Biology subjects

Marcel, T. C.

Publications and source records attributed to Marcel, T. C..

6 recordsLinked to original sources

bioRxiv2023

Estimating the frequency of virulence against an Stb gene in Zymoseptoria tritici populations by bulk phenotyping on checkerboard microcanopies of wheat NILs

Monitoring virulent strains within fungal pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in genomes based on high-throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms and in planta phenotyping remains necessary. We developed a method for bulk phenotyping on checkerboard microcanopies of wheat near-isogenic lines (BPC) for estimating the frequency of virulence against an Stb gene in populations of Zymoseptoria tritici, the causal agent of Septoria tritici blotch in wheat, without the need for strain-by-strain phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines - one with the resistance gene and the other without it - with a multi-strain cocktail representative of the population to be characterized, followed by the differential quantification of infection points (lesions). Using Stb16q, a resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, and synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with recently developed molecular methods.

microbiology↗

bioRxiv2023

Can higher aggressiveness effectively compensate for a virulence deficiency in plant pathogen? A case study of Puccinia triticina's fitness evolution in a diversified varietal landscape

Plant resistances impose strong selective pressure on plant pathogen populations through the deployment of resistance genes, which leads to the emergence of new virulences. The pathogen adaptation also involves other parasitic fitness traits, especially aggressiveness components. A previous study on Puccinia triticina, the causal agent of wheat leaf rust, revealed that the distribution frequency of virulences in the French pathogen population cannot be fully explained by the major resistance genes deployed in the landscape. From 2012 to 2015, two dominant pathotypes (distinguished by their combination of virulences) were equally frequent despite the theoretical advantage conferred to one pathotype (166 317 0) by its virulence to Lr3, frequent in the cultivated landscape, whereas the other (106 314 0) is avirulent to this gene. To explain this apparent contradiction, we assessed three components of aggressiveness -- infection efficiency, latency period and sporulation capacity -- for 23 isolates representative of the most frequent genotype within each pathotype (106 314 0-G2 and 166 317 0-G1, identified by their combination of microsatellite markers). We tested these isolates on seedlings of Michigan Amber, a naive wheat cultivar that has never been grown in the landscape, Apache, a neutral cultivar with no selection effect on the landscape-pathotype pattern, and several cultivars that were frequently grown. We found that 106 314 0-G2 was more aggressive than 166 317 0-G1, with a consistency for the three components of aggressiveness. Our results show that aggressiveness plays a significant role in driving evolution in pathogen populations by acting as a selective advantage, even offsetting the disadvantage of lacking virulence towards a major Lr gene. Higher aggressiveness represents a competitive advantage that is likely even more pronounced when exhibited at the landscape scale as the expression of its multiple components is amplified by the polycyclic nature of epidemics.

plant biology↗

bioRxiv2022

A highly multiplexed assay to monitor virulence, fungicide resistance and gene flow in the fungal wheat pathogen Zymoseptoria tritici

Crop pathogens pose severe risks to global food production due to the rapid rise of resistance to pesticides and host resistance breakdowns. Predicting future risks requires monitoring tools to identify changes in the genetic composition of pathogen populations. Here we report the design of a microfluidics-based amplicon sequencing assay to multiplex 798 loci targeting virulence and fungicide resistance genes, and randomly selected genome-wide markers for the fungal pathogen Zymoseptoria tritici. The fungus causes one of the most devastating diseases on wheat showing rapid adaptation to fungicides and host resistance. We optimized the primer design by integrating polymorphism data from 632 genomes of the same species. To test the performance of the assay, we genotyped 192 samples in two replicates. Analysis of the short-read sequence data generated by the assay showed a fairly stable success rate across samples to amplify a large number of loci. The performance was consistent between samples originating from pure genomic DNA as well as material extracted directly from infected wheat leaves. In samples with mixed genotypes, we found that the assay recovers variations in allele frequencies. We also explored the potential of the amplicon assay to recover transposable element insertion polymorphism relevant for fungicide resistance. As a proof-of-concept, we show that the assay recovers the pathogen population structure across French wheat fields. Genomic monitoring of crop pathogens contributes to more sustainable crop protection and yields.

genomics↗

bioRxiv2022

Is virulence phenotype evolution driven exclusively by Lr gene deployment in French Puccinia triticina populations?

