Transcriptomic Analysis of Resistant and Susceptible Eggplant Genotypes (Solanum melongena L.) Provides Insights into Phytophthora capsici Infection Defense Mechanisms

Phytophthora fruit rot caused by Phytophthora capsici is a devastating disease in many solanaceous vegetables, resulting in tremendous yield and economic losses. However, the underlying resistance or susceptibility to P. capsici in eggplant remains obscure. In this study, the transcriptomic analysis was performed between the resistant (G42) and susceptible (EP28) eggplant genotypes at 0, 1, 3 and 5 days post-inoculation (dpi). Taking 0 dpi as the control, a total of 4111, 7496 and 7325 DEGs were expressed at 1, 3 and 5 dpi, respectively, in G42 and 5316, 12675 and 12048 DEGs were identified at 1, 3 and 5 dpi, respectively, in EP28. P. capsici infection induced substantial transcriptional changes in the inoculated fruits. The analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) identified defense-related pathways including ‘plant-pathogen interactions’, ‘mitogen-activated protein kinase (MAPK)’ and ‘hormone biosynthesis and signal transduction’. The hormone-related genes encompassing ethylene, abscisic acid, auxins and gibberellins showed differential expression between G42 and EP28 eggplant genotypes, signifying their important roles in plant disease resistance. P. capsici infection induced the expression of major transcription factors such as MYB, NAC/NAM, bHLH, WRK, HSF, HD-ZIPAP2/ERF and Mad-box. qRT-PCR validation of the selected genes corroborates with RNA-seq, depicting the precision and consistency of the transcriptomic data. According to qRT-PCR and RNA-seq analyses, the expression of the pathogenesis-related gene transcriptional activator, SmPTI6 (Smechr0603020), is upregulated in G42 and downregulated in EP28. This differential expression suggests a potential role in the resistance to P. capsici. Functional analysis via a virus-induced gene silencing (VIGS) system found that silencing SmPTI6 in G42 enhanced infection by P. capsici, indicating that SmPTI6 performs a critical role in response to pathogen attack. The comprehensive results obtained in this study provide a valuable resource for understanding the molecular mechanisms underlying eggplant resistance to P. capsici and for establishing breeding resistant eggplant genotypes to P. capsici.