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International audience; Each season, crops face simultaneous or successive multiple infections. Yet cultivar resistance is often bred against one pest at a time, and screened under single infections. This raises the question of resistance expression bred under mono-infections when exposed to multiple infections. We tackled this question by measuring the level of quantitative resistance of potato cultivars to either Globodera pallida or Phytophthora infestans under single or multiple infections, using potato virus Y (PVY) or Rhizoctonia solani as the co-infector. Overall, co-infection resulted in less multiplication of the target pathogen compared to single infection, although this reduction did not always reach statistical significance. A preliminary assessment of defence gene expression in plants infected with P. infestans alone or together with PVY or R. solani suggested that P. infestans repressed defence genes previously triggered by PVY, but boosted the expression of these genes when primed by R. solani. Together, these data support the view that resistance expression is impacted by co-infection, and that it should be screened under multiple infection situations to be best assessed and exploited as a component of Integrated Pest Management strategies.

International audience

Our knowledge of the diversity of potato cyst nematodes in their native areas still remains patchy and should be improved. A previous study based on 42 Peruvian Globodera pallida populations revealed a clear south to north phylogeographic pattern, with five well‐supported clades and maximum diversity observed in the south of Peru. In order to investigate this phylogeographic pattern more closely, we genotyped a larger collection of Peruvian populations using both cathepsin L gene sequence data and a new set of 13 microsatellite loci. Using different genetic analyses (STRUCTURE, DAPC), we consistently obtained the same results that led to similar conclusions: the presence of a larger genetic diversity than previously known suggesting the presence of cryptic species in the south of Peru. These investigations also allowed us to clarify the geographic borders of the previously described G. pallida genetic clades and to update our knowledge of the genetic structure of this species in its native area, with the presence of additional clades. A distance‐based redundancy analysis (dbRDA) was also carried to understand whether there was a correlation between the population genetic differentiation and environmental conditions. This analysis showed that genetic distances observed between G. pallida populations are explained firstly by geographic distances, but also by climatic and soil conditions. This work could lead to a revision of the taxonomy that may have strong implications for risk assessment and management, especially on a quarantine species.

International audience; Cyst nematodes are sedentary endoparasites of plants which cause important economic losses worldwide. New nematode control measures are needed since the removal of effective chemical nematicides from the market due to their negative impact on environment and human health. Induced hatching of second-stage juveniles in the absence of host plant using root exudates, also named "suicide hatching", could be a sustainable alternative method to reduce nematode population densities in infested soils. Unfortunately, biocontrol methods are often less effective in agricultural fields than in laboratory or greenhouse and this could be due to, among other reasons, a different susceptibility of nematode populations to root exudate stimulation. Testing this intra-specific variability would help to anticipate any drop in the efficiency of this new biocontrol strategy. A selection of root exudates from different plant species, maximizing the hatching level highlighted in a previous study, was tested on the hatching of representative populations of the genetic diversity for Globodera pallida, Heterodera schachtii and Heterodera carotae. Results showed significant differences between populations for given nematode species but not correlated with the genetic structure. Overall, root exudates tested provide a high level of hatching of these three nematode species. Surprisingly, the root exudate from broccoli induces hatching of European populations of the potato cyst nematode G. pallida.

International audience; The cyst nematode Heterodera carotae, which parasitizes carrot roots, has been recorded in many countries in Europe (Italy, The Netherlands, Switzerland, France, Denmark, …), in South Africa and in North America (Canada, USA). To date, there is a lack of knowledge about the genetic structure of the populations of this economically important nematode. The aim of this work was to study the structuration of the genetic diversity of the carrot cyst nematode at the European scale. We have developed a set of thirteen polymorphic microsatellite markers and used it to genotype seventeen European populations of H. carotae coming from France, Switzerland, Italy, Denmark and one non-European population from Canada. As previously showed for other cyst nematode species, the H. carotae populations were characterised by a strong heterozygote deficit. A Bayesian clustering analysis revealed two distinct genetic clusters, with one group located in the north of Europe and a second one located in the south of Europe. Moreover, our results highlighted rather limited gene flow at small spatial scale and some events of long distance migration. This first investigation of the genetic diversity of H. carotae populations would be useful to develop sustainable control strategies.

