Identification of Novel Basil Downy Mildew Resistance Genes Using De Novo Comparative Transcriptomics

Sweet basil (Ocimum basilicum) production is threatened by the oomycete pathogen Peronospora belbahrii, causing basil downy mildew (BDM). BDM-resistant cultivar 'Mrihani' (MRI) was identified in a germplasm screen and bred with BDM-susceptible 'Newton' (SB22) to produce resistant cultivars, but the molecular mechanisms conferring resistance in MRI and the progeny remained unknown. A comparative transcriptomic approach was used to identify candidate resistance genes and potential mechanisms for BDM resistance. To differentiate the host-pathogen interactions in resistant and susceptible plants, RNA samples from BDM-infected MRI and SB22 plants were harvested at four time points during the first 3 days of infection, with mock-inoculated controls for both genotypes. Three categories of genes uniquely transcribed in the resistant MRI upon pathogen challenge were identified: nucleotide-binding leucine-rich repeat proteins (NLRs), multifunctional receptor-like kinases (RLKs), and secondary metabolic enzymes. Validation of the top resistance candidate NLR gene confirmed its unique presence in MRI and two of four resistant MRI × SB22 F₂ progeny. In MRI, pathogen challenge also induced differential regulation in members of the salicylic acid synthesis pathway, suggesting its role in BDM resistance. Overall, our study demonstrates the utility of de novo comparative transcriptomics to identify resistance genes and mechanisms in non-model crops.