Integrated Epigenomic and Transcriptomic Profiling of the Resistance Response of Common Bean (Phaseolus vulgaris) to Bean Rust (Uromyces appendiculatus)

Common bean (Phaseolus vulgaris L.) is one of the most important grain legumes consumed directly as part of the diet, serving as an important source for dietary minerals and micronutrients. A better understanding of bean responses to abiotic and biotic stresses is important for continued understanding of tolerance/resistance mechanisms in this important crop. Epigenetic regulation as those caused by small RNAs, DNA methylation, and histone modifications are important for understanding the effect of the epigenome on the genome and transcriptome. With the release of the common bean genome, we now have the capacity to understand the interplay between genome-wide DNA methylation, histone-DNA interactions, and the effect of these two factors on the transcriptome.  Bean rust caused by the fungal pathogen Uromyces appendiculatus is a major concern for bean production worldwide, and in this work, we sought to understand histone-DNA interactions combined with transcriptome analysis during the resistance response of common bean inoculated with bean rust.  We developed a chromatin immunoprecipitation technique for common bean followed by high throughput sequencing (ChIP-seq).  We report on the integrated analysis of genomic wide interactions of two histone modification marks, dimethylation at H3K9 (repressive mark) and acetylation at H4K12 (activation mark) combined with transcriptomic analysis of the common bean rust resistance response. We additionally show progress towards comparison of two methylation analysis methods-sodium bisulfite sequencing and methylated DNA immunoprecipitation sequencing (MeDIP-seq), which combined with the understanding of histone-DNA interactions will help in a better understanding and annotation of the bean genome.