Isolation of putative pepper defense-related genes against the pathogen Phytophthora capsici using suppression subtractive hybridization/macroarray and RNA-sequencing analyses

The oomycete Phytophthora capsici Leonian is one of the most economically important pathogens limiting pepper (Capsicum annuum) production in many regions around the world. Insights into the defense mechanisms of pepper against P. capsici would be helpful in the breeding of resistant cultivars. However, little is still known about the defense system in pepper against P. capsici. We used suppression subtractive hybridization (SSH) followed by macro-array screening to isolate the putative candidate defense genes (PSH, Phytophthora Subtractive Hybridization) in pepper that are differentially expressed between the resistant cultivar (CM334) and the susceptible cultivar (Chilsungcho) following P. capsici infection. A total of 72 PSH genes were identified and categorized based on their putative functions. Semi-quantitative RT-PCR analyses using 11 selected genes confirmed their differential expressions between the resistant and susceptible cultivars along the time course of infection with P. capsici. Furthermore, RNA-seq analyses were performed to understand the possible roles of PSH genes in the defense response to P. capsici as well as three viruses, including two tobacco mosaic virus strains and one Pepper Mottle Virus strain. We found that 37 genes out of 72 displayed differential expression in our RNA-seq-based heatmap between ‘CM334’ and ‘Chilsungcho’ upon pathogen infection. In particular, two genes, CA00g99220 and CA00g96010, and one gene, CA12g16620, were shown to be strongly and uniquely expressed in the resistant cultivar, CM334, against P. capsici and two viruses, respectively. Thus, we consider that this combined approach using SSH/macro-array screening and RNA-seq analyses is a relevant tool for isolation of candidate defense-related genes upon pathogen infection. Data in this study provide a good source for further study on the defense mechanisms against pathogens in chili pepper.