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Valerie Caffier - One of the best experts on this subject based on the ideXlab platform.
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Slow erosion of a quantitative apple resistance to Venturia inaequalis based on an isolate-specific Quantitative Trait Locus
Infection Genetics and Evolution, 2016Co-Authors: Valerie Caffier, Bruno Le Cam, Mehdi Al Rifai, Marie-noëlle Bellanger, Morgane Comby, Caroline Denance, Frederique Didelot, Pascale Expert, Tifenn Kerdraon, Arnaud LemarquandAbstract:Quantitative plant resistance affects the aggressiveness of pathogens and is usually considered more durable than qualitative resistance. However, the efficiency of a quantitative resistance based on an isolate-specific Quantitative Trait Locus (QTL) is expected to decrease over time due to the selection of isolates with a high level of aggressiveness on resistant plants. To test this hypothesis, we surveyed scab incidence over an eight-year period in an orchard planted with susceptible and quantitatively resistant apple genotypes. We sampled 79 Venturia inaequalis isolates from this orchard at three dates and we tested their level of aggressiveness under controlled conditions. Isolates sampled on resistant genotypes triggered higher lesion density and exhibited a higher sporulation rate on apple carrying the resistance allele of the QTL T1 compared to isolates sampled on susceptible genotypes. Due to this ability to select aggressive isolates, we expected the QTL T1 to be non-durable. However, our results showed that the quantitative resistance based on the QTL T1 remained efficient in orchard over an eight-year period, with only a slow decrease in efficiency and no detectable increase of the aggressiveness of fungal isolates over time. We conclude that knowledge on the specificity of a QTL is not sufficient to evaluate its durability. Deciphering molecular mechanisms associated with resistance QTLs, genetic determinants of aggressiveness and putative trade-offs within pathogen populations is needed to help in understanding the erosion processes
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differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population a case study in an apple Venturia inaequalis pathosystem
New Phytologist, 2013Co-Authors: Valerie Caffier, Amandine Le Van, Pauline Lasserrezuber, Aurelie ChauveauAbstract:Summary Understanding how pathogens evolve according to pressures exerted by their plant hosts is essential for the derivation of strategies aimed at the durable management of resistant cultivars. The spectrum of action of the resistance factors in the partially resistant cultivars is thought to be an important determinant of resistance durability. However, it has not yet been demonstrated whether the pressures exerted by quantitative resistance are different according to their spectrum of action. To investigate selection pressures exerted by apple genotypes harbouring various resistance quantitative trait loci (QTLs) on a mixed inoculum of the scab disease agent, Venturia inaequalis, we monitored V. inaequalis isolate proportions on diseased apple leaves of an F1 progeny using quantitative pyrosequencing technology and QTL mapping. Broad-spectrum resistances did not exert any differential selection pressures on the mixed inoculum, whereas narrow-spectrum resistances decreased the frequencies of some isolates in the mixture relative to the susceptible host genotypes. Our results suggest that the management of resistant cultivars should be different according to the spectrum of action of their resistance factors. The pyramiding of broad-spectrum factors or the use of a mixture of apple genotypes that carry narrow-spectrum resistance factors are two possible strategies for the minimization of resistance erosion.
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revision of the nomenclature of the differential host pathogen interactions of Venturia inaequalis and malus
Annual Review of Phytopathology, 2011Co-Authors: Vincent G M Bus, Erik H A Rikkerink, Valerie Caffier, Charleseric Durel, Kim M PlummerAbstract:The apple scab (Venturia inaequalis–Malus) pathosystem was one of the first systems for which Flor’s concept of gene-for-gene (GfG) relationships between the host plant and the pathogen was demonstrated. There is a rich resource of host resistance genes present in Malus germplasm that could potentially be marshalled to confer durable resistance against this most important apple disease. A comprehensive understanding of the host-pathogen interactions occurring in this pathosystem is a prerequisite for effectively manipulating these host resistance factors. An accurate means of identification of specific resistance and consistent use of gene nomenclature is critical for this process. A set of universally available, differentially resistant hosts is described, which will be followed by a set of defined pathogen races at a later stage. We review pertinent aspects of the history of apple scab research, describe the current status and future directions of this research, and resolve some outstanding issues.
