The Venturia apple pathosystem: pathogenicity mechanisms and plant defense responses

Hyperspectral imaging reveals small-scale water gradients in apple leaves due to minimal cuticle perforation by Venturia inaequalis conidiophores

Effects of Venturia inaequalis on water relations of apple leaves were studied under controlled conditions without limitation of water supply to elucidate their impact on the non-haustorial biotrophy of this pathogen. Leaf water relations, namely leaf water content and transpiration, were spatially resolved by hyperspectral imaging and thermography; non-imaging techniques-gravimetry, a pressure chamber, and porometry-were used for calibration and validation. Reduced stomatal transpiration 3-4 d after inoculation coincided with a transient increase of water potential. Perforation of the plant cuticle by protruding conidiophores subsequently increased cuticular transpiration even before visible symptoms occurred. With sufficient water supply, cuticular transpiration remained at elevated levels for several weeks. Infections did not affect the leaf water content before scab lesions became visible. Only hyperspectral imaging was suitable to demonstrate that a decreased leaf water content was strictly limited to sites of emerging conidiophores and that cuticle porosity increased with sporulation. Microscopy confirmed marginal cuticle injury; although perforated, it tightly surrounded the base of conidiophores throughout sporulation and restricted water loss. The role of sustained redirection of water flow to the pathogen's hyphae in the subcuticular space above epidermal cells, to facilitate the acquisition and uptake of nutrients by V. inaequalis, is discussed.

Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab (Venturia inaequalis) in apple cultivars (Malus × domestica)

Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent "-omics" approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different "-omics" approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.

Antifungal Activity of Hop Leaf Extracts and Xanthohumol on Two Strains of Venturia inaequalis with Different Sensitivities to Triazoles

Hop cones are well-known for their antimicrobial properties, attributed to their specialized metabolites. Thus, this study aimed to determine the in vitro antifungal activity of different hop parts, including by-products such as leaves and stems, and some metabolites against Venturia inaequalis, the causal agent of apple scab. For each plant part, two types of extracts, a crude hydro-ethanolic extract and a dichloromethane sub-extract, were tested on spore germination of two strains with different sensitivities to triazole fungicides. Both extracts of cones, leaves and stems were able to inhibit the two strains, whereas rhizomes did not show activity. The apolar sub-extract of leaves appeared as the most active modality tested with half maximal inhibitory concentrations (IC₅₀) of 5 and 10.5 mg·L^-1 on the sensitive strain and the strain with reduced sensitivity, respectively. Differences in activity level between strains were noticed for all active modalities tested. Sub-extracts of leaves were then separated into seven fractions by preparative HPLC and tested on V. inaequalis. One fraction, containing xanthohumol, was especially active on both strains. This prenylated chalcone was then purified by preparative HPLC and showed significant activity against both strains, with IC₅₀ of 1.6 and 5.1 mg·L^-1. Therefore, xanthohumol seems to be a promising compound to control V. inaequalis.

Cell Wall Carbohydrate Dynamics during the Differentiation of Infection Structures by the Apple Scab Fungus, Venturia inaequalis

Scab, caused by the biotrophic fungal pathogen Venturia inaequalis, is the most economically important disease of apples. During infection, V. inaequalis colonizes the subcuticular host environment, where it develops specialized infection structures called runner hyphae and stromata. These structures are thought to be involved in nutrient acquisition and effector (virulence factor) delivery, but also give rise to conidia that further the infection cycle. Despite their importance, very little is known about how these structures are differentiated. Likewise, nothing is known about how these structures are protected from host defenses or recognition by the host immune system. To better understand these processes, we first performed a glycosidic linkage analysis of sporulating tubular hyphae from V. inaequalis developed in culture. This analysis revealed that the V. inaequalis cell wall is mostly composed of glucans (44%) and mannans (37%), whereas chitin represents a much smaller proportion (4%). Next, we used transcriptomics and confocal laser scanning microscopy to provide insights into the cell wall carbohydrate composition of runner hyphae and stromata. These analyses revealed that, during subcuticular host colonization, genes of V. inaequalis putatively associated with the biosynthesis of immunogenic carbohydrates, such as chitin and β-1,6-glucan, are downregulated relative to growth in culture, while on the surface of runner hyphae and stromata, chitin is deacetylated to the less-immunogenic carbohydrate chitosan. These changes are anticipated to enable the subcuticular differentiation of runner hyphae and stromata by V. inaequalis, as well as to protect these structures from host defenses and recognition by the host immune system. IMPORTANCE Plant-pathogenic fungi are a major threat to food security. Among these are subcuticular pathogens, which often cause latent asymptomatic infections, making them difficult to control. A key feature of these pathogens is their ability to differentiate specialized subcuticular infection structures that, to date, remain largely understudied. This is typified by Venturia inaequalis, which causes scab, the most economically important disease of apples. In this study, we show that, during subcuticular host colonization, V. inaequalis downregulates genes associated with the biosynthesis of two immunogenic cell wall carbohydrates, chitin and β-1,6-glucan, and coats its subcuticular infection structures with a less-immunogenic carbohydrate, chitosan. These changes are anticipated to enable host colonization by V. inaequalis and provide a foundation for understanding subcuticular host colonization by other plant-pathogenic fungi. Such an understanding is important, as it may inform the development of novel control strategies against subcuticular plant-pathogenic fungi.