A previous version of this article has been peer-reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100132); International audience; Understanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no or minor parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.

Despite their ability to infect both plant species, natural populations ofPhytophthora infestans, the pathogen causing late blight on potato and tomato, are usually separated into genetically distinct lineages that are mainly restricted to either host. Laboratory cross-inoculation tests revealed a host-related local adaptation between genotypes, with asymmetric fitness performance between generalist lineages, mainly present on tomato, and specialist lineages confined to potato. To further understand the basis of host-related adaptation inP. infestans, we combined experimental evolution and analysis of effectors involved in pathogenicity and cell death modulation. We aimed to check in this way (i) if natural host adaptation ofP. infestansis reversible during one growing season and (ii) if this process is accompanied by changes in pathogenicity-related gene expression. Two isolates differing substantially by their level of specialization were passaged for nine generations on susceptible potato (cv. Bintje), tomato (cv. Marmande) or alternately on both hosts. Pathogenic fitness and the expression of eight pathogen effectors with known host targets (AVRblb2, EPIC2B, EPI1, PexRD2, SNE1, PiNPP, INF1 and Pi03192) and the candidate effector carbonic anhydrase (CA) were quantified before and after experimental evolution on these hosts. Fitness and gene expression varied during the experimental evolution experiment, but independently of the subculturing host. However, the level of host-related specialization of both isolates was stable over time and linked to distinct expression patterns of antagonistic host cell death regulator genes, such asSNE1andPiNPP. Relations between fitness and effector expression proved to be host- and/or isolate-dependent. Altogether, our results demonstrate host adaptation ofP. infestansto be a rather stable trait that is not prone to fluctuate by transitory host changes. They further suggest that pathogenicity ofP. infestansstrongly depends on its ability to establish a steady biotrophic interaction with its hosts by regulating effector gene expression.Author SummaryThe infamous Irish potato famine pathogenPhytophthora infestanscauses late blight on potato and tomato, and extensive losses on both crops worldwide. Isolates causing tomato late blight markedly differ in genotype and phenotype from isolates causing potato late blight: under controlled conditions, isolates from tomato perform well on both hosts, while isolates highly pathogenic from potato struggle to produce large lesions on tomato. Mechanisms explaining these differences are unknown, but might provide clues to better understand the fundamental process of host specialization in pathogens.P. infestansis known to secrete many effectors, modulating the outcome of the interaction with its hosts. We thus coupled experimental evolution, by subculturing isolates nine times on different hosts, and expression of host cell death regulating effectors to explain pathogenic specialization. We showed that the level of pathogenic specialization depends on the pathogen ability to maintain a biotrophic interaction with its host, and hence to suppress cell death. Host specialization was not altered during serial passages, irrespective of the hosts, although overall pathogenicity increased. These findings show thatP. infestansis primarily a biotrophic pathogen, feeding on living host tissue, and open ground for new breeding targets for improved resistance to late blight.

International audience; Plant-parasitic nematodes are a costly burden of crop production. Ubiquitous in nature, phytoparasitic nematodes are associated with nearly every important agricultural crop and represent a significant constraint on global food security. Population genetics is a key discipline in plant nematology to understand aspects of the life strategies of these parasites, in particular their modes of reproduction, geographic origins, evolutionary histories, and dispersion abilities. Advances in high-throughput sequencing technologies have enabled a recent but active effort in genomic analyses of plant-parasitic nematodes. Such genomic approaches applied to multiple populations are providing new insights into the molecular and evolutionary processes that underpin the establishment of these nematodes and into a better understanding of the genetic and mechanistic basis of their pathogenicity and adaptation to their host plants. In this review, we attempt to update information about genome resources and genotyping techniques useful for nematologists who are thinking about initiating population genomics or genome sequencing projects. This review is intended also to foster the development of population genomics in plant-parasitic nematodes through highlighting recent publications that illustrate the potential for this approach to identify novel molecular markers or genes of interest and improve our knowledge of the genome variability, pathogenicity, and evolutionary potential of plant-parasitic nematodes.