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A proposal for the nomenclature of Venturia inaequalis races
2007Co-Authors: Vincent Bus, C Gessler, Valerie Caffier, Charleseric Durel, Eric Rikkerink, Herb Aldwinckle, S. Gardiner, R. Groenwold, Francois Laurens, Bruno Le CamAbstract:The Venturia inaequalis-Malus pathosystem was one of the first for which gene-for-gene relationships were demonstrated following the discovery of such relationships between Melampsora lini and flax by Flor in the 1950s. An understanding of these relationships forms the basis for monitoring pathotypes of V. inaequalis at the population level and is employed to assess the usefulness of resistance genes for breeding durable resistance to scab. These pathotypes are difficult to accommodate in the current system of nomenclature for V. inaequalis races where each new combination of avirulence alleles is assigned a simple numerical descriptor as its name. We propose a system that is better suited to the increasing complexities of combinations of genes involved in both race-specific and race-nonspecific recognition by the host, while at the same time updating the name of scab resistance loci (Rvik) and QTL loci (Qvik) to international standards. For the race-specific interactions, the basic premise is that each Rvik-AvrRvik and Qvik-AvrQvik relationship should be represented by a differential host (k), abbreviated to h(k), carrying only the specific Rvik or (major) Qvik resistance allele and an isolate of the pathogen having lost only the complementary allele at the AvrRvik or AvrQvik locus, race (k), with k representing the number of the specific interaction. Races lacking more than one avirulence gene at different loci will be identified as race (k,l,m,...) and apple hosts carrying multiple scab resistance genes as host (k,l,m,...). The proposed system has some continuity with the current system, but should simplify the presentation and interpretation of studies on avirulence alleles in V. inaequalis at the population level. Gene-for-gene relationships reported to date for this pathosystem are reviewed, some inconsistencies clarified, and several new interactions added. The gene-for-gene relationships of European isolates collected in the last decade have been studied in order to establish a new set of reference isolates that represent various V.inaequalis races.
Kim M Plummer - One of the best experts on this subject based on the ideXlab platform.
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Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range
BMC Genomics, 2017Co-Authors: Cecilia H. Deng, Carl H Mesarich, Kim M Plummer, Jason Shiller, Patrick Kastner, Darcy A. B. Jones, Adam P. Taranto, Andrew J. Robinson, Nathan E. Hall, Matthew D TempletonAbstract:Background Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis , which infects apple, and V. pirina , which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. Results Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia , with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. Conclusions Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.
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revision of the nomenclature of the differential host pathogen interactions of Venturia inaequalis and malus
Annual Review of Phytopathology, 2011Co-Authors: Vincent G M Bus, Erik H A Rikkerink, Valerie Caffier, Charleseric Durel, Kim M PlummerAbstract:The apple scab (Venturia inaequalis–Malus) pathosystem was one of the first systems for which Flor’s concept of gene-for-gene (GfG) relationships between the host plant and the pathogen was demonstrated. There is a rich resource of host resistance genes present in Malus germplasm that could potentially be marshalled to confer durable resistance against this most important apple disease. A comprehensive understanding of the host-pathogen interactions occurring in this pathosystem is a prerequisite for effectively manipulating these host resistance factors. An accurate means of identification of specific resistance and consistent use of gene nomenclature is critical for this process. A set of universally available, differentially resistant hosts is described, which will be followed by a set of defined pathogen races at a later stage. We review pertinent aspects of the history of apple scab research, describe the current status and future directions of this research, and resolve some outstanding issues.
