Gene expression profiling and characterization of black rot resistance in Dendrobium Sonia 'Earsakul': a comparison of the non-mutagenized control and the resistant mutagenized line.

backgroundBlack rot, caused by Phytophthora parasitica, poses a significant threat to the commercial cultivation of Dendrobium spp., particularly the cultivar 'Earsakul'. However, the black rot resistance mechanisms in Dendrobium Sonia 'Earsakul' remain unexplored. This study elucidates the molecular mechanisms underlying black rot resistance by comparing a resistant ethyl methanesulfonate (EMS)-mutagenized line, SUT13E18301 with a susceptible non-mutagenized control, SUT16C014 in control (without pathogen inoculation) and inoculated conditions.

resultsResistance phenotyping using detached leaf assay revealed stark contrasts in disease severity, prompting comprehensive transcriptomic analyses via RNA sequencing at 12- and 24-hours post-inoculation (hpi), compared with control condition. Bioinformatic analysis identified 4,190 significantly differentially expressed genes (DEGs), most of which were associated with defense responses. At the early stage (12 hpi), the genes related to signaling pathway, transcriptional reprogramming, and cell wall modification were differentially expressed. At the later infection stage (24 hpi), results highlighted genes with important roles in pathogen recognition, hormone signaling, cell wall modification, antimicrobial compounds/defense proteins production, hypersensitive response, and detoxification, all related to disease resistance mechanisms. Among these, nearly all of twenty-three candidate genes, including peroxidase (POD) 51-like, beta-glucosidase 11-like, pectinesterase, chitinase 2-like, transcription factor MYB6, and fasciclin-like arabinogalactan protein 11 (FLA11) showed up-regulation in the resistant line, whereas reduced responses in the susceptible line. Quantitative real-time PCR (qPCR) validation confirmed these expression patterns, showing strong positive correlation (R = 0.94). Furthermore, a highly significant increase in POD activity was observed at 24 hpi compared to 0 and 12 hpi in the resistant line. Conversely, the susceptible line showed no significant differences across the time points. Additionally, the weighted gene co-expression network analysis (WGCNA) and the regulatory network of candidate genes indicated that resistance is mediated by complex interactions among multiple regulatory components, rather than a single predominant pathway, and integration of structural and chemical defenses.

conclusionsThese findings provide crucial insights into the genetic basis of black rot resistance and identify valuable molecular targets for breeding black rot resistance in Dendrobium.