International audience; Global trading of plant materials, in combination with agricultural practices, may facilitate the spreading of cyst nematodes to so far non-infected areas. Recently Potato Cyst Nematode (PCN) was recognized to be present in Indonesia and both diversity and distribution require further study. Assessment of PCN populations was done by collecting soil samples, determination of morphological characteristics in combination with ITS rDNA and COI mtDNA sequencing. Thirty-seven soil samples were collected from potato fields in the Indonesia archipelago. The results showed the presence ofGlobodera rostochiensisin 22 out of 37 sampling fields, namely North Sumatra (6 fields), Central Java (12 fields), East Java (3 fields), and -for the first time- in Sulawesi (North Sulawesi) (1 field). The highest observed density was found in Banjarnegara (Central Java), i.e., 872 cysts 100 ml soil(-1).Globodera pallidawas not recovered. Both ITS and COI characterisation of Indonesian PCN (G. rostochiensis) revealed the virtual absence of sequence variation as compared to most PCN from the rest of the world; the COI sequences were identical to the most common and mostly distributed haplotype around the world. Microsatellite genotyping indicated a higher genetic diversity for populations from East Java than for populations from North Sumatra, suggesting that cysts at the origin of populations in North Sumatra were coming from populations in East Java. These data on species identification, population density, genetic diversity, and distribution of potato cyst nematode over the Indonesian archipelago constitute the very basis for the design of environmentally-sound and effective PCN control strategies.

International audience; Management of plant pests is probably the most serious challenge in sustainable food production and the maintenance of food security. Due to the strict regulation of or ban on major categories of pesticide, the potato cyst nematode Globodera pallida has been managed by a combination of crop rotation and the potato resistance locus Grp1, a relatively narrow range resistance gene which was introgressed into a range of commercial potato cultivars in Europe. However, in 2014, G. pallida populations were described that can no longer be controlled by Grp1. Most likely similar highly virulent populations will also emerge in all major potato growing areas in North Western Europe where production practices are very similar. Except for laborious, costly and often moderately accurate pot experiments, there is currently no rapid and reliable method to identify virulent populations. This represents a strong limitation and prevents an accurate and durable management of infestations. The PalAdapt project funded by EFSA represents the first step of a European battle plan against the emergence of virulent G. pallida populations and aims at improving the methods and tools for a fast identification of virulence outbreaks. Four main research questions were investigated during the project: (i) Do resistance breaking populations correspond to novel introductions into Europe? (ii) Can miniaturized in vitro tests be used to get more rapidly an accurate identification of the virulence status?, (iii) Is cyst size a life history trait useful to estimate the virulence status of a population?, (iv) Can we identify polymorphism to design molecular tools for an accurate virulence monitoring? The EFSA partnering grants initiative was an accurate way to improve the EU risk assessment capacity through a knowledge exchange among partners having complementary resources and expertise.

International audience; Plant-parasite coevolution has generated much interest and studies to understand and manage diseases in agriculture. Such a reciprocal evolutionary process could lead to a pattern of local adaptation between plants and parasites. Based on the phylogeography of each partner, the present study tested the hypothesis of local adaptation between the potato cyst nematode Globodera pallida and wild potatoes in Peru. The measured fitness trait was the hatching of cysts which is induced by host root exudates. Using a cross-hatching assay between 13 populations of G. pallida and root exudates from 12 wild potatoes, our results did not show a strong pattern of local adaptation of the parasite but the sympatric combinations induced better hatching of cysts than allopatric combinations, and there was a negative relationship between the hatching percentage and the geographical distance between nematode populations and wild potatoes. Moreover, a strong effect of the geographic origin of root exudates was found, with root exudates from south of Peru inducing better hatching than root exudates from north of Peru. These results could be useful to develop new biocontrol products or potato cultivars to limit damages caused by G. pallida.