A Melanin-Deficient Isolate of Venturia inaequalis Reveals Various Roles of Melanin in Pathogen Life Cycle and Fitness

Venturia inaequalis is the ascomycetous pathogen causing apple scabs and forms dark-pigmented spores and partially melanised infection structures. Although melanin is considered to be essential for the infection of host tissue, a spontaneously occurring melanin-deficient mutant was isolated from an abaxial side of an apple leaf and can be cultivated in vitro as well as in vivo. The morphology and development of the melanin-deficient-isolate SW01 on leaves of susceptible apple plants were compared to that of the corresponding wild-type isolate HS1. White conidia of SW01 were often wrinkled when dry and significantly increased their volume in suspension. Germination and formation of germtubes and appressoria were not impaired; however, the lack of melanisation of the appressorial ring structure at the interface with the plant cuticle significantly reduced the infection success of SW01. The colonisation of leaf tissue by non-melanised subcuticular hyphae was not affected until the initiation of conidiogenesis. Non-melanised conidiophores penetrated the plant cuticle from inside less successfully than the wild type, and the release of white conidia from less solid conidiophores above the cuticle was less frequent. Melanin in the outer cell wall of V. inaequalis was not required for the survival of conidia under ambient temperature or at -20 °C storage conditions, however, promoted the tolerance of the pathogen to copper and synthetic fungicides affecting the stability and function of the fungal cell wall, plasma membrane, respiration (QoIs) and enzyme secretion, but had no effect on the sensitivity to sulphur and SDHIs. The roles of melanin in different steps of the V. inaequalis life cycle and the epidemiology of apple scabs are discussed.

Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers

Apple scab is a serious disease that restricts the growth of cultivated apples. The objective of this study is to investigate the genetic variations and genetic structure of Venturia inaequalis in Gansu Province, China. 108 isolates of the pathogen V. inaequalis from the Jingning, Lingtai, Jingchuan, Xifeng, Ning and Maiji regions were collected, and their genetic diversity was analyzed using AFLP molecular marker technique. The results showed that genetic diversity was present among the isolates but was not statistically significant. Genetic distance values ranged from 0.0095 to 0.0762. Cluster analysis results showed that the 108 isolates could be divided into two clusters using a similarity coefficient of 0.69. A total of 104 isolates were contained in cluster I while four isolates were contained in Cluster II. From the AMOVA analysis, 98% of variations were observed within the same region, while 2% were observed across different regions. The analysis of population structure showed that 108 isolates had two common ancestors, with the Jingning isolates mainly being derived from the red ancestor. PCoA analysis showed that the Jingning isolates were independent to a certain extent. The different geographical location caused the genetic difference of the isolates. The genetic diversity of apple scab in Gansu Province is greatly aided by this work, which also offers a theoretical foundation for the use of molecular markers in assisted breeding to create novel resistant types.

