Abstract
BackgroundScab, caused by the fungus Venturia inaequalis, is one of the most important diseases of cultivated apple. While a few scab resistance genes (R genes) governing qualitative resistance have been isolated and characterized, the biological roles of genes governing quantitative resistance, supposed to be more durable, are still unknown. This study aims to investigate the molecular mechanisms involved in the partial resistance of the old Belgian apple cultivar ‘Président Roulin’ against V. inaequalis.ResultsA global gene expression analysis was conducted in ‘Président Roulin’ (partially resistant) and in ‘Gala’ (susceptible) challenged by V. inaequalis by using the cDNA-AFLP method (cDNA-Amplified Fragment Length Polymorphism). Transcriptome analysis revealed significant modulation (up- or down-regulation) of 281 out of approximately 20,500 transcript derived fragments (TDFs) in ‘Président Roulin’ 48 hours after inoculation. Sequence annotation revealed similarities to several genes encoding for proteins belonging to the NBS-LRR and LRR-RLK classes of plant R genes and to other defense-related proteins. Differentially expressed genes were sorted into functional categories according to their gene ontology annotation and this expression signature was compared to published apple cDNA libraries by Gene Enrichment Analysis. The first comparison was made with two cDNA libraries from Malus x domestica uninfected leaves, and revealed in both libraries a signature of enhanced expression in ‘Président Roulin’ of genes involved in response to stress and photosynthesis. In the second comparison, the pathogen-responsive TDFs from the partially resistant cultivar were compared to the cDNA library from inoculated leaves of Rvi6 (HcrVf2)-transformed ‘Gala’ lines (complete disease resistance) and revealed both common physiological events, and notably differences in the regulation of defense response, the regulation of hydrolase activity, and response to DNA damage. TDFs were in silico mapped on the ‘Golden Delicious’ apple reference genome and significant co-localizations with major scab R genes, but not with quantitative trait loci (QTLs) for scab resistance nor resistance gene analogues (RGAs) were found.ConclusionsThis study highlights possible candidate genes that may play a role in the partial scab resistance mechanisms of ‘Président Roulin’ and increase our understanding of the molecular mechanisms involved in the partial resistance against apple scab.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1043) contains supplementary material, which is available to authorized users.
Highlights
Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of cultivated apple
Fungal development across post inoculation time points Microscopic observations revealed no significant difference between ‘Président Roulin’ and ‘Gala’ for pathogen development at the early stages of infection
As for any transcriptome study, a genome-wide screen for differentially expressed genes based on cDNA-AFLP requires that as many transcripts as possible are analyzed in a unique way, and that the data obtained are informative enough to allow characterization of the transcripts. Considering criteria such as the genomic region of the restriction sites, the redundancy and the length of the transcript derived fragments (TDFs) being produced, we showed in silico that the restriction enzyme pair EcoRI/ MseI was the most appropriate for our cDNA-AFLP analysis
Summary
Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of cultivated apple. Apple scab caused by the hemi-biotrophic ascomycete Venturia inaequalis (Cke.) Wint. Multiple applications of fungicides are required for effective control in commercial orchards planted with susceptible cultivars. For apple orchards in France, pesticide treatments costs account for about 10% of the fixed production expenses, representing a substantial cost per kg of apple (0.031 €) [2]. This intensive use of fungicides in orchards raises ecological problems and human health concerns in addition to the economic cost
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