Putative SET domain-containing proteins play significant roles in regulating sporulation and pathogenicity in Phytophthora capsici

Phytophthora capsici is a filamentous oomycete responsible for root rot, fruit rot, leaf blight, and other economically destructive diseases in multiple plant species, including pepper (Capsicum annuum), tomato (Solanum lycopersicum), squash (Cucurbita pepo), eggplant (Solanum melongena), faba bean (Vicia faba), and lima bean (Phaseolus lunatus), among others. The pathogen causes significant yield losses in fruit and vegetable crops globally. Multiple molecular parameters, including effector proteins and epigenetic modulators, play vital roles in modulating the physio pathological development of P. capsici. Here, we identified 56 SET domain-containing proteins in P. capsici, with 35 predicted as potential effectors. Transcriptomic analysis revealed the upregulation of 13 candidate effector genes during infection, suggesting their roles in pathogenicity. We successfully deleted one effector, PcSET-C (DVH05_022087), and two non-effector proteins, PcSET-B (DVH05_004260), and PcSET-A (DVH05_000194), using CRISPR-Cas9 and homologous recombination strategies. Phenotypic analysis showed that targeted deletion of the PcSET-A, and PcSET-B gene significantly impaired vegetative growth, while ΔPcset-C strains displayed growth like wild-type strains. Additionally, we showed that targeted disruption of all three genes resulted in reduced asexual sporulation and almost completely abolished the pathogenicity or virulence of ΔPcset-A, ΔPcset-B, and ΔPcset-C strains on different P. capsici-susceptible plants. However, targeted replacement of the three SET domain-containing genes investigated in this study has no significant adverse effects on zoospore release in P. capsici. These findings provide insights into the crucial role of SET domain-containing proteins in both morphological and pathological development of P. capsici and underscore PcSETs as potential targets for disease control.