Insights of Phaseolus vulgaris’ response to infection by Uromyces appendiculatus using an RNA-seq approach

Rust, caused by the obligate biotrophic fungal pathogen <i>Uromyces appendiculatus</i> (Pers.:Pers.) Unger, is one of the most destructive diseases of common bean (<i>Phaseolus vulgaris</i> L.) causing yield losses in production areas worldwide. This study explores the use of RNA sequencing (RNA-seq) as a breeding prediction tool through the assessment of gene expression patterns of common bean susceptible (Golden Gate Wax) and resistant (Teebus-RR-1) varieties to <i>U. appendiculatus</i> virulent strain race 31-1 at two time points (14- and 21- days post infection; dpi). <i>U. appendiculatus</i> induced stress-responsive genes such as heat shock proteins (HSPs: <i>HSP17.6II</i> and <i>ATHSP22.0</i>), receptor-like kinases (RLKs: <i>CRK29</i>), cytochrome monooxygenases (<i>CYP76C4</i>, <i>CYP82C4</i> and <i>CYP94B1</i>) and terpene synthases (<i>TPS21</i> and <i>TPS14</i>) at 14-dpi, while <i>BIA</i> and <i>WRKY70</i> transcription factors, among others were regulated differentially in both varieties at 21-dpi. Genes <i>RPS2</i>, <i>CAR1</i> and <i>DM2H</i> were among the identified potential biomarkers associated with <i>U. appendiculatus</i> resistance. Enrichment of signaling receptor activity, response to stress, sesquiterpenoid and triterpenoid biosynthesis, and plant hormone signal transduction were unique to Teebus-RR-1. Overall, the findings of this study indicate varying gene expression patterns between varieties in response to <i>U. appendiculatus</i>. Insights provided by the RNA-Seq approach used in this study on mechanisms of <i>P. vulgaris'</i> response to <i>U. appendiculatus</i> can be used for biomarker discovery and possible development of resistant varieties.