RNA-Seq based transcriptome analysis of melon (Cucumis melo L.) for the identification of candidate genes involved in the resistance towards Fusarium oxysporum f. sp. melonis race 1,2.

Fusarium wilt of melon is one of the most important diseases of melon worldwide and one of the less controllable, because the pathogen remains viable in the infected soil. Among the eight formae speciales that attack Cucurbits, only F. oxysporum f. sp. melonis Snyder & Hans. (FOM) is specific to melon (Cucumis melo L.). Four races of the pathogen (0, 1, 2 and 1,2) have been defined according to host resistance genes overcome by variants of the pathogen. FOM race 1,2 is the most widespread and harmful race causing economic losses up to 100% of the yield. Resistance to race 1,2 is complex and appears to be controlled by multiple recessive genes and strongly affected by environment. Partial resistance was found in several Far-Eastern lines and introgressed into the cultivar “Isabelle” from which two doubled-haploid (DH) resistant lines Nad-1 and Nad-2 were derived. At present, only partial resistant genotypes are commercially available, mainly as rootstock, to contrast FOM race 1,2 damage and being breeding for fully resistant cultivars a long and costly process, resistance sources are still inadequate. Using cDNA-AFLP analysis differentially expressed transcripts associated with the infection process in the binomial interaction between melon cultivar “Charentais Fom-2” and FOM races 1 and 1,2 were identified. With the objective of studying the melon-FOM race 1,2 pathosystem a RNA-Seq analysis was conducted to outline gene expression profiling during the incompatible (resistant) and compatible (susceptible) interactions and to identify candidate resistance genes towards FOM race 1,2. The DH resistant line Nad-1 (NAD) and the susceptible genotype “Charentais-T” (CHT) were analyzed at two time points, 24 and 48 hour post inoculation (hpi). In the resistant line, 2023 and 568 differentially expressed genes (DEGs) resulted to be up-regulated in response to FOM infection at 24 and 48 hpi, respectively. This approximately 3-fold ratio was reversed in the susceptible genotype in which 882 and 2237 DEGs were called at 24 and 48 hpi, respectively. It is notable that the defence responses of the two genotypes during the two time points were largely different, with only 79 DEGs in common. Gene ontology (GO) enrichment analyses revealed a total of 57 GO terms enriched in both varieties and consistent with response to fungal infection, such as “defence response to fungus”, “response to chitin”, respiratory burst involved in defence response”, “cell wall”, “regulation of plant hypersensitive response”. Furthermore, several GO terms were genotype and time points specific. In particular, 33 GO terms were enriched solely in NAD at 24 hpi among which “defence response, incompatible interaction” is the most remarkable suggesting an early activation of the resistance response. In NAD, only 2 GO were shared by the two points, “pectin esterase activity” and “manganese ion binding”, whereas, 18 GO resulted NAD 48 hpi specific. In particular, the “lipoxygenase”, “response to jasmonic acid stimulus”, “oxylipin biosynthetic process” represent the most relevant GO groups. Global transcriptome profiling and GO enrichment analysis of resistant and susceptible non-inoculated plants, allowed identification of 26 and 14 GO groups belonging to NAD at 24 and 48 hpi respectively, while “response to stress” and “defence response” are the only 2 GO terms shared by the two time points. This suggests that the resistant plant NAD is already predisposed to activate the defence mechanism to FOM. The resistant plant is able to modulate a higher amount of genes at the early stage of infection that are responsible for the initial immunization against FOM. This study represents a preliminary approach to pose the basis for the identification of resistance mechanisms and resistance candidate genes to FOM race 1,2.