Plant-parasitic nematodes are among the most harmful pests of cultivated crops causing important economic losses. The ban of chemical nematicides requires the development of alternative agroecological approaches to protect crops against nematodes. For cyst nematodes, egg hatching is stimulated by host plant root exudates. Inducing “suicide hatching” of nematode second-stage juveniles (J2), using root exudates in the absence of the host plant, may constitute an effective and innovative biocontrol method to control cyst nematodes. However, before considering the development of this approach, understanding the effect of soil biotic component on cyst nematode hatching by root exudates is a major issue. The effectiveness of this approach could be modulated by other soil organisms consuming root exudates for growth as soil microbiota, and this must be evaluated. To do that, four different native agricultural soils were selected based on their physicochemical properties and their microbiota composition were characterized by rDNA metabarcoding. To disentangle the effect of microbiota from that of soil on hatching, four recolonized artificial soils were obtained by inoculating a common sterile soil matrix with the microbiota proceeding from each agricultural soil. Each soil was then inoculated with cysts of the potato cyst nematode, Globodera pallida, and low or high doses of potato root exudates (PREs) were applied. After 40 days, viable J2 remaining in cysts were counted to determine the efficiency of root exudates to stimulate hatching in different soils. Results showed that (i) when physicochemical and microbiota compositions varied among native soils, the hatching rates remained very high albeit small differences were measured and no dose effect was detected and (ii) when only microbiota composition varied among recolonized soils, the hatching rates were also high at the highest dose of PREs, but a strong dose effect was highlighted. This study shows that abiotic and biotic factors may not compromise the development of methods based on suicide hatching of cyst nematodes, using root exudates, molecules inducing J2 hatch, or trap crops.

International audience

International audience; Evidence of strong gene flow among French populations of the carrot cyst nematode [i]Heterodera carotae[/i]

The effective size of a population is the size of an ideal population which would undergo genetic drift at the same rate as the real population. The balance between selection and genetic drift depends on the effective population size (Ne), rather than the real numbers of individuals in the population (N). The objectives of the present study were to estimateNein the potato cyst nematodeGlobodera pallidaand to explore the causes of a lowNe/Nratio in cyst nematodes using artificial populations. Using a temporal analysis of 24 independent populations, the medianNewas 58 individuals (minNe= 25 and maxNe= 228).Neis commonly lower thanNbut in the case of cyst nematodes, theNe/Nratio was extremely low. Using artificial populations showed that this low ratio did not result from migration, selection and overlapping generations, but could be explain by the fact thatG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a lowNe, resulting in a strong intensity of genetic drift, could be important for their control becauseG. pallidapopulations will have a low capacity to adapt to changing environments.

International audience; The negative relationship between offspring size and number is a classic example of trade-off between life-history traits, reported many times in animal and plant species. Here, we wanted to ascertain whether such a trade-off occurred in the oomycete Phytophthora infestans, and whether it was impacted by biotic and abiotic factors. We thus conducted three infection experiments under controlled conditions and measured the number and the size of sporangia (asexual propagules) produced on potato by different P. infestans isolates. In all experiments, we observed a negative relationship between sporangia size and number, demonstrating the existence of a trade-off. Moreover, although the potato host cultivar, temperature and host of origin (tomato or potato) all affected sporangia number, sporangia size or both, none of these biotic and abiotic factors did change the trade-off. Therefore, the trade-off between sporangia size and number could maintain the polyphenism for these traits in P. infestans populations, and favors the coexistence of distinct reproductive strategies within this species. Our results emphasize the relevance to focus on the relationship between offspring size and number in other fungal plant pathogens, as well as to study the impact of offspring size on fitness-linked traits (virulence and disease lesion development) in these organisms.

