Applied Agriculture Sciences
Agriculture and food sciences | Online ISSN: 3066-3407
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Volume 4 Number 1 2026
REVIEWS (Open Access)
Multi-Omics Approaches in Orphan Crops: Bridging the Gap Between Botanical Diversity and Global Food Security
Zahir Uddin 1*
Applied Agriculture Sciences 4 (1) 1-8 https://doi.org/10.25163/agriculture.4110911
Submitted: 29 June 2026 Revised: 16 August 2026 Accepted: 24 August 2026 Published: 26 August 2026
Abstract
Modern agriculture leans, perhaps too heavily, on a narrow handful of staple species, and that dependence is beginning to look less like efficiency and more like fragility. As climate volatility intensifies and diets grow monotonous, orphan or underutilized crops - long overlooked by formal breeding programs - are being reconsidered as a practical route toward dietary diversification and climate resilience. This narrative review synthesizes literature published between 2011 and 2026, drawing on genomic, pangenomic, transcriptomic, metabolomic, and phenomic studies of underutilized crop species, alongside research on CRISPR/Cas-based domestication and AI-driven phenotyping frameworks. The evidence indicates that long-read sequencing and graph-based pangenomes have begun resolving structural variation once hidden by single reference genomes, revealing presence-absence variants tied to drought, heat, and nutritional traits in species such as finger millet, tef, and pigeonpea. Precision editing tools, particularly CRISPR/Cas9 and base/prime editors, have already converted several wild or semi-domesticated relatives into agronomically workable crops, while machine-learning-assisted phenomics has improved trait prediction accuracy considerably. Taken together, these findings support an integrated De novo domestication-Speed breeding-AI-empowered Phenomics (DSAP) strategy as a credible, though not yet fully proven, roadmap for repositioning orphan crops within global food systems, provided that open-access genomic infrastructure and participatory breeding are pursued alongside the technology itself.
Keywords: orphan crops; multi-omics integration; pangenomics; CRISPR/Cas gene editing; food security
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