Puccinia triticina is a highly damaging wheat pathogen. The efficacy of leaf rust control by genetic resistance is mitigated by the adaptive capacity of the pathogen, expressed as changes in its virulence combinations (pathotypes). An extensive P. triticina population survey has been carried out in France over the last 30 years, describing the evolution dynamics of this pathogen in response to cultivar deployment. We analyzed the dataset for the 2006-2016 period to determine the relationship between the Lr genes in the cultivars and virulence in the pathotypes. Rust populations were dominated by a small number of pathotypes, with variations in most of the virulence frequencies related to the corresponding Lr gene frequencies in the cultivated landscape. Furthermore, the emergence and spread of a new virulence matched the introduction and use of the corresponding Lr gene (Lr28), confirming that the deployment of qualitative resistance genes is an essential driver of evolution in P. triticina populations. However, PCA revealed that certain pathotype-cultivar associations cannot be explained solely by the distribution of Lr genes in the landscape. This conclusion is supported by the predominance of a few pathotypes on some cultivars, with the persistence of several other compatible pathotypes at low frequencies. Specific interactions are not, therefore, sufficient to explain the distribution of virulence in rust populations. Our findings suggest that aggressiveness is a driver of changes in pathotype frequencies. Accordingly, the hypothesis of "dual selection", based on both qualitative and quantitative interactions between P. triticina populations and bread wheat cultivars, is favored.

microbiology↗

bioRxiv2020

Life story of Tunisian durum wheat landraces revealed by their genetic and phenotypic diversity

Durum wheat (Triticum turgidum L. subsp. durum) landraces represent a prominent genetic resource for Mediterranean farming systems and breeding programs. Fourteen landraces sampled in Tunisia were genotyped with 9 microsatellite markers and characterized with 15 morphological descriptors, including resistance to the fungal disease Septoria tritici blotch (STB). The genetic diversity, nearly was as important within landraces populations (45%) than between populations (54%). It was structured in seven genetic groups and was only partly explained by the variety name or the locality of origin. Populations were also greatly diversified phenotypically (Shannon-Weaver H=0.54) with traits related to spike and awn colours being the most diversified. Resistance to STB was either qualitative in two populations or with varying degrees of quantitative resistance in the others. A Pst-Fst comparison indicate a local adaptation of the populations. Overall, the genetic structure of Tunisian durum wheat landraces revealed a complex selection trajectory and seed exchanges between farmers.

plant biology↗

bioRxiv2019

Differential tolerance to changes in moisture regime during early infection stages in the fungal pathogen Zymoseptoria tritici

Foliar plant pathogens require liquid or vapour water for at least part of their development, but their response and their adaptive tolerance to moisture conditions have been much less studied than other meteorological factors to date. We examined the impact on the wheat-Zymoseptoria tritici interaction of altering optimal moisture conditions conducive to infection. We assessed the responses in planta of 48 Z. tritici strains collected in two climatologically distinct locations (Ireland and Israel) to four high moisture regimes differing in the timing and the duration of uninterrupted exposure to saturated relative humidity (100% RH) during the first three days of infection. Individual- and population-level moisture reaction norms expressing how the sporulating area of a lesion change with the RH conditions were established based on visual assessments of lesion development at 14, 17 and 20 days post-inoculation (dpi). Our findings highlighted: (i) a critical time-dependent effect on lesion development of uninterrupted periods of exposure to 100% RH during these earliest infection stages; (ii) a marked interindividual variation in the sensitivity to RH conditions both in terms of strain average moisture response and plasticity; (iii) a higher tolerance - expressed at 14 dpi, not later - of the Israeli population to early interruption of optimal moisture conditions. By indicating that sensitivity to sub-optimal moisture conditions may vary greatly between Z. tritici individuals and populations, this study highlights the evidence of moisture adaptation signature in a plant pathogen. This suggests that understanding such variation will be critical to predict their response to changing climatic conditions.

microbiology↗