RNA-sequencing analysis to identify candidate genes associated with responses to fruit tree canker in apple

Neonectria ditissima (formerly Neonectria galligena, anamorph Cylindrocarpon heteronema) is the causal agent of fruit tree canker, which is regarded as a serious economic problem in horticulture. This fungus occurs in a wide range of temperatures but is closely associated with wet weather, and geographic distribution is therefore strongly associated with local climate. Notable damage to apple trees is especially common in some regions like North-Western Europe. Significant efforts Fungicide and culture measures to control the disease usually are not very successful. An alternative approach could be the culture of more resistant cultivars. However, breeding for resistance is hard, resistance tests being time-lasting and labor intensive and resistance being quantitative in nature. Availability of molecular markers for resistance could greatly enhance the prospects of breeding. Currently, nothing is known on the genetic bases of resistance as present in some cultivars. Therefore a focused genomics approach was initiated in order to facilitate the identification of resistance genes. In this study, the transcriptomes of a partially resistant and highly susceptible cultivar are compared for healthy and infected wood. Samples were taken at three different time points, i.e., 5, 15, and 30 days after inoculation.This comparison enabled us to identify a list of candidate genes in response to fungus attack in apple trees. This information will be used in the study of signaling pathways are possibly involved in resistance to fruit tree canker.