Abstract/Summary

European canker, caused by the fungal pathogen Neonectria ditissima, is a devastating disease in commercial apple production. N. ditissima is principally a wood pathogen, which causes trunk cankers and dieback in apple orchards. Due to a lack of efficient cultural and chemical methods to control European canker, host resistance remains one of the most effective means of limiting disease spread. Despite its importance to the apple growing community, the genetic basis underlying this resistance is still not well understood which hinders efficient breeding of cultivars with improved tolerance to the disease. The work in this thesis was conducted to aid the development of apple cultivars with a high tolerance to infection by N. ditissima. This was done by exploring the genetics behind host resistance in apple scion germplasm as well as investigating the potential of developing apple cultivars with canker-suppressing endophytic microbiomes. This thesis describes the identification of seven quantitative trait loci (QTL) associated with resistance to European canker in apple through Bayesian analysis. Single nucleotide polymorphism (SNP) haplotypes associated with resistant alleles for each QTL are also reported. The molecular basis of this quantitative resistance was further explored through a transcriptome analysis. The host response to Neonecria infection was studied in two partially tolerant cultivars; the scion variety ‘Golden Delicious’ and the rootstock cultivar ‘M9’. Furthermore, a comparative transcriptome analysis of full-sibling apple genotypes carrying resistant and susceptible alleles at six resistance QTL was conducted to identify candidate genes underlying the quantitative resistance to this wood pathogen. Host resilience to plant pathogens is not only dependent on host resistance but can also be influenced by microbial communities colonising the phyllosphere. The work within this thesis therefore further explores the feasibility to breed apple cultivars amenable to endophyte colonization through a QTL analysis in a bi-parental population of apple.