The potential for breeding apple varieties with propensity for apple canker resilient microbiome recruitment

Abstract: Apple canker caused by Neonectria ditissima is one of the most devastating diseases of apple worldwide. It infects apple trees through wounds and can cause tree death and reduction of yield and quality. The withdrawal of chemical control products and high density plantings of highly susceptible cultivars requires the development of new management approaches. Bacterial and fungal endophytes may help their host by improving tolerance to abiotic and biotic stresses and enhancing growth. Their communities are shaped by environment but also by host genotype. Here we used canker inoculated F1 sibling population of cv ‘Aroma’ × ‘Golden delicious’ bi-parental cross, endophyte sequencing, and quantitative trial loci mapping to identify genetically controlled endophytes with canker control potential. We found principal components of apple leaf scar endophytes, as well as individual fungal or bacterial operational taxonomic units that were partially genetically controlled, correlated with canker resistant phenotypes and associated with quantitative trial loci (QTL). Most interesting were bacterial endophytes from the Sphingomonas genus that were associated with strong QTL (50 % effect), positively correlated with canker tolerant phenotypes and are known to increase plant growth and disease tolerance. SNP markers associated with Sphingomonas abundance could be used to aid selection of new varieties with enhanced propensity for recruitment of apple canker tolerant bacterial endophytes.