Studying phenotypic and genomic modifications associated with pathogen adaptation to resistance is a crucial step to better understand and anticipate resistance breakdown. This short review summarizes recent results obtained using experimentally evolved populations of the potato cyst nematode Globodera pallida. In a first step, the variability of resistance durability was explored in four different potato genotypes carrying the resistance quantitative trait loci (QTL) GpaV(vrn) originating from Solanum vernei but differing by their genetic background. The consequences of the adaptation to resistance in terms of local adaptation, cross-virulence and virulence cost were then investigated. Finally, a genome scan approach was performed in order to identify the genomic regions involved in this adaptation. Results showed that nematode populations were able to adapt to the QTL GpaV(vrn), and that the plant genetic background has a strong impact on resistance durability. A trade-off between the adaptations to different resistant potato genotypes was detected, and we also showed that adaptation to the resistance QTL GpaV(vrn) from S. vernei did not allow adaptation to the colinear locus from S. sparsipilum (GpaV(spl)). Unexpectedly, the adaptation to resistance led to an increase of virulent individual's fitness on a susceptible host. Moreover, the genome scan approach allowed the highlighting of candidate genomic regions involved in adaptation to host plant resistance. This review shows that experimental evolution is an interesting tool to anticipate the adaptation of pathogen populations and could be very useful for identifying durable strategies for resistance deployment.

Rapport de l’Expertise scientifique collective réalisée par l’INRA à la demande du métaprogramme INRA "Gestion durable de la santé des cultures" et de l'Institut technique de l'agriculture biologique

SummaryThe effective size of a population is the size of an ideal population which would drift at the same rate as the real population. The balance between selection and genetic drift depends on the population size expressed as the genetically effective population size (Ne), rather than the real numbers of individuals in the population (N).The objectives of the present study were to estimate Nein the potato cyst nematodeGlobodera pallidausing artificial populations and to explore the link between Neand the durability of plant resistances.Using a temporal method on 24 independent pairs of initial and final populations, the median Newas 58 individuals.Neis commonly lower than N but in our case the Ne/N ratio was extremely low becauseG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex-ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a low Necould be important for the control of phytoparasitic nematodes becauseG. pallidapopulations will have a low capacity to adapt to changing environments unless selection intensity is very strong, which could be greatly beneficial for long-term use of plant resistances.

International audience; Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaV(vm), has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a) virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.

In the current agronomical context of pesticide use reduction, deciphering the genetic bases of pathogen adaptation to plant resistances is of major importance to improve their durability. Knowledge of the virulence gene frequencies in pathogens populations could indeed allow the prediction of their durability before deployment. Globodera pallida is a major pest of potato crop for which a promising resistance QTL, GpaVvrn, has been identified in Solanum vernei. An experimental evolution study, in which G. pallida lineages evolved on resistant or susceptible potato genotypes for up to eight generations, previously showed that G. pallida was able to rapidly overcome GpaVvrn resistance. However it was not known if enough genetic mixing occurred in these lineages to be able to detect islands of differentiation in a genome scan approach. Here, we investigated this question using 53 polymorphic microsatellite markers distributed along the genome and three different tests based on genetic differentiation and heterozygosity. We identified eight outlier loci, indicative of genomic regions putatively involved in host adaptation. Several loci were identified by multiple detection methods and/or in two independent adapted lineages. We also showed that some identified candidate genomic regions seem to be also involved in the overcoming of nematode resistance in a genotype harbouring the same resistance QTL in a different genetic background. These results validate the feasibility of a genome scan approach on a biological material coming from short experimental evolution, and encourage to perform a high coverage genome scan using whole genome resequencing. This article is protected by copyright. All rights reserved.

International audience; Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multilocus genotypes. Cross-inoculations on potato and tomato leaflets showed that all isolates were pathogenic on both hosts. However, tomato isolates performed much better on tomato than did potato isolates, which performed better on potato than did tomato isolates, thus revealing a clear pattern of local adaptation. Potato isolates were significantly fitter on potato than on tomato, and are best described as potato specialists; tomato isolates appear to be generalists, with similar pathogenicity on both hosts. Niche separation in the field may thus result mainly from the large fitness gap on tomato between generalists and unadapted potato specialists, while the small, but significant fitness difference on potato between both types of isolates may prevent population invasion by generalists. Extreme specialization to potato seems very costly relative to performance loss on the alternative host. This study therefore shows that local adaptation and niche separation, commonly expected to involve and generate specialists, can occur with generalists.