The Use of Mycoendophyte-Based Bioformulations to Control Apple Diseases: Toward an Organic Apple Production System in the Aurès (Algeria)

The present study aims to investigate the effectiveness of bioformulations based on endophytic fungi to control apple scab and Valsa canker disease in two orchards in the Aurès region (Algeria). In both orchards, the results showed that the treatment of senescent apple leaves by invert emulsions containing Trichoderma longibrachiatum and Chaetomium globosum harmed the ascogenesis of winter forms of Venturia inaequalis by reducing the number of ascospore-ejecting asci, the number of morphologically mature asci, and a considerable increase in the immature asci number. This antifungal activity was more essential in soil-incorporated leaves, showing the importance of the combination of treatments with cultural practices to efficiently control the apple scab disease. Furthermore, the disease incidence decreased by 52.63% and 50.68% in R'haouat and Bouhmama orchards, respectively. Moreover, the treatment of Valsa ceratosperma cankers with a biogel containing the endophytic yeast Metschnikowia sp. led to wound healing varying from 43.52% and 87.97% after 120 days but remained more considerable than conventional treatment with Folicur (tebuconazol). The current results open real opportunities concerning the implementation of eco-friendly and potent apple protection systems.

The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Background

Scab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth by V. inaequalis, as well as in activating, suppressing, or circumventing resistance protein-mediated defences in apple, is required.

Results

We generated the first comprehensive RNA-seq transcriptome of V. inaequalis during colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid, or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector from Leptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi.

Conclusions

Our study reveals the transcriptomic profile underpinning subcuticular growth by V. inaequalis and provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01442-9.

Comparative transcriptomics unravels new genes imparting scab resistance in apple (Malus x domestica Borkh.)

Apple scab is caused by an ascomycete fungus, Venturia inaequalis (Cke.) Wint., which is one of the most severe disease of apple (Malus × Domestica Borkh.) worldwide. The disease results in 30-40% fruit loss annually and even complete loss in some places. Owing to the evolving susceptibility of resistant apple genotypes harboring R-genes to new variants of V. inaequalis, a comparative transcriptome analysis using Illumina (HiSeq) platform of three scab-resistant (Florina, Prima, and White Dotted Red) and three susceptible (Ambri, Vista Bella, and Red Delicious) apple genotypes was carried out to mine new scab resistance genes. The study led to the identification of 822 differentially expressed genes in the tested scab-resistant and scab-susceptible apple genotypes. The most upregulated genes uniformly expressed in resistant varieties compared to susceptible ones were those coding for 17.3 kDa class II heat shock protein-like, chaperone protein ClpB1, glutathione S-transferase L3-like protein, B3 domain-containing protein At3g18960-like, transcription factor bHLH7, zinc finger MYM-type protein 1-like, and nine uncharacterized proteins, besides three lncRNAs. The genes that were downregulated in susceptible and upregulated in resistant cultivars were those coding for non-specific lipid transfer protein GPI-anchored 1, rust resistance kinase Lr10-like, disease resistance protein RPS6-like, and many uncharacterized proteins. DESeq2 analysis too revealed 20 DEGs that were upregulated in scab-resistant cultivars. Furthermore, a total of 361 genes were significantly upregulated in scab-susceptible variety, while 461 were found downregulated (P value < 0.05 and Log2 (FC) > 1). The differentially expressed genes (DEGs) were related to various pathways, i.e., metabolic, protein processing, biosynthesis of secondary metabolites, plant hormone signal transduction, autophagy, ubiquitin-mediated proteolysis, plant-pathogen interaction, lipid metabolism, and protein modification pathways. Real-time expression of a set of selected twelve DEGs further validated the results obtained from RNA-seq. Overall, these findings lay the foundation for investigating the genetic basis of apple scab resistance and defense pathways that might have a plausible role in governing scab resistance in apple against V. inaequalis.

CRISPR-Cas9 gene editing and rapid detection of gene-edited mutants using high-resolution melting in the apple scab fungus, Venturia inaequalis

