Abstract
Background
The fungal pathogen Neonectria ditissima causes wood cankers on a wide range of dicotyledonous species, and is a major disease threat to apple production globally. However, understanding of host response and genetic mechanisms underlying resistance remains limited. A transcriptome analysis of RNA sequencing data from infected apple stems was used to assess the response of apple to a single isolate of N. ditissima. The analysis was performed on two partially resistant cultivars; the scion variety ‘Golden Delicious’ and the rootstock cultivar ‘M9 EMLA’. Furthermore, we conducted a comparative transcriptome analysis of full-sibling apple genotypes carrying partial resistant (QTL-R) and susceptible (QTL-S) alleles at six resistance quantitative trait loci (QTL) to study the genetic mechanisms underlying quantitative resistance to this wood pathogen.
Results
The transcriptome profiling of ‘Golden Delicious’ and ‘M9 EMLA’ trees during infection with N. ditissima show that >5,000 genes were differentially expressed in the two cultivars during fungal infection. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG) and protein family (PFAM) enrichment analyses of the differentially regulated genes suggest that secondary metabolism, hormone signalling, pathogen recognition, and metabolism of sugar and carbon are involved in the response to infection. The comparative transcriptome analysis of QTL-R/QTL-S progeny revealed differential expression of genes functioning in pathogen recognition, secondary metabolism, and detoxification within the QTL intervals.
Notable candidate genes encompass putative 4-Coumarate-CoA Ligases (4CL) located within the QTL on chromosome 16, as well as clusters of putative Wall Associated Kinases (WAK) and Wall Associated Kinase Like (WAKL) situated within the QTLs on chromosomes 10 and 2, respectively.
Conclusion
Our study indicate that the host's reaction to N. ditissima involves both intracellular and extracellular immune receptors and that the presence of the pathogen triggers hormone signalling and modifies the metabolism of sugars, carbon, and secondary metabolites. The exploration of candidate genes within resistance QTL highlighted genes that can be used in marker development for breeding. Our findings identifies candidate genes associated with partial resistance to European canker that exhibit a broad impact on pathogen interaction, potentially extending their role to confer resistance against other apple diseases.