Identification and validation of stem rot disease resistance genes in passion fruit (Passiflora edulis)

Stem rot disease poses a significant challenge in passion fruit production, necessitating the identification of resistant genes for the development of stem rot resistant varieties. In this study, we conducted artificial inoculation of <i>Fusarium solani</i> on leaves of two passion fruit varieties, ‘Huangjinguo’ and ‘Ziguo 7’. Leaf samples were collected at 0 h, 24 h, and 48 h post-inoculation for RNA-sequencing (RNA-seq) analysis, and 3 370, 4 464, and 3 974 differentially expressed genes (DEGs) were identified at these stages. Gene Ontology (GO) analysis revealed associations with functions such as response to reactive oxygen species (ROS), response to hydrogen peroxide, and protein complex oligomerisation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted the enrichment of DEGs in the phenylpropanoid biosynthesis pathway, including genes such as <i>ZX.06G0025070</i>,<i> ZX.01G0064640</i>,<i> ZX.04G0011040</i>,<i> ZX.05G0011380</i>, all implicated in lignin biosynthesis. Weighted gene co-expression network analysis (WGCNA) identified three modules significantly associated with passion fruit stem rot resistance. Network analysis highlighted<i> ZX.08G0013660</i> as the gene with the highest connectivity in these modules, featuring a leucine-rich repeat domain. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis further validated <i>ZX.08G0013660</i> and other genes as potential candidates for passion fruit stem rot resistance. Overall, genes related to ROS, phenylpropanoid biosynthesis and leucine-rich repeat domain protein likely play critical roles in passion fruit stem rot resistance. This study provides new insights for breeding passion fruit varieties resistant to stem rot disease.