In the current agronomical context of reduced use of pesticides, deciphering the genetic bases of pathogen adaptation to plant resistances is of major importance as it could help us to improve durability of these resistances. Globodera pallida is a major pest of potato and for which the promising resistance factor, QTL GpaVvrn, has been identified in Solanum vernei and introduced into several new resistant cultivars in Europe.

To understand the mechanisms leading to the breakdown of plant resistance by potato cyst nematodes (PCN; Globodera rostochiensis and G. pallida), an understanding of the genetic structure and variation in populations and the processes that govern their evolution is required.

International audience; The main objective of this investigation was to test the always more aggressive' hypothesis, often advocated to explain lineage replacements in clonal populations of the potato late blight oomycete Phytophthora infestans. To this end, genotypic and pathogenicity data on 1274 French isolates of P. infestans, collected over the period 2001-2008, were analysed. Overall, the populations sampled showed limited genetic diversity, with four multilocus lineages (1_A1, 2_A1, 8_A1 and 13_A2) accounting for over 80% of the isolates collected. As in other West European countries, drastic changes in these dominant clonal lineages were observed over the course of the 8years, particularly in the appearance and propagation of the clone 13_A2. However, invasiveness of clones was not associated with higher aggressiveness; on the contrary, dominant clones had generally low or moderate aggressiveness relative to others present at the same time within the same populations. This finding challenges the link between invasive behaviour and increased aggressiveness often assumed for this biotrophic pathogen, and could reflect the existence of a trade-off between intra-season and inter-season transmission. This would be consistent with the concept of inclusive fitness, which involves the abilities to both reproduce and survive.

Summary Genetic resistance provides efficient control of crop diseases, but is limited by pathogen evolution capacities which often result in resistance breakdown. It has been demonstrated recently, in three different pathosystems, that polygenic resistances combining a major-effect gene and quantitative resistance controlled by the genetic background are more durable than monogenic resistances (with the same major gene in a susceptible genetic background), but the underlying mechanisms are unknown. Using the pepper–Potato virus Y system, we examined three mechanisms that could account for the greater durability of the polygenic resistances: (i) the additional quantitative resistance conferred by the genetic background; (ii) the increase in the number of mutations required for resistance breakdown; and (iii) the slower selection of adapted resistance-breaking mutants within the viral population. The three mechanisms were experimentally validated. The first explained a large part of the variation in resistance breakdown frequency and is therefore expected to be a major determinant of resistance durability. Quantitative resistance factors also had an influence on the second mechanism by modifying the virus mutational pathways towards resistance breakdown and could also have an influence on the third mechanism by increasing genetic drift effects on the viral population. The relevance of these results for other plant–pathogen systems and their importance in plant breeding are discussed.

The variability of resistance durability in different potato genotypes harbouring the same resistance QTL but differing by their genetic background was explored. The indirect consequences of the resistance adaptation in terms of local (i.e. genotype-specific) adaptation and cross-virulence was also investigated. Following the virulence of the potato cyst nematode Globodera pallida in a long-term experimental evolution protocol, the results showed that nematode populations were able to adapt to the resistance of four potato genotypes carrying the QTL GpaV from Solanum vernei, and that the plant genetic background has an impact upon the durability of resistance. The pattern of local adaptation observed here indicates that divergent selection has occurred during the experimental evolution performed from the same initial nematode population, and revealed a trade-off between the adaptation to a resistant potato genotype and the adaptation to another resistant genotype differing in its genetic background. In terms of cross-virulence between potato genotypes derived from different resistance sources (S. sparsipilum and S. spegazzinii), this study shows that the adaptation to resistance QTL GpaVvrn does not necessarily allow the adaptation to collinear GpaV loci. The results presented here could be useful for predicting evolution of nematode populations in natural agro-ecosystems and identifying durable strategies for resistance deployment.

