Comprehensive RNA-seq analyses reveal tissue-wide resistance mechanism under Phytophthora capsici infection in chile pepper (Capsicum annuum L.)

Chile pepper rot caused by the oomycete Phytophthora capsici is an important disease affecting chile pepper production globally. Comparative transcriptomic analyses using RNA sequencing was performed to identify differentially expressed genes (DEGs) and shared genetic resistance mechanisms across different tissues upon infection to the pathogen. RNA sequencing revealed the dynamic transcriptome of leaf, tissue, and roots from resistant (R; CM-334) and susceptible (S; Early Jalapeno) genotypes under different times of infection by P. capsici. There were 149,531 differentially expressed genes (DEGs) from 39 different R vs. S, time vs. time, and tissue vs. tissue contrasts. A total of 75,520 DEGs (51%) was upregulated, whereas 74,011 (49%) were downregulated. The total number of upregulated DEGs for the different tissue samples decreased across times of infection, where the 72h post-inoculation showed the least number of genes. The roots generally showed higher number of DEGs compared to the stem and the leaf tissues. Network analyses of DEGs for the R vs. S constrast demonstrated that genes with functions related to defense response to fungus were also involved with carbohydrate metabolism and ADP binding. Genes related to immune response to fungal infection and amino acid metabolism (e.g., homoserkine kinase activity) were upregulated across all times of infection and tissue samples indicating the presence of a tissue-wide resistance (TWR) mechanism against P. capsici. This is the first known report of the existence of a TWR mechanism which can be leveraged for breeding and selection for broad-spectrum resistance for P. capsici in current Capsicum germplasm.