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Pyricularia oryzae (syn. Magnaporthe oryzae), is a filamentous ascomycete that causes a major disease called blast on cereal crops, as well as on a wide variety of wild and cultivated grasses. Blast diseases have a tremendous impact worldwide particularly on rice and on wheat, where the disease emerged in South America in the 1980s, before spreading to Asia and Africa. Its economic importance, coupled with its amenability to molecular and genetic manipulation, have inspired extensive research efforts aiming at understanding its biology and evolution. In the past 40 years, this plant-pathogenic fungus has emerged as a major model in molecular plant–microbe interactions. In this review, we focus on the clarification of the taxonomy and genetic structure of the species and its host range determinants. We also discuss recent molecular studies deciphering its lifecycle. Taxonomy: Kingdom: Fungi, phylum: Ascomycota, sub-phylum: Pezizomycotina, class: Sordariomycetes, order: Magnaporthales, family: Pyriculariaