Gene expression profiling by cDNA-AFLP reveals potential candidate genes for partial resistance of ‘Président Roulin’ against Venturia inaequalis

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.

Mapping of Quantitative Trait Loci for Scab Resistance in Apple (Malus × Domestica)

“…The number of heterozygous polymorphic markers for chromosomes varied from one for chromosome 6, 13 and 14 to four for chromosome 1,2,5 and 11. Chromosomes 3,4,7,10,12 and 17 had two polymorphic markers, each. Chromosome 8, 9 and 15 were analyzed with three markers each.…”

“…In contrast, partial resistance confers a reduction rather than complete arrest of the disease, and is controlled by Quantitative Trait Loci (QTLs). Partial resistance is presumed to be more durable than complete resistance as there is relatively low selection pressure on pathogen isolates [4], and therefore, becomes an attractive alternative for controlling apple scab.…”

“…QTLs associated with apple scab have been mapped on 10 different linkage groups (LGs) [4]. However, the nature of these QTLs remains largely unknown, in spite of the availability of whole genome sequence assembly of Malus x domestica.…”

Changes in transcript and protein expression levels in the barley — Cochliobolus sativus interaction

“…Similarly, proteomics can be used to compare changes in levels of many proteins under particular genetic and environmental conditions. However, proteomic studies provide information on post-translational modifications, which cannot be obtained from mRNA expression profiles; these have proven critical to our understanding of proper physiological protein function, translocation, and subcellular localization (Bastiaanse et al 2014;Liu and Aebersold 2016). Understanding the mutual regulatory interactions between transcriptome and proteome necessitates an approach that encompasses the simultaneous monitoring of expression at both the RNA and protein levels (Cheng et al 2016).…”