Genetic basis of downy mildew resistance in cucumber: Identification of candidate genes and ethylene-mediated defense mechanism

The present study aimed to reveal the the genetic factors underlying downy mildew (DM) resistance in cucumber. We established three mapping populations, including two recombinant inbred lines (dm2.1-F ₇ and dm2.2-F ₇ ) and one near isogenic line (dm5.1-BC ₄ F ₂ ), all derived from the cross between TH118FLM (DM-resistant) and WMEJ (DM-susceptible). These lines exhibited a skewed susceptibility distribution, suggesting the involvement of crucial recessive genes in DM-resistance. A quantitative trait locus (QTL)-seq analysis of the pooled populations of these lines effectively refined the genomic regions of dm2.1 , dm2.2 , and dm5.1 . Subsequent single-nucleotide polymorphism mining further refined these regions and identified candidate genes, with dm2.1 , dm2.2 , and dm5.1 spanning 61.7, 84.7, and 80 Kb and encompassing 7, 10, and 5 putative genes, respectively. Finally, CsaV3_2G012920 ( CsACO , 1-aminocyclopropane-1-carboxylate oxidase), CsaV3_2G030320 ( CsCA , carbonic anhydrase), and CsaV3_5G015170 ( CsSTPK , serine/threonine-protein kinase) were identified as candidate DM-resistance genes, based on sequence and expression differences between DM-resistant and DM-susceptible lines. Furthermore, in silico 3D modeling revealed structural variations in CsaV3_5G015170 but not CsaV3_2G012920 and CsaV3_2G030320 . Based on the presumed functions and transcriptional responses of these genes to ethephon treatment, we proposed an ethylene-mediated defense mechanism for DM-resistance. According to this model, Pseudoperonospora cubensis first induces CsACO expression, leading to ethylene production, and then induces CsCA and CsSTPK expression, resulting in stomatal closure preventing pathogenic hyphal penetration and ethylene-mediated signaling pathway activation, respectively. These findings enhance our understanding of the genetic mechanisms underlying DM-resistance in cucumbers and further support our efforts to combat this destructive disease.