Screening and identification of candidate Fusarium wilt-resistance genes from pumpkin

Pumpkin (Cucurbita moschata) has been widely used as cucumber (Cucumis sativus L.) rootstock to defend against Fusarium wilt (FW) and increase cucumber yields and profits. However, the resistance genes and mechanisms underlying the FW tolerance in pumpkin are poorly understood. Here we analyzed the transcriptome of pumpkin inoculated with the cucumber FW causal agent Fusarium oxysporum f. sp. cucumerinum (Foc), and obtained 3 152 and 4 735 upregulated genes induced by Foc at 24 h after Foc inoculation compared with at 0 h and 24 h non-inoculated control, respectively. Next, 404 common differentially expressed genes (DEGs) were screened using the criterion log2 FPKM (fold change) ≥ 2. In total, 206 of 404 DEGs were predominantly expressed in roots, which is the first tissue that Foc contacts and invades. 140 DEGs were selected and classified into four groups (pathogenesis resistance, secondary metabolism-related, transcription factor and signal binding) based on their functional descriptions. Then, 29 genes having high expression levels were selected to investigate the expression patterns induced by a Foc inoculation. Among them, 16 genes were significantly induced by Foc and showed high expression levels at various treatment time points. These candidate genes may act as positive regulators of FW resistance in pumpkin and provide effective resources for improving cucumber FW resistance through breeding programs.