Apple scab, caused by the fungal pathogen Venturia inaequalis, is the most economically important disease of apple (Malus x domestica) worldwide. To develop durable control strategies against this disease, a better understanding of the genetic mechanisms underlying the growth, reproduction, virulence and pathogenicity of V. inaequalis is required. A major bottleneck for the genetic characterization of V. inaequalis is the inability to easily delete or disrupt genes of interest using homologous recombination. Indeed, no gene deletions or disruptions in V. inaequalis have yet been published. Using the melanin biosynthesis pathway gene trihydroxynaphthalene reductase (THN) as a target for inactivation, which has previously been shown to result in a light-brown colony phenotype when transcriptionally silenced using RNA interference, we show, for the first time, that the CRISPR-Cas9 gene editing system can be successfully applied to the apple scab fungus. More specifically, using a CRISPR-Cas9 single guide RNA (sgRNA) targeted to the THN gene, delivered by a single autonomously replicating Golden Gate-compatible plasmid, we were able to identify six of 36 stable transformants with a light-brown phenotype, indicating an ∼16.7% gene inactivation efficiency. Notably, of the six THN mutants, five had an independent mutation. As part of our pipeline, we also report a high-resolution melting (HRM) curve protocol for the rapid detection of CRISPR-Cas9 gene-edited mutants of V. inaequalis. This protocol identified a single base pair deletion mutation in a sample containing only 5% mutant genomic DNA, indicating high sensitivity for mutant screening. In establishing CRISPR-Cas9 as a tool for gene editing in V. inaequalis, we have provided a strong starting point for studies aiming to decipher gene function in this fungus. The associated HRM curve protocol will enable CRISPR-Cas9 transformants to be screened for gene inactivation in a high-throughput and low-cost manner, which will be particularly powerful in cases where the CRISPR-Cas9-mediated gene inactivation efficiency is low.

Genetic diversity of Venturia inaequalis isolates (Apple scab) in China and U.K. determined by SSR markers

Apple scab caused by Venturia inaequalis is a serious disease of cultivated apple worldwide. In this study, we collected 132 V. inaequalis isolates from Shaanxi, Gansu, Xinjiang, and the U.K. and analyzed their genetic diversity by using 13 microsatellite markers. Cluster analysis based on population structure and genetic distances suggested high similarity among the four regions. Population differentiation values ranged from 0.044 to 0.155, indicating there is a high level of kinship among the four regions. All isolates could be divided into 5 lineages with a 0.76 similarity coefficient. Among the four regions, Shaanxi had only one lineage, Group II; Gansu had four lineages, Group I, Group II, Group IV, and Group V; Xinjiang had all five lineages, Group I, Group II, Group III, Group IV, and Group V; and the U.K. had three lineages, Group I, Group II and Group IV. High molecular variance was detected for populations in the four regions, with 91% of the variance occurring within the populations and 9% among the populations. Structure analysis there are three common ancestors of these four regions. The results of the present study shed light on the genetic diversity of V. inaequalis in Shaanxi, Gansu and Xinjiang, which will lead to the development of more effective management strategies and new resistant apple cultivars through molecular marker-assisted selection.

Influence of plant immunity inducers on the degree of apple scab development when applied in plant protection systems in the zone of humid subtropics of Abkhazia

One of the ways to reduce pesticide load and prevent emergence of pathogen resistance can be the use of plant immunity inducers in plant protection systems. The purpose of these studies was to evaluate an efficiency of natural plant immunity inducers Albit® (poly-beta-hydroxybutyric acid), Immunocytophite® (arachidonic acid ethyl ether) and Ecogel® (chitosan lactate) in apple scab protection systems in Abkhazia. The maximum resistance of apple trees to this phytopathogen was recorded in the experimental variants with Albit® and Ecogel® application in half dosages of fungicides and in the variant of production processing (biological efficiency reached 79.4 %). Plant immunity inducers used on apple trees showed cultivar-specificity. For the four-year research period, the greatest efficiency of immunity inducers was achieved on the susceptible cultivar Idared in the second year of the experiment, while on the relatively scab-resistant cultivar Golden Rangers – it was achieved only in the third year. The greatest stability in the efficiency for a four-year period was observed for the tank mix Albit with half dosages of fungicides. Immunocytophyte® was characterized by lower inducing activity, which is associated with its activation of the jasmonate pathway for the formation of non-specific induced immunity.

Cinnamate-CoA ligase is involved in biosynthesis of benzoate-derived biphenyl phytoalexin in Malus × domestica 'Golden Delicious' cell cultures

Apple (Malus sp.) and other genera belonging to the sub-tribe Malinae of the Rosaceae family produce unique benzoic acid-derived biphenyl phytoalexins. Cell cultures of Malus domestica cv. 'Golden Delicious' accumulate two biphenyl phytoalexins, aucuparin and noraucuparin, in response to the addition of a Venturia inaequalis elicitor (VIE). In this study, we isolated and expressed a cinnamate-CoA ligase (CNL)-encoding sequence from VIE-treated cell cultures of cv. 'Golden Delicious' (M. domestica CNL; MdCNL). MdCNL catalyses the conversion of cinnamic acid into cinnamoyl-CoA, which is subsequently converted to biphenyls. MdCNL failed to accept benzoic acid as a substrate. When scab-resistant (cv. 'Shireen') and moderately scab-susceptible (cv. 'Golden Delicious') apple cultivars were challenged with the V. inaequalis scab fungus, an increase in MdCNL transcript levels was observed in internodal regions. The increase in MdCNL transcript levels could conceivably correlate with the pattern of accumulation of biphenyls. The C-terminal signal in the MdCNL protein directed its N-terminal reporter fusion to peroxisomes in Nicotiana benthamiana leaves. Thus, this report records the cloning and characterisation of a cinnamoyl-CoA-forming enzyme from apple via a series of in vivo and in vitro studies. Defining the key step of phytoalexin formation in apple provides a biotechnological tool for engineering elite cultivars with improved resistance.

