Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics

Authors: ALLEN, KELLY - University Of Massachusetts, Amherst; DELULIO, GREGORY - University Of Massachusetts, Amherst; PYNE, ROBERT - Rutgers University; MAMAN, JACOB - University Of Massachusetts, Amherst; GUO, LI - Peking University; LYON, REBECCA - Former ARS Employee; Johnson, Eric; WICK, ROBERT - University Of Massachusetts, Amherst; SIMON, JAMES - Rutgers University; GERSHENSON, ANNE - University Of Massachusetts, Amherst; MA, LI-JUN - University Of Massachusetts, Amherst

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2025
Publication Date: 7/4/2025
Citation: Allen, K.S., Delulio, G.A., Pyne, R., Maman, J., Guo, L., Lyon, R.M., Johnson, E.T., Wick, R.L., Simon, J.E., Gershenson, A., Ma, L. 2025. Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics. Molecular Plant-Microbe Interactions. https://doi.org/10.1094/PHYTO-11-24-0369-R.
DOI: https://doi.org/10.1094/PHYTO-11-24-0369-R

Interpretive Summary: Downy mildews are leaf diseases caused by several species of fungus-like organisms that can only live in plants. These diseases cause substantial economic losses on numerous crops including basil, which is a specialty crop with high economic value. Basil cultivars resistant to the basil downy mildew disease-causing organism, Peronospora belbahrii, have been developed, but the mechanisms for this resistance remain largely unknown. This study compared the responses of a sweet basil cultivar, which is susceptible to basil downy mildew disease, and Mrihani basil, which is resistant to this disease, when challenged with basil downy mildew pathogen. The study identified several groups of genes that were turned on in the downy mildew resistant cultivar but not in the downy mildew susceptible cultivar. One gene known to contribute to disease defense responses in other plants was turned on in the resistant basil cultivar but not in the susceptible basil cultivar. Genes involved in the biosynthesis of salicylic acid were also turned on in disease resistant basil cultivar, but not in disease susceptible basil cultivar. Salicylic acid plays an important role in plant defense against pathogens. The genes identified in this study can serve as guides for developing downy mildew resistant sweet basils in the future which can help growers reduce losses caused by P. belbahrii.

Technical Abstract: Sweet basil (Ocimum basilicum L.) 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 fertile resistant progeny were produced through a breeding program with BDM-susceptible ‘Newton’ (SB22), but the molecular mechanisms conferring resistance in MRI and 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 three 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), multi-functional 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 MRIxSB22 F2 progeny. In MRI, pathogen challenge also induced differential regulation in members of the salicylic acid synthesis pathway, suggesting its role in BDM resistance and demonstrating the utility of de novo comparative transcriptomics to identify resistance genes and mechanisms in non-model crops.