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two novel Venturia inaequalis genes induced upon morphogenetic differentiation during infection and in vitro growth on cellophane
Fungal Genetics and Biology, 2008Co-Authors: Nataliya Kucheryava, Paul W Sutherland, Joshua Jeremy Conolly, Carl H Mesarich, Erik H A Rikkerink, Eric Kemen, Kim M Plummer, Joanna K. Bowen, Matthias Hahn, Matthew D TempletonAbstract:Abstract Venturia inaequalis is a hemibiotrophic ascomycete that causes apple scab. Germ tubes, from conidia or ascospores, penetrate the leaf or fruit surface directly via appressoria-like swellings; subsequently the hyphae divide laterally to form a stroma between the cuticle and the outer wall of the epidermal cells. This morphological switch can be mimicked by growing the fungus in vitro on cellophane discs. The aim of this work was to identify genes upregulated in planta using growth on cellophane as a model. Four cDNA clones were found to be induced by growth on cellophane, and qRT-PCR showed two of these genes were up-regulated over a thousand fold in infected apple leaves compared to liquid culture. The predicted proteins for both genes possess putative signal peptides for secretion but have no similarity to sequences in publicly available databases. Both genes encode proteins with novel, imperfect repeat domain structures, the number of which vary in an isolate-specific fashion. Cin1 has seven or eight repeats of about 60 amino acids with four conserved cysteine residues per repeat, while Cin3 has four or five repeats of 32 amino acids with no cysteines. Both proteins appear to have evolved through internal duplication. Cin3, in particular, shows considerable between-strain variation in domain structure, indicating a high degree of recombination at this locus and revealing that the repeat structure has most likely arisen by unequal crossing-over. Results of this study support the hypothesis that cellophane-grown V. inaequalis mimics aspects of biotrophic infection and provide the first insights into novel fungal genes expressed during apple scab infection and their mechanisms of evolution.
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the vh8 locus of a new gene for gene interaction between Venturia inaequalis and the wild apple malus sieversii is closely linked to the vh2 locus in malus pumila r12740 7a
New Phytologist, 2005Co-Authors: Vincent G M Bus, Erik H A Rikkerink, Francois Laurens, Eric W Van De Weg, Rachel L Rusholme, Susan E Gardiner, H Bassett, Linda P Kodde, Kim M PlummerAbstract:The wild apple (Malus sieversii) is a large-fruited species from Central Asia, which is used as a source of scab resistance in cultivar breeding. Phytopathological tests with races of Venturia inaequalis were performed to differentiate scab-resistance genes in Malus as well as an avirulence gene in the pathogen. A novel gene-for-gene interaction between V. inaequalis and Malus was identified. The locus of the scab-resistance gene Vh8 is linked with, or possibly allelic to, that of the Vh2 gene in Malus pumila Russian apple R12740-7A, at the lower end of linkage group 2 of Malus. Race 8 isolate NZ188B.2 is compatible with Vh8, suggesting the loss or modification of the complementary AvrVh8 gene, while isolate 1639 overcomes both Vh2 and Vh8, but is incompatible with at least one other gene not detected by any of the other race isolates tested. Our research is the first to differentiate scab-resistance genes in a putative gene cluster in apple with the aid of races of V. inaequalis.
Awais Khan - One of the best experts on this subject based on the ideXlab platform.
