title: Gene expression profiling by cDNA-AFLP reveals potential candidate genes for partial resistance of 'Président Roulin' against Venturia inaequalis.
abstract: BACKGROUND
  Scab, 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Life Sciences Department, Breeding and Biodiversity Unit, Walloon Agricultural Research Center, Rue de Liroux, 4, 5030 Gembloux, Belgium. bastiaanse.h@gmail.com.
authors.forename: Héloïse
authors.initials: H
authors.lastname: Bastiaanse
authors.forename: Yordan
authors.initials: Y
authors.lastname: Muhovski
authors.forename: Olivier
authors.initials: O
authors.lastname: Parisi
authors.forename: Roberta
authors.initials: R
authors.lastname: Paris
authors.forename: Dominique
authors.initials: D
authors.lastname: Mingeot
authors.forename: Marc
authors.initials: M
authors.lastname: Lateur
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D001203:Ascomycota; D016172:DNA Fingerprinting; D018076:DNA, Complementary; D060467:Disease Resistance / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D054884:Host-Pathogen Interactions / Q000235:genetics*; D027845:Malus / Q000235:genetics* / Q000378:metabolism / Q000382:microbiology; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D018384:Oxidative Stress; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D018076:DNA, Complementary