A MultiOmics approach for better understanding and comprehensive management of durum and soft wheat kernels quality and safety in the Italian Peninsula

Wheat is one of the most cultivated cereal crops in the Mediterranean basin area, with both durum and soft wheat representing strategic resources for food security. Climate and environmental changes endanger the cultivation of key crops by influencing their growth and yield. This is related also to changes in the microbiome composition and the plant metabolome. By examining the kernel’s metabolome and microbiome composition, it is possible to assess sample quality before planting or food processing. As plant microbiome influences the host’s performance, it is crucial to gain a comprehensive understanding of its composition. Identification of the presence of species that produce toxins, or, of beneficial microbials that can limit pathogen growth may lead to the development of new strategies to protect the agricultural market and consumer health. To conduct this research, a multi-omics approach was applied to study several durum and soft wheat varieties harvested in Italian peninsula in 2023. Untargeted metabolomics (LC-Orbitrap) analyses were performed to explore chemical signatures linked to wheat variety, quality and traceability and to find possible correlations with metagenomic and agronomic data. Metabolic fingerprints tend to cluster samples according to their eco-geographical origin, suggesting that environmental conditions have a stronger influence on the metabolome than the wheat genotype. A metagenomic analysis through metabarcoding sequencing using Oxford Nanopore Technology was performed in parallel with in vitro isolation of fungal endophytes, revealing both emerging pathogens and promising biocontrol agents, which are being investigated in co-culture assays against wheat pathogens, supporting future applications in sustainable disease management.