Transcriptomic and volatilomic profiles reveal Neofabraea vagabunda infection-induced changes in susceptible and resistant apples during storage

Bull’s eye rot is one of the most severe diseases that may affect apple fruit during post-harvest storage. It is caused by the fungus Neofabraea vagabunda, and the mechanism by which the pathogen infects the fruits is only partially understood. In particular, very little is known about the molecular mechanisms regulating the interaction between the pathogen and the host during symptoms development. Despite different apple cultivars show divergent levels of resistance to the pathogen, the genetic basis of these responses is still unknown. In order to better understand the molecular mechanisms occurring in the apple fruit during N. vagabunda infection, a large-scale transcriptome study by RNA-Seq analysis was performed, comparing fruits of the sensitive ‘Roho’ cultivar and the resistant cultivar ‘Ariane’ after artificial infection with N. vagabunda and a storage period of four months. Transcriptomic analyses revealed the regulation of several classes of genes during this period, some of which may be involved in apple-pathogen interaction, such as superoxide dismutases and heat shock proteins (HSPs), ethylene-responsive transcription factors (ERFs), carboxylesterases and NAC transcription factors gene families. Moreover, a volatile analysis was performed, revealing differences in the volatile profile between the resistant and the susceptible cultivar that may help to elucidate the resistance mechanism. RNA-Seq data highlighted several classes of pathogen-related genes, such as genes coding for enzymes involved in cell wall disruption and in reactive oxygen species (ROS) homeostasis, being differentially regulated between resistant and susceptible fruits and between diseased and healthy fruits of the same cultivar, indicating that apples are capable of perceiving and triggering a molecular response to N. vagabunda infection. Some volatiles, as ethanol and methanol, but also furan and formaldehyde, might be potential markers for N. vagabunda infection; others, such as hexenal and methyl acetate, were found to be putatively involved in regulating apple-fungi interaction