Epigenetic Regulators of Plant Stress Responses in Legumes: A Case Study of the Bean-Bean Rust Interaction

Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber and micronutrient contents. Bean-rust, caused by the fungal pathogen Uromyces appendiculatus is a major constraint in common bean production. Integrating the information extracted from next generation sequencing (NGS) approaches aid in understanding regulatory mechanisms associated with disease-resistance in common bean. The inoculated (I) and mock-inoculated (MI) leaf samples were collected at 0, 12 and 84 hour-after-inoculation (hai). This study utilized chromatin immunoprecipitation sequencing (ChIP-Seq), RNA sequencing (RNA-Seq), and small RNA sequencing (small RNA-Seq). The bioinformatic tools used for these analyses were Bowtie, SICER, HOMER, TopHat, Cufflinks and miRPlant. We identified five important classes of epigenetic modulators in gene expression that include DNA methylation (279), histone methylation (45), histone acetylation (145), chromatin remodeling (26) and Polycomb Group (225) proteins. Four differentially expressed stress responsive genes identified were early-responsive to dehydration (ERD) stress family protein, chloroplast drought-induced stress protein, oxidative stress 3 and stress induced alpha-beta barrel domain protein between 0, 12 and 84 hai. The R proteins marked by both methylation and acetylation modifications were pleiotropic drug resistant protein 12, LRR family, NB-ARC domain containing and TIR-NBS-LRR proteins. Some key defense responsive genes (calmodulin, cytochrome p450, chitinase, DNA Pol II, and LRR) and transcription factors (WRKY, bZIP, MYB, HSFB3, GRAS, NAC, and NMRA) were also identified. This is the first comprehensive report in understanding the role of epigenetic regulation in bean-rust interaction and can be exploited in other non-model species under biotic and abiotic stresses.