application of multi-omics provides a powerful, data-driven toolkit for holistically improving both pre-harvest mushroom quality and yield, and post-harvest longevity and value.