Molecular cloning and functional analysis of a biphenyl phytoalexin-specific O-methyltransferase from apple cell suspension cultures

This manuscript describes the cloning and functional characterization of a biphenyl phytoalexin biosynthetic gene, 3,5-dihydroxybiphenyl O-methyltransferase from elicitor-treated cell cultures of scab resistant apple cultivar 'Florina'. Apples belong to the subtribe Malinae of the Rosaceae family. Biphenyls and dibenzofurans are the specialized phytoalexins of Malinae, of which aucuparin is the most widely distributed biphenyl. The precursor of aucuparin, 3,5-dihydroxybiphenyl, is a benzoate-derived polyketide, which is formed by the sequential condensation of three molecules of malonyl-CoA and one molecule of benzoyl-CoA in a reaction catalyzed by biphenyl synthase (BIS). This 3,5-dihydroxybiphenyl then undergoes sequential 5-O-methylation, 4-hydroxylation, and finally 3-O-methylation to form aucuparin. A cDNA encoding O-methyltransferase (OMT) was isolated and functionally characterized from the cell cultures of scab-resistant apple cultivar 'Florina' (Malus domestica cultivar 'Florina'; MdOMT) after treatment with elicitor prepared from the apple scab causing fungus Venturia inaequalis. MdOMT catalyzed the regiospecific O-methylation of 3,5-dihydroxybiphenyl at the 5-position to form 3-hydroxy-5-methoxybiphenyl. The enzyme showed absolute substrate preference for 3,5-dihydroxybiphenyl. The elicitor-treated apple cell cultures showed transient increases in the MdOMT (GenBank ID MF740747) and MdBIS3 (GenBank ID JQ390523) transcript levels followed by the accumulation of biphenyls (aucuparin and noraucuparin) and dibenzofuran (eriobofuran) phytoalexins. MdOMT fused with N- and C-terminal yellow fluorescent protein showed cytoplasmic localization in the epidermis of Nicotiana benthamiana leaves. In scab inoculated greenhouse-grown 'Florina' plants, the expression of MdOMT was transiently induced in the stem followed by the accumulation of biphenyl phytoalexins.

Comparative metabolomics of scab-resistant and susceptible apple cell cultures in response to scab fungus elicitor treatment

Apple scab disease caused by the fungus Venturia inaequalis is a devastating disease that seriously affects quality and yield of apples. In order to understand the mechanisms involved in scab resistance, we performed gas chromatography-mass spectrometry based metabolomics analysis of the cell culture of scab resistant cultivar 'Florina' and scab susceptible cultivar 'Vista Bella' both prior -to and -following treatment with V. inaequalis elicitor (VIE). A total 21 metabolites were identified to be altered significantly in 'Florina' cell cultures upon VIE-treatment. Among 21 metabolites, formation of three new specialized metabolites aucuparin, noraucuparin and eriobofuran were observed only in resistant cultivar 'Florina' after the elicitor treatment. The score plots of principal component analysis (PCA) exhibited clear discrimination between untreated and VIE-treated samples. The alteration in metabolite levels correlated well with the changes in the transcript levels of selected secondary metabolite biosynthesis genes. Aucuparin, noraucuparin and eriobofuran isolated from the 'Florina' cultures showed significant inhibitory effect on the conidial germination of V. inaequalis. The results expand our understanding of the metabolic basis of scab-resistance in apple and therefore are of interest in apple breeding programs to fortify scab resistance potential of commercially grown apple cultivars.

