Approccio integrato alla difesa sostenibile del riso nei confronti del brusone e della fusariosi: resistenza varietale, diagnostica innovativa e mezzi di difesa green

The intensification of rice cultivation in Europe has increased the crop’s vulnerability to fungal pathogens such as Fusarium fujikuroi, causal agent of rice bakanae disease, and Pyricularia oryzae, causative agent of rice blast disease, causing economically significant yield losses. At the same time, the EU’s Farm to Fork strategy mandates a 50 % reduction in chemical pesticide use by 2030, highlighting the urgency for sustainable, non‑chemical disease management strategies. This PhD thesis addresses this challenge by combining biological control, genetic resistance and pathogen population monitoring to develop integrated, environmentally friendly approaches for rice disease management. Chapter 2 describes the isolation and in vivo screening of 135 bacterial and fungal endophytes from rice seeds and shoots against F. fujikuroi. A total of 17 isolates significantly reduced bakanae severity; after excluding potential human or plant pathogens, five strains of Epicoccum layuense, E. catenisporum, Microbacterium testaceum and Methylobacterium oryzae species were shown to only slightly inhibit F. fujikuroi via diffusible and volatile compounds in vitro, despite their significant efficacy in vivo, confirmed by observing also significant effects on disease incidence and total biomass. Chapter 3 explores the modes of action of promising BCAs by profiling rice defense‑related gene expression over time. Using qRT‑PCR and multivariate analyses, expression of a chitinase (CH1), a germin-like PR gene (GL8) and a MAPK kinase (MKK) was monitored in the susceptible cultivar ‘Carnise’ at three timepoints post‑germination following seed treatment with M. testaceum, E. catenisporum and a recently patented strain of Sphingomonas yabuuchiae. Strain‑specific transcriptional signatures of induced systemic resistance (ISR) were identified and correlated with reductions in disease severity, incidence and biometric parameters. Non‑metric multidimensional scaling (NMDS) and correlation analyses revealed co‑regulation of cell‑wall‑degrading enzymes and MAPK signaling, providing molecular biomarkers for biocontrol mode of action (MOA) based selection of BCAs. Chapter 4 investigates the local population structure of P. oryzae in Italy to support the deployment of resistant cultivars. A collection of isolates from five regions (2011–2012, 2020–2022) was genotyped using SSR markers. Cluster analyses of 200 unique multilocus genotypes revealed five genetic groups whose distribution was shaped by geography and time. In Piedmont, correlations between climatic variables and allele frequencies suggest environmental drivers of local adaptation. Virulence assays showed the disappearance of a less‑virulent cluster over time, underscoring the pathogen’s capacity to overcome host resistance. Together, these studies advance the understanding of rice–pathogen–microbe interactions at multiple levels. These findings support the integration of biological control, targeted resistance breeding and population surveillance into sustainable rice disease management strategies compatible with evolving regulatory frameworks.