Toward multi-omics dissection of fungal disease resistance in oat ( Avena sativa L.): current evidence, knowledge gaps, and a comparative cereal roadmap

Common oat (Avena sativa L.) is a nutritionally important cereal constrained by fungal pathogens including rusts, powdery mildew, and Fusarium head blight. Unlike wheat and barley, whose defenses are characterized across multiple omics levels, oat resistance research was long hindered by its complex hexaploid genome. Critically, despite expanding genomic resources, no genuine multi-omics integration has yet been achieved for any oat–fungal pathosystem. This review synthesizes oat-specific evidence across individual omics layers, spanning genomic inventories of resistance genes and meta-QTL, transcriptomic reprogramming of defense signaling, and limited proteomic and metabolomic data, and identifies knowledge gaps relative to wheat and barley. Oat-specific defenses, including steroidal saponins and induced avenanthramide phytoalexins, are distinguished from the benzoxazinoid chemistry of wheat. An evidence matrix shows that of six pathosystems surveyed, only Fusarium head blight is characterized at all three post-genomic levels, whereas crown rust, despite over 90 cataloged resistance genes, lacks any proteomic or metabolomic data. Three priorities are identified: (i) genome sequencing of oat-specific pathogens for dual-genome analyses; (ii) proteomic and metabolomic profiling of resistant versus susceptible genotypes; and (iii) adoption of single-cell transcriptomics, spatial metabolomics, and CRISPR/Cas9 validation. The genomic resources now available provide the foundation for genuine multi-omics integration in this crop.