Antifungal activity of essential oils on two Venturia inaequalis strains with different sensitivities to tebuconazole

The antifungal activity of seven essential oils (eucalyptus, clove, mint, oregano, savory, tea tree, and thyme) was studied on Venturia inaequalis, the fungus responsible for apple scab. The composition of the essential oils was checked by gas chromatography-mass spectrometry. Each essential oil had its main compound. Liquid tests were performed to calculate the IC₅₀ of essential oils as well as their majority compounds. The tests were made on two strains with different sensitivities to tebuconazole: S755, the sensitive strain, and rs552, the strain with reduced sensitivity. Copper sulfate was selected as the reference mineral fungicidal substance. IC₅₀ with confidence intervals were calculated after three independent experiments. The results showed that all essential oils and all major compounds had in vitro antifungal activities. Moreover, it was highlighted that the effectiveness of four essential oils (clove, eucalyptus, mint, and savory) was higher than copper sulfate on both strains. For each strain, the best activity was obtained using clove and eucalyptus essential oils. For clove, the IC₅₀ obtained on the sensitive strain (5.2 mg/L [4.0-6.7 mg/L]) was statistically lower than the IC₅₀ of reduced sensitivity strain (14 mg/L [11.1-17.5 mg/L]). In contrast, for eucalyptus essential oil, the IC₅₀ were not different with respectively 9.4-13.0 and 12.2-17.9 mg/L for S755 and rs552 strains. For mint, origano, savory, tea tree, and thyme, IC₅₀ were always the best on rs552 strain. The majority compounds were not necessarily more efficient than their corresponding oils; only eugenol (for clove) and carvacrol (for oregano and savory) seemed to be more effective on S755 strain. On the other hand, rs552 strain seemed to be more sensitive to essential oils than S755 strain. In overall, it was shown that essential oils have different antifungal activities but do not have the same antifungal activities depending on the fungus strain used.

When a Plant Resistance Inducer Leaves the Lab for the Field: Integrating ASM into Routine Apple Protection Practices

Plant resistance inducers, also called elicitors, could be useful to reduce the use of pesticides. However, their performance in controlling diseases in the field remains unsatisfactory due to lack of specific knowledge of how they can integrate crop protection practices. In this work, we focused on apple crop and acibenzolar-S-methyl (ASM), a well-known SAR (systemic acquired resistance) inducer of numerous plant species. We provide a protocol for orchard-effective control of apple scab due to the ascomycete fungus Venturia inaequalis, by applying ASM in combination with a light integrated pest management program. Besides we pave the way for future optimization levers by demonstrating in controlled conditions (i) the high influence of apple genotypes, (ii) the ability of ASM to prime defenses in newly formed leaves, (iii) the positive effect of repeated elicitor applications, (iv) the additive effect of a thinning fruit agent.

Biology and Epidemiology of Venturia Species Affecting Fruit Crops: A Review

The fungal genus Venturia Sacc. (anamorph Fusicladium Bonord.) includes plant pathogens that cause substantial economic damage to fruit crops worldwide. Although Venturia inaequalis is considered a model species in plant pathology, other Venturia spp. also cause scab on other fruit trees. Relative to the substantial research that has been conducted on V. inaequalis and apple scab, little research has been conducted on Venturia spp. affecting other fruit trees. In this review, the main characteristics of plant-pathogenic species of Venturia are discussed with special attention to V. inaequalis affecting apple, V. pyrina affecting European pear, V. nashicola affecting Asian pear, V. carpophila affecting peach and almond, Fusicladium oleagineum affecting olive, F. effusum affecting pecan, and F. eriobotryae affecting loquat. This review has two main objectives: (i) to identify the main gaps in our knowledge regarding the biology and epidemiology of Venturia spp. affecting fruit trees; and (ii) to identify similarities and differences among these Venturia spp. in order to improve disease management. A thorough review has been conducted of studies regarding the phylogenetic relationships, host ranges, biologies, and epidemiologies of Venturia spp. A multiple correspondence analysis (CA) has also been performed on the main epidemiological components of these Venturia spp. CA separated the Venturia spp. into two main groups, according to their epidemiological behavior: the first group included V. inaequalis, V. pyrina, V. nashicola, and V. carpophila, the second F. oleagineum and F. eriobotryae, with F. effusum having an intermediate position. This review shows that Venturia spp. affecting fruit trees are highly host-specific, and that important gaps in understanding the life cycle exist for some species, including V. pyrina; gaps include pseudothecia formation, ascospore and conidia germination, and mycelial growth. Considering the epidemiological information reviewed, this paper shows that the use of Mills tables to predict infection periods should be avoided for Venturia spp. other than V. inaequalis.