SUMMARY Evolutionary processes responsible for parasite adaptation to their hosts determine our capacity to manage sustainably resistant plant crops. Most plant–parasite interactions studied so far correspond to gene-for-gene models in which the nature of the alleles present at a plant resistance locus and at a pathogen pathogenicity locus determine entirely the outcome of their confrontation. The interaction between the pepper pvr2 resistance locus and Potato virus Y (PVY) genome-linked protein VPg locus obeys this kind of model. Using synthetic chimeras between two parental PVY cDNA clones, we showed that the viral genetic background surrounding the VPg pathogenicity locus had a strong impact on the resistance breakdown capacity of the virus. Indeed, recombination of the cylindrical inclusion (CI) coding region between two PVY cDNA clones multiplied by six the virus capacity to break down the pvr23-mediated resistance. High-throughput sequencing allowed the exploration of the diversity of PVY populations in response to the selection pressure of the pvr23 resistance. The CI chimera, which possessed an increased resistance breakdown capacity, did not show an increased mutation accumulation rate. Instead, selection of the most frequent resistance-breaking mutation seemed to be more efficient for the CI chimera than for the parental virus clone. These results echoed previous observations, which showed that the plant genetic background in which the pvr23 resistance gene was introduced modified strongly the efficiency of selection of resistance-breaking mutations by PVY. In a broader context, the PVY CI coding region is one of the first identified genetic factors to determine the evolvability of a plant virus.

BACKGROUND: Management of grapevine powdery mildewErysiphenecator Schw. requires fungicide treatments such as sterol demethylation inhibitors (DMIs) or mitochondrial inhibitors (QoIs). Recently, reduction in the efficacy of DMIs or QoIs was reported in Europe and the United States. The aim of the present study was to develop real-time qPCR tools to detect and quantify several CYP51 gene variants of E. necator: (i) A versus B groups (G37A) and (ii) sensitive versus resistant to sterol demethylase inhibitor fungicides (Y136F). RESULTS: The efficacy of the qPCR tools developed was better than the CAPS method, with a limit of 2 pg for En ecatorDNA, 0.06 ng for genetic group A and 1.4 ng for the DMI-resistant allele. The detection limits of qPCR protocols (LOD) ranged from 0.72 to 0.85%, and the quantification limits (LOQ) ranged from 2.4 to 2.85% for the two alleles G47A and Y136F respectively. The application of qPCR to field isolates from French vineyards showed the presence of DMI-resistant and/or QoI-resistant alleles in French pathogen populations, linked to genetic group B. CONCLUSION: The real-time PCR assay developed in this study provides a potentially useful tool for efficient quantification of different alleles of interest for fungicide monitoring and for population structure ofE.necator. c � 2010 Society of Chemical Industry

To understand why the Pvr4 resistance of pepper against Potyvirus spp. remained durable in field conditions while virulent Potato virus Y (PVY) variants could be selected in the laboratory, we studied the molecular mechanisms which generated these variants and the consequences on viral fitness. Using a reverse genetics approach with an infectious cDNA clone of PVY, we found that the region coding for the NIb protein (RNA-dependent RNA polymerase) of PVY was the avirulence factor corresponding to Pvr4 and that a single nonsynonymous nucleotide substitution in that region, an adenosine to guanosine substitution at position 8,424 of the PVY genome (A8424G), was sufficient for virulence. This substitution imposed a high competitiveness cost to the virus against an avirulent PVY variant in plants devoid of Pvr4. In addition, during serial passages in susceptible pepper plants, the only observed possibility of the virulent mutant to increase its fitness was through the G8424A reversion, strengthening the high durability potential of the Pvr4 resistance. This is in accordance with the fact that the NIb protein is one of the most constrained proteins expressed by the PVY genome and, more generally, by Potyvirus spp., and with a previously developed model predicting the durability of virus resistances as a function of the evolutionary constraint applied on corresponding avirulence factors.