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new north american isolates of Venturia inaequalis can overcome apple scab resistance of malus floribunda 821
Plant Disease, 2020Co-Authors: David Papp, Jugpreet Singh, David M Gadoury, Awais KhanAbstract:Apple scab, caused by Venturia inaequalis, is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Thus, development of scab resistant cultivars is one of the highest priorities of apple breeding programs. The principal source of resistance for breeding programs has been the scab resistance gene Rvi6 that originated from the Japanese crabapple Malus floribunda (Sieb.) sel. 821. Isolates of V. inaequalis able to overcome Rvi6 have been identified in Europe, but have not yet been reported on the American continents. We recently discovered scab infection on M. floribunda 821 trees in a research orchard at Geneva, NY, U.S.A., where approximately 10% of the leaves bore profusely sporulating apple scab lesions, many of which had coalesced to cover entire leaves. We observed both chlorosis, typical to Rvi6, and pinpoint pitting symptoms typical to failed infections by V. inaequalis on hosts bearing the Rvi7 gene. We assessed genetic diversity and population genetic structure of 11 V. inaequalis isolates in total, of North American and European origin, isolated from M. floribunda 821, 'Nova Easygro', 'Golden Delicious', TSR33T239, 'Schone van Boskoop', and 'Prima', using 16,321 genome-wide SNPs. Population genetic structure and PCA separated the isolates into distinct European and U.S. groups. The forgoing suggests that the new Rvi6 virulent isolates emerged within U.S. populations, rather than being transported from Europe. The complete resistance breakdown in M. floribunda 821 but not in descendant cultivars, which kept their field resistance, suggests that durable resistance to apple scab will require a more comprehensive understanding of Rvi6 mediated resistance in diverse genetic backgrounds.
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new north american isolates of Venturia inaequalis can overcome apple scab resistance of malus floribunda 821
bioRxiv, 2019Co-Authors: David Papp, Jugpreet Singh, David M Gadoury, Awais KhanAbstract:Abstract Apple scab, caused by Venturia inaequalis (Cke.) Wint., is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Thus, development of scab resistant cultivars is one of the highest priorities of apple breeding programs. The principal source of resistance for breeding programs has been the scab resistance gene Rvi6 that originated from the Japanese crabapple Malus floribunda (Sieb.) sel. 821. Isolates of V. inaequalis able to overcome Rvi6 have been identified in Europe, but have not yet been reported on the American continents. We recently discovered scab infection on M. floribunda 821 trees in a research orchard at Geneva, New York, USA, where approximately 10% of the leaves bore profusely sporulating apple scab lesions, many of which had coalesced to cover entire leaves. Chlorosis and pinpoint pitting symptoms typical of failed infections by V. inaequalis on hosts bearing the Rvi6 and Rvi7 genes were also observed. We assessed genetic diversity and population genetic structure of six V. inaequalis isolates collected from M. floribunda 821, one isolate from ‘Nova Easygro’, one isolate from ‘Golden Delicious’ and two isolates from Europe (11 isolates in total) using 16,321 genome-wide SNPs. Population genetic structure and PCA separated the isolates into distinct European and USA groups. The forgoing suggests that the new Rvi6 virulent isolates emerged within USA populations, rather than being transported from Europe. The overcoming of resistance in M. floribunda 821 but not in descendant cultivars suggests that durable resistance to apple scab will require a more comprehensive understanding of Rvi6 mediated resistance in diverse genetic backgrounds.
Ehlert Katja - One of the best experts on this subject based on the ideXlab platform.
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Epidemiologische Untersuchungen zum Apfelschorf (Venturia inaequalis) und die biologische Validierung einer neuen Regensensorik zur Prognose
Julius Kühn-Institut, 2017Co-Authors: Ehlert KatjaAbstract:Ein Ziel dieser Arbeit war die Entwicklung und biologische Evaluierung einer Sensorik zur Verbesserung der Prognose des Apfelschorfs. Als Grundlage für die Schorfprognose dient nach dem Modell von Mills die Länge der Blattnässedauer in Abhängigkeit von der Lufttemperatur. Es wurden mehrjährige Vergleiche verschiedener käuflicher Blattnässesensoren durchgeführt und in Zusammenarbeit mit der Firma Thies Clima ein Sensor für Wasserbenetzung entwickelt. Der Vergleich der käuflichen Sensoren zeigte deutliche Unterschiede in der Anzeige der Nässedauer zwischen den verschiedenen getesteten Sensoren. Die Eignung dieser Sensoren für die Prognose war sehr verschieden. Der im Rahmen des Verbundprojektes entwickelte Sensor ist zuverlässig, wetterfest, korrosionsbeständig und wartungsarm. Die einzelnen Prototypen wurden nach der Evaluierung in der Klimakammer im Freiland getestet und die Einstellungen anhand von Bioassays auf ihre Eignung zur Prognose überprüft. Der marktreife Prototyp kann ohne weitere Modellierung zur Erfassung der Blattnässe von Apfelblättern in die Prognose eingebunden werden. Ein weiteres Ziel der vorliegenden Arbeit war es, die Zusammenhänge der diurnalen Rhythmik der Sporenausschleuderung von Venturia inaequalis zu untersuchen. Im Freiland wurden die Ascosporenflüge unter natürlichen Bedingungen und mit Störlicht registriert. Im Labor wurde der Sporenausstoß unter dem Einfluss der Beleuchtungsstärke und Wellenlängen-Zusammensetzung untersucht. Sowohl im Freiland als auch im Labor konnte eine Aufhebung der Dunkelhemmung des Sporenausstoßes erreicht werden. Der sichtbare Anteil des Lichts konnte auch bei Helligkeiten von über 10000 Lux als Auslöser des Sporenausstoßes ausgeschlossen werden. Durch die Bestrahlung der Pseudothecien tragenden Blätter mit nicht sichtbaren infraroten Lichtanteilen wurde eine Freisetzung der Ascosporen auch im Dunkeln erreicht und die diurnale Rhythmik der Sporenausschleuderung im Freiland wurde aufgelöst.Ein Ziel dieser Arbeit war die Entwicklung und biologische Evaluierung einer Sensorik zur Verbesserung der Prognose des Apfelschorfs. Als Grundlage für die Schorfprognose dient nach dem Modell von Mills die Länge der Blattnässedauer in Abhängigkeit von der Lufttemperatur. Es wurden mehrjährige Vergleiche verschiedener käuflicher Blattnässesensoren durchgeführt und in Zusammenarbeit mit der Firma Thies Clima ein Sensor für Wasserbenetzung entwickelt. Der Vergleich der käuflichen Sensoren zeigte deutliche Unterschiede in der Anzeige der Nässedauer zwischen den verschiedenen getesteten Sensoren. Die Eignung dieser Sensoren für die Prognose war sehr verschieden. Der im Rahmen des Verbundprojektes entwickelte Sensor ist zuverlässig, wetterfest, korrosionsbeständig und wartungsarm. Die einzelnen Prototypen wurden nach der Evaluierung in der Klimakammer im Freiland getestet und die Einstellungen anhand von Bioassays auf ihre Eignung zur Prognose überprüft. Der marktreife Prototyp kann ohne weitere Modellierung zur Erfassung der Blattnässe von Apfelblättern in die Prognose eingebunden werden. Ein weiteres Ziel der vorliegenden Arbeit war es, die Zusammenhänge der diurnalen Rhythmik der Sporenausschleuderung von Venturia inaequalis zu untersuchen. Im Freiland wurden die Ascosporenflüge unter natürlichen Bedingungen und mit Störlicht registriert. Im Labor wurde der Sporenausstoß unter dem Einfluss der Beleuchtungsstärke und Wellenlängen-Zusammensetzung untersucht. Sowohl im Freiland als auch im Labor konnte eine Aufhebung der Dunkelhemmung des Sporenausstoßes erreicht werden. Der sichtbare Anteil des Lichts konnte auch bei Helligkeiten von über 10000 Lux als Auslöser des Sporenausstoßes ausgeschlossen werden. Durch die Bestrahlung der Pseudothecien tragenden Blätter mit nicht sichtbaren infraroten Lichtanteilen wurde eine Freisetzung der Ascosporen auch im Dunkeln erreicht und die diurnale Rhythmik der Sporenausschleuderung im Freiland wurde aufgelöst
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Epidemiologische Untersuchungen zum Apfelschorf (Venturia inaequalis) und die biologische Validierung einer neuen Regensensorik zur Prognose
2017Co-Authors: Ehlert KatjaAbstract:Ein Ziel dieser Arbeit war die Entwicklung und biologische Evaluierung einer Sensorik zur Verbesserung der Prognose des Apfelschorfs. Als Grundlage für die Schorfprognose dient nach dem Modell von Mills die Länge der Blattnässedauer in Abhängigkeit von der Lufttemperatur. Es wurden mehrjährige Vergleiche verschiedener käuflicher Blattnässesensoren durchgeführt und in Zusammenarbeit mit der Firma THIES Clima ein Sensor für Wasserbenetzung entwickelt. Der Vergleich der käuflichen Sensoren zeigte deutliche Unterschiede in der Anzeige der Nässedauer zwischen den verschiedenen getesteten Sensoren. Die Eignung dieser Sensoren für die Prognose war sehr verschieden. Der im Rahmen des Verbundprojektes entwickelte Sensor ist zuverlässig, wetterfest, korrosionsbeständig und wartungsarm. Die einzelnen Prototypen wurden nach der Evaluierung in der Klimakammer im Freiland getestet und die Einstellungen anhand von Bioassays auf ihre Eignung zur Prognose überprüft. Der marktreife Prototyp kann ohne weitere Modellierung zur Erfassung der Blattnässe von Apfelblättern in die Prognose eingebunden werden. Ein weiteres Ziel der vorliegenden Arbeit war es, die Zusammenhänge der diurnalen Rhythmik der Sporenausschleuderung von Venturia inaequalis zu untersuchen. Im Freiland wurden die Ascosporenflüge unter natürlichen Bedingungen und mit Störlicht registriert. Im Labor wurde der Sporenausstoß unter dem Einfluss der Beleuchtungsstärke und Wellenlängen-Zusammensetzung untersucht. Sowohl im Freiland als auch im Labor konnte eine Aufhebung der Dunkelhemmung des Sporenausstoßes erreicht werden. Der sichtbare Anteil des Lichts konnte auch bei Helligkeiten von über 10000 Lux als Auslöser des Sporenausstoßes ausgeschlossen werden. Durch die Bestrahlung der Pseudothecien tragenden Blätter mit nicht sichtbaren infraroten Lichtanteilen wurde eine Freisetzung der Ascosporen auch im Dunkeln erreicht und die diurnale Rhythmik der Sporenausschleuderung im Freiland wurde aufgelöst
Amandine Le Van - One of the best experts on this subject based on the ideXlab platform.
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differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population a case study in an apple Venturia inaequalis pathosystem
New Phytologist, 2013Co-Authors: Valerie Caffier, Amandine Le Van, Pauline Lasserrezuber, Aurelie ChauveauAbstract:Summary Understanding how pathogens evolve according to pressures exerted by their plant hosts is essential for the derivation of strategies aimed at the durable management of resistant cultivars. The spectrum of action of the resistance factors in the partially resistant cultivars is thought to be an important determinant of resistance durability. However, it has not yet been demonstrated whether the pressures exerted by quantitative resistance are different according to their spectrum of action. To investigate selection pressures exerted by apple genotypes harbouring various resistance quantitative trait loci (QTLs) on a mixed inoculum of the scab disease agent, Venturia inaequalis, we monitored V. inaequalis isolate proportions on diseased apple leaves of an F1 progeny using quantitative pyrosequencing technology and QTL mapping. Broad-spectrum resistances did not exert any differential selection pressures on the mixed inoculum, whereas narrow-spectrum resistances decreased the frequencies of some isolates in the mixture relative to the susceptible host genotypes. Our results suggest that the management of resistant cultivars should be different according to the spectrum of action of their resistance factors. The pyramiding of broad-spectrum factors or the use of a mixture of apple genotypes that carry narrow-spectrum resistance factors are two possible strategies for the minimization of resistance erosion.
