Transcriptome profiling reveals tissue-wide gene expression in chili pepper (Capsicum annuum L.) under infection by Phytophthora capsici

Phytophthora blight, manifested by root, stem, and fruit rot, caused by the oomycete <i>Phytophthora capsici</i>, is an important disease affecting Chili pepper production globally. RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs) and shared genetic resistance mechanisms across different tissues upon infection by the pathogen. RNA-seq revealed the dynamic transcriptome of leaf, stem, and root tissues from resistant (R; CM-334) and susceptible (S; Early Jalapeño) varieties under different times of infection by <i>P. capsici</i>. There were 149,531 differentially expressed genes (DEGs) from 39 different R vs. S, time vs. time, and tissue vs. tissue comparisons. A total of 75,520 DEGs (51%) showed higher expression, whereas 74,011 (49%) demonstrated lower expression across all tissues and times of post-inoculation. The total number of DEGs with higher expression for the different tissue samples decreased across times of post-inoculation, where the 72h post-inoculation showed the least number of genes. The roots generally showed a higher number of DEGs compared to the stems and the leaves. Network analyses of DEGs demonstrated that genes with functions related to defense response to fungal infection were also involved with carbohydrate metabolism and ADP binding. Genes related to immune response to fungal infection and amino acid metabolism (e.g., homoserine kinase activity) showed higher gene expression across all times of infection and tissue samples. Chili pepper transcriptome under <i>P. capsici</i> infection provides evidence of shared gene expression across multiple tissues which can be leveraged for breeding and selection for broad-spectrum resistance in current <i>Capsicum</i> germplasm.