UC Riverside

The generalist soil-borne fungal pathogen Macrophomina phaseolina is known to cause a disease most widely known as charcoal rot. Despite the widespread damage this pathogen has caused on over 500 species of plants including important crops, the mechanism of its virulence is still unclear, and effective methods of control are still lacking. In this study, M. phaseolina interaction with the model plant Arabidopsis thaliana is described using a plate-based infection assay which allows for image analysis-based quantitative assessment of disease progression. From a panel of A. thaliana inbred lines derived from natural populations, we observed significant quantitative deviation in growth inhibition caused by M. phaseolina. In order to gain insight to the genetic architecture behind M. phaseolina resistance, we sought to utilize the natural genetic variation represented in the panel of 87 natural A. thaliana accessions. Genome-wide association approaches combined with RNA-sequencing identified multiple genomic loci and candidate genes which could potentially contribute to the phenotypic variance. Seedling root transcriptomes captured at three time points post-infection revealed that resistant and susceptible A. thaliana genotypes have distinct patterns in defense gene expression. Surprisingly, in the two resistant accessions examined, a rapid decline in up-regulation of many defense genes were observed between 12 and 48 hours post-infection. Genes previously associated with plant immunity, as well as genes involved in processes that have not been seen in M. phaseolina response, were identified in this study, providing a robust pool of candidate genes which will be a useful resource for increasing M. phaseolina tolerance in host plants.