Biology subjects

Duplaix, C.

Publications and source records attributed to Duplaix, C..

7 recordsLinked to original sources

bioRxiv2025

Ancient MAX Effector Variants of a Fungal Pathogen Evade Apoplastic Immunity in Apple

Venturia inaequalis is an Ascomycota fungus responsible for apple scab, the main disease in apple orchards. During infection, the pathogen colonizes the subcuticular space and secretes effectors to promote virulence. To mitigate disease impact, resistance genes such as Rvi6, which encodes a membrane-localized receptor-like protein, have been introduced into apple cultivars. However, over the past three decades, Rvi6-mediated resistance has been circumvented in orchards, with the emergence of virulent V. inaequalis strains. Through comparative genomics analyses and functional validation by complementation, we identified AvrRvi6 as the fungal determinant that activates Rvi6-mediated immunity. Screening 122 V. inaequalis strains worldwide, we identified 20 distinct AvrRvi6 alleles, of which only five are not recognized by Rvi6. Evolution analysis demonstrated that the emergence of these virulent alleles predates the domestication of apple, thus revealing that wild Malus species constitute a reservoir of virulence. Using AlphaFold structural modeling, we showed that AvrRvi6 belongs to an expanded family that adopts a MAX effector fold, originally described for cytoplasmic effectors of the blast fungus Pyricularia oryzae. Transient expression in Nicotiana benthamiana demonstrated that AvrRvi6 triggers allele-specific apoplastic immunity and validated three different molecular mechanisms (mutation, partial deletion and transposon insertion in the promoter) that V. inaequalis employs to circumvent Rvi6 recognition. This study delivers the first characterization of a V. inaequalis avirulence factor, uncovers an unexpected apoplastic role for a MAX effector, and demonstrates how ancestral virulence diversity maintained in wild populations compromises resistance durability in apple.

microbiology↗

bioRxiv2022

Preventing multiple resistance above all: new insights for managing fungal adaptation

Sustainable crop protection is crucial for food security, but is threatened by the adaptation of diverse, evolving pathogen population. Resistance can be managed by maximizing selection pressure diversity, by dose variation and the spatial and temporal combination of active ingredients. We explored the interplay between operational drivers for maximizing management strategy sustainability relative to the resistance status of fungal populations. We applied an experimental evolution approach to three artificial populations of an economically important wheat pathogen, Zymoseptoria tritici, differing in initial resistance status. We revealed that diversified selection pressure limited the selection of resistance in naive populations and those with low frequencies of single. Increasing the number of modes of action delayed resistance development most effectively -- ahead of increasing the number of fungicides, fungicide choice based on resistance risk and temporal variation in fungicide exposure -- but favored generalism in the evolved populations. However, the prior presence of multiple resistant resistant isolates and their subsequent selection in populations overrode the effects of diversity in management strategies, incidentally invalidating any universal ranking. Initial resistance composition must therefore be considered specifically in sustainable resistance management, to address real-world field situation. Abbreviated summaryExperimental evolution is a relevant tool for exploring the determinants of antifungal adaptation in fungi. Here, using the model species Z. tritici and two fungicidal modes of action associated with contrasting resistance risks, we have demonstrated that initial population composition, and in particular the presence of multiple resistance, represents the main determinant of adaptive trajectories. Originality-Significance StatementPesticides are part of microbe environment in agricultural systems and may select for resistance. This adaptation of pathogens is a burden for plant health. Using an original multicriteria assessment and experimental evolution, we revealed that multi-fungicide use, selecting for multiple resistance, trumped any other driver of selection, invalidating any universal ranking of management strategies, a dispute extensively illustrated in literature and still inconclusive, especially in agriculture. This outcome refocuses the debate on population diversity and evolution rather than on the intrinsic properties of strategies, as mostly acclaimed in literature. From a practical point of view, our results highlight the importance of considering local population composition when recommending spraying programs. This practice is currently not generalized in agriculture but may be timely to effectively delay resistance evolution and reduce pesticide load in agricultural systems, a growing social demand, since resistance monitoring at relatively fine spatial scales and at low frequency may become commonplace in a near future with the rise of new molecular biology technologies

evolutionary biology↗

bioRxiv2021

I alternate therefore I generalize: how the intrinsic resistance risk of fungicides counterbalances their durability

The evolution of resistance to pesticides is a major burden in agriculture. Resistance management involves maximizing selection pressure heterogeneity, particularly by combining active ingredients with different modes of action. We tested the hypothesis that alternation may delay the build-up of resistance not only by spreading selection pressure over longer periods, but also by decreasing the rate of evolution of resistance to alternated fungicides, by applying an experimental evolution approach to the economically important crop pathogen Zymoseptoria tritici. Our results show that alternation is either neutral or slows the overall resistance evolution rate, relative to continuous fungicide use, but results in higher levels of generalism in evolved lines. We demonstrate that the nature of the fungicides, and therefore their relative intrinsic risk of resistance may underly this trade-off, more so than the number of fungicides and the rhythm of alternation. This trade-off is also dynamic over the course of resistance evolution. These findings open up new possibilities for tailoring resistance management effectively while optimizing interplay between alternation components.

evolutionary biology↗

bioRxiv2020

Large-scale study reveals regional fungicide applications as a major determinant of resistance evolution in the wheat pathogen Zymoseptoria tritici in France.

O_LIResearch rationale: In modern cropping systems, the near-universal use of plant protection products selects for resistance in pest populations. The emergence and evolution of this adaptive trait threaten treatment efficacy. We identified determinants of fungicide resistance evolution and quantified their effects at a large spatiotemporal scale. C_LIO_LIMethods: We focused on Zymoseptoria tritici, which causes leaf blotch in wheat. Phenotypes of qualitative or quantitative resistance to various fungicides were monitored annually, from 2004 to 2017, at about 70 sites throughout 22 regions of France (territorial units of 25 000km2 on average). We modelled changes in resistance frequency with regional anti-Septoria fungicide use, yield losses due to the disease and the regional area under organic wheat. C_LIO_LIKey results: The major driver of resistance dynamics was fungicide use at the regional scale. We estimated its effect on the increase in resistance and relative apparent fitness of each resistance phenotype. The predictions of the model replicated the spatiotemporal patterns of resistance observed in field populations (R2 from 0.56 to 0.82). C_LIO_LIMain conclusion: The evolution of fungicide resistance is mainly determined at the regional scale. This study therefore showed that collective management at the regional scale could effectively complete local actions. C_LI

evolutionary biology↗

bioRxiv2019

The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host-specialized and generalist populations

The host plant is often the main variable explaining population structure in fungal plant pathogens, because specialization contributes to reduce gene flow between populations associated with different hosts. Previous population genetic analysis revealed that French populations of the grey mould pathogen Botrytis cinerea were structured by hosts tomato and grapevine, suggesting host specialization in this highly polyphagous pathogen. However, these findings raised questions about the magnitude of this specialization and the possibility of specialization to other hosts. Here we report specialization of B. cinerea populations to tomato and grapevine hosts but not to other tested plants. Population genetic analysis revealed two pathogen clusters associated with tomato and grapevine, while the other clusters co-occurred on hydrangea, strawberry and bramble. Measurements of quantitative pathogenicity were consistent with host specialization of populations found on tomato, and to a lesser extent, populations found on grapevine. Pathogen populations from hydrangea and strawberry appeared to be generalist, while populations from bramble may be weakly specialized. Our results suggest that the polyphagous B. cinerea is more accurately described as a collection of generalist and specialist individuals in populations. This work opens new perspectives for grey mold management, while suggesting spatial optimization of crop organization within agricultural landscapes.

microbiology↗

bioRxiv2017

Stability in the genetic structure of a Zymoseptoria tritici population from epidemic to interepidemic stages at a small spatial scale

Subpopulations of the wheat pathogen Zymoseptoria tritici (26 sample groups composed of 794 strains) were collected in two nearby wheat fields in the Paris basin, during both epidemic and inter-epidemic periods of three successive years (2009-2013). In addition to the type of inoculum (ascospores vs. pycnidiospores), the alternative presence of wheat debris allowed taking into account its putative origin (local vs. distant). We used a molecular epidemiology approach, based on population genetic indices derived from SSR marker analysis, to describe putative changes in the structure and genotypic diversity of these subpopulations over three years, at a spatiotemporal scale consistent with epidemiological observations. Genetic structure was stable over time (within and between years) and between fields. All subpopulations displayed very high levels of gene and genotypic diversity. The low levels of linkage disequilibrium and the very low clonal fraction at all stages were consistent with the regular occurrence of sexual reproduction in the two fields. A significant increase of the MAT1-1/MAT1-2 ratio was observed over the course of the epidemics, suggesting a competitive advantage of MAT1-1 strains consistently with their greater pathogenicity reported in the literature. Finally, we found that the period, the type of inoculum and its putative origin had little effect on the short term evolution of the local population of Z. tritici. Fungal population size and diversity are apparently large enough to prevent genetic drift at this fine spatiotemporal scale, and more likely short distance migration contributes strongly to the stabilization of genetic diversity among and within plots.

epidemiology↗

bioRxiv2017

Plasticity of the MFS1 promoter leads to multi drug resistance in the wheat pathogen Zymoseptoria tritici

The ascomycete Zymoseptoria tritici is the causal agent of septoria leaf blotch on wheat. Disease control relies mainly on resistant wheat cultivars and on fungicide applications. The fungus displays a high potential to circumvent both methods. Resistance against all unisite fungicides has been observed over decades. A different type of resistance has emerged among wild populations with multi-drug resistant (MDR) strains. Active fungicide efflux through overexpression of the major-facilitator gene, MFS1, explains this emerging resistance mechanism. In this study, we identified as responsible mutations three types of inserts in the MFS1 promoter, two of which harboring potential transcription factor binding sites. We show, that type I insertion leads to MFS1 overexpression and consequently to MDR. Interestingly, all three inserts correspond to repeated elements of the Z. tritici genome.\n\nThese results underline the plasticity of repeated elements leading to fungicide resistance in Z. tritici and which contribute to its adaptive potential.

microbiology↗