New biotechnological tools to accelerate scab-resistance trait transfer to apple

Apple is a fruit crop cultivated worldwide. Apple orchards are exposed to a diverse set of environmental and biological factors that affect the productivity and sustainability of the culture. Many of the efforts and costs for apple production rely on reducing the incidence of fungal diseases, and one of the main diseases is apple scab caused by the fungus Venturia inaequalis. The economic impact of scab on apple productivity has guided many breeding programs to search for cultivars resistant to apple scab. Introgression from wild relatives has been successful to some extent, and genetic engineering for resistant cultivars has even been employed. This review presents the techniques used to the present time to obtain pathogen-resistant apple cultivars and introduces new biotechnological approaches based on plant plasmids that show promising results for delivering genetic traits with a short-term perspective.

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

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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1043) contains supplementary material, which is available to authorized users.

De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen

Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.

Venturia inaequalis: the causal agent of apple scab

The fungus Venturia inaequalis infects members of the Maloideae, and causes the disease apple scab, the most important disease of apple worldwide. The early elucidation of the gene-for-gene relationship between V. inaequalis and its host Malus has intrigued plant pathologists ever since, with the identification of 17 resistance (R)-avirulence (Avr) gene pairings. The Avr gene products are presumably a subset of the total effector arsenal of V. inaequalis (predominantly proteins secreted in planta assumed to facilitate infection). The supposition that effectors from V. inaequalis act as suppressors of plant defence is supported by the ability of the pathogen to penetrate the cuticle and differentiate into large pseudoparenchymatous structures, termed stromata, in the subcuticular space, without the initiation of an effective plant defence response. If effectors can be identified that are essential for pathogenicity, the corresponding R genes will be durable and would add significant value to breeding programmes. An R gene cluster in Malus has been cloned, but no V. inaequalis effectors have been characterized at the molecular level. However, the identification of effectors is likely to be facilitated by the resolution of the whole genome sequence of V. inaequalis.

TAXONOMY

Teleomorph: Venturia inaequalis Cooke (Wint.); Kingdom Fungi; Phylum Ascomycota; Subphylum Euascomycota; Class Dothideomycetes; Family Venturiaceae; genus Venturia; species inaequalis. Anamorph: Fusicladium pomi (Fr.) Lind or Spilocaea pomi (Fr.). LIFE CYCLE: V. inaequalis is a hemibiotroph and overwinters as pseudothecia (sexual fruiting bodies) following a phase of saprobic growth in fallen leaf tissues. The primary inoculum consists of ascospores, which germinate and penetrate the cuticle. Stromata are formed above the epidermal cells but do not penetrate them. Cell wall-degrading enzymes are only produced late in the infection cycle, raising the as yet unanswered question as to how V. inaequalis gains nutrients from the host. Conidia (secondary inoculum) arise from the upper surface of the stromata, and are produced throughout the growing season, initiating multiple rounds of infection. VENTURIA INAEQUALIS AS A MODEL PATHOGEN OF A WOODY HOST: V. inaequalis can be cultured and is amenable to crossing in vitro, enabling map-based cloning strategies. It can be transformed readily, and functional analyses can be conducted by gene silencing. Expressed sequence tag collections are available to aid in gene identification. These will be complemented by the whole genome sequence, which, in turn, will contribute to the comparative analysis of different races of V. inaequalis and plant pathogens within the Dothideomycetes.

Current trends and future prospects of biotechnological interventions through tissue culture in apple

Apple (Malus domestica Borkh.), which is a widely cultivated, important economic fruit crop with nutritive and medicinal importance, has emerged as a model horticultural crop in this post-genomic era. Apple cultivation is heavily dependent on climatic condition and is susceptible to several diseases caused by fungi, bacteria, viruses, insects, etc. Extensive research work has been carried out to standardize tissue culture protocols and utilize them in apple improvement. We review the in vitro shoot multiplication, rooting, transformation and regeneration methodologies in apple and tabulate various such protocols for easy reference. The utility and limitation of transgenesis in apple improvement have also been summarized. The concepts of marker-free plants, use of non-antibiotic resistance selectable markers, and cisgenic and intragenic approaches are highlighted. Furthermore, the limitations, current trends and future prospects of tissue culture-mediated biotechnological interventions in apple improvement are discussed.