Comparative RNA sequencing analysis of resistant and susceptible Dendrobium "Earsakul" under black rot challenge

Dendrobium, a highly popular ornamental plant with immense economic significance, is increasingly threatened by black rot disease caused by Phytophthora parasitica. The sole reliance on the use of chemicals to control this disease highlights the need for developing strategies to generate sustainable, genetically resistant Dendrobium varieties.

In this study, we conducted comparative transcriptomic profiling to elucidate the molecular basis of black rot resistance in Dendrobium "Earsakul" by analyzing resistant (SUT13E18305) and susceptible (SUT16C007) lines at 0, 12, and 24 h post-inoculation.

Phenotypic evaluation revealed clear divergence between the two lines by 5 days after inoculation (DAI): the resistant line exhibited limited disease symptoms, while the susceptible line showed severe disease progression by 7 DAI. RNA sequencing analysis showed rapid and dynamic defense response in the resistant genotype, including activation of genes encoding pathogen recognition receptors such as chitin elicitor-binding protein-like and receptor-like kinases, which triggered the immune response. Key transcription factor genes (WRKY43, WRKY75, and MYB6) were strongly upregulated, and these upregulated genes mediated coordinated activation of signaling pathways. Defense-related genes involved in the biosynthesis of pathogenesis-related proteins and antimicrobial compounds, reactive oxygen species management, strengthening of the cell wall, and phenylpropanoid metabolism were also significantly induced in the resistant genotype. In contrast, the susceptible genotype exhibited delayed immune activation, suppressed expression of defense-related genes, and inadequate cell wall remodeling, ultimately leading to extensive colonization of the pathogen. Notably, quantitative real-time polymerase chain reaction confirmed stage-specific expression patterns of multiple genes in both genotypes.

The findings of this study demonstrate the utility of transcriptomics in elucidating complex defense responses in non-model crops and offer broader insights into plant-hemibiotrophic pathogen interactions, providing a molecular framework for breeding disease-resistant Dendrobium cultivars.