Integrated soybean transcriptomics, metabolomics, and chemical genomics reveal the importance of the phenylpropanoid pathway and antifungal activity in resistance to the broad host range pathogen Sclerotinia sclerotiorum
Sclerotinia sclerotiorum, a predominately necrotrophic fungal pathogen with a broad host range, causes a significant yield limiting disease of soybean called Sclerotinia stem rot (SSR). Resistance mechanisms against SSR are poorly understood, thus hindering the commercial deployment of SSR resistant varieties. We used a multiomic approach utilizing RNA-sequencing, Gas chromatography-mass spectrometry-based metabolomics and chemical genomics in yeast to decipher the molecular mechanisms governing resistance to S. sclerotiorum in soybean. Transcripts and metabolites of two soybean recombinant inbred lines, one resistant, and one susceptible to S. sclerotiorum were analyzed in a time course experiment. The combined results show that resistance to S. sclerotiorum in soybean is associated in part with an early accumulation of JA-Ile ((+)-7-iso-Jasmonoyl-L-isoleucine), a bioactive jasmonate, increased ability to scavenge reactive oxygen species (ROS), and importantly, a reprogramming of the phenylpropanoid pathway leading to increased antifungal activities. Indeed, we noted that phenylpropanoid pathway intermediates such as, 4-hydroxybenzoate, ferulic acid and caffeic acid were highly accumulated in the resistant line. In vitro assays show that these metabolites and total stem extracts from the resistant line clearly affect S. sclerotiorum growth and development. Using chemical genomics in yeast, we further show that this antifungal activity targets ergosterol biosynthesis in the fungus, by disrupting enzymes involved in lipid and sterol biosynthesis. Overall, our results are consistent with a model where resistance to S. sclerotiorum in soybean coincides with an early recognition of the pathogen, leading to the modulation of the redox capacity of the host and the production of antifungal metabolites.\n\nAuthor SummaryResistance to plant fungal pathogens with predominately necrotrophic lifestyles is poorly understood. In this study, we use Sclerotinia sclerotiorum and soybean as a model system to identify key resistance components in this crop plant. We employed a variety of omics approaches in combination with functional studies to identify plant processes associated with resistance to S. sclerotiorum. Our results suggest that resistance to this pathogen is associated in part with an earlier induction of jasmonate signaling, increased ability to scavenge reactive oxygen species, and importantly, a reprogramming of the phenylpropanoid pathway resulting in increased antifungal activities. These findings provide specific plant targets that can exploited to confer resistance to S. sclerotiorum and potentially other pathogens with similar lifestyle.