Understanding Disease Resistance Signaling in Common Bean (Phaseolus vulgaris L.) through Integrated Epigenomic and Transcriptomic Analyses

Common bean (Phaseolus vulgaris L.) is one of the most important food legumes in the world. Due to its high protein and fiber content, this crop serves as an economically important and reliable food source to many people around the world.  Bean rust caused by the fungal pathogen Uromyces appendiculatus is an important disease that can severely affect bean yields.  Disease resistance in the common bean cultivar Sierra to race 53, an incompatible race of bean rust, is mediated through a hypersensitive response.  In order to understand the interplay between the epigenome and the transcriptome in the disease resistance response, we have undertaken a multi-pronged approach which includes global analysis of histone deacetylases (HDACs), DNA methyltransferases, chromatin immunoprecipation-  and transcriptome sequencing (ChIP-seq and RNA-seq) from leaves of mock inoculated and inoculated plants collected at 0, 12, and 84 hours after treatment with the bean rust pathogen. We detected differences in differential expression of HDACs and binding of DNA by two histone modification marks H3K9_me2 and H4K12_ac (which represent closed and open chromatin respectively) both between and within time points.  In RNA-seq analyses, in addition to the expected defense related genes, we found differential up- and down-regulation of genes from many other signaling networks.  This work serves as a first step to understanding the regulation and complex interplay of signaling pathways in the bean-bean rust response.