International audience; Environmental factors such as temperature strongly impact microbial communities. In the current context of global warming, it is therefore crucial to understand the effects of these factors on human, animal, or plant pathogens. Here, we used a common-garden experiment to analyze the thermal responses of three life-history traits (latent period, lesion growth, spore number) in isolates of the potato late blight pathogen Phytophthora infestans from different climatic zones. We also used a fitness index (FI) aggregating these traits into a single parameter. The experiments revealed patterns of local adaptation to temperature for several traits and for the FI, both between populations and within clonal lineages. Local adaptation to temperature could result from selection for increased survival between epidemics, when isolates are exposed to more extreme climatic conditions than during epidemics. We also showed different thermal responses among two clonal lineages sympatric in western Europe, with lower performances of lineage 13_A2 compared to 6_A1, especially at low temperatures. These data therefore stress the importance of thermal adaptation in a widespread, invasive pathogen, where adaptation is usually considered almost exclusively with respect to host plants. This must now be taken into account to explain, and possibly predict, the global distribution of specific lineages and their epidemic potential.

International audience; Trade-offs between virulence (defined as the ability to infect a resistant host) and life-history traits are of particular interest in plant pathogens for durable management of plant resistances. Adaptation to plant resistances (i.e., virulence acquisition) is indeed expected to be associated with a fitness cost on susceptible hosts. Here, we investigated whether life-history traits involved in the fitness of the potato cyst nematode Globodera pallida are affected in a virulent lineage compared to an avirulent one. Both lineages were obtained from the same natural population through experimental evolution on resistant and susceptible hosts, respectively. Unexpectedly, we found that virulent lineages were more fit than avirulent lineages on susceptible hosts: they produced bigger cysts, containing more larvae and hatching faster. We thus discuss possible reasons explaining why virulence did not spread into natural G. pallida populations.

International audience; A trade-off between pathogenicity and transmission is often postulated to explain the persistence of pathogens over time. If demonstrated, it would help to predict the evolution of pathogenicity across cropping seasons, and to develop sustainable control strategies from this prediction. Unfortunately, experimental demonstration of such trade-offs in agricultural plant pathogens remains elusive. We measured asexual transmission of Phytophthora infestans isolates differing in pathogenicity in two sets of artificial infection experiments under controlled, semi-outdoor conditions. Higher foliar pathogenicity decreased mean daughter tuber weight, increased infection severity in daughter tubers, and increased stem mortality before emergence. The most pathogenic isolates thus suffer a double penalty for asexual transmission: a lower survival probability within small and severely infected tubers; and a lower infection probability of neighbouring healthy plants due to fewer infected stems produced by surviving tubers. Moderate tuber resistance favoured transmission of the least pathogenic isolates, while high levels of resistance almost abolished transmission of all isolates. These data demonstrate a trade-off between foliar pathogenicity and asexual transmission over seasons in P. infestans, which should stabilise pathogenicity over time in the potato late blight pathosystem and possibly favour clone replacement by less pathogenic lineages after demographic bottlenecks.

Ascochyta blight, caused by the necrotrophic ascomycete Didymella pinodes , is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population of D. pinodes , suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520 D. pinodes strains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses. IMPORTANCE Ascochyta blight, caused by Didymella pinodes , is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population of D. pinodes , suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic.

International audience; Tobacco cyst nematode is a sexually diploid species composed of three subspecies, Globodera tabacum subsp. tabacum (Gtt), G. tabacum subsp. virginiae (Gtv) and G. tabacum subsp. solanacearum (Gts). In Europe, only Gtt have been reported to date. Here, we report from a plant in a French tobacco field, the identification of a mixture between cysts of the subspecies Gtt and cysts genetically different. The objective of the present study was to determine the subspecies status of those particular cysts. To this aim, we performed CAPS analyses on two genes and a principal component analysis on microsatellite data. The results obtained with both CAPS and microsatellite markers demonstrate for the first time the occurrence of G. tabacum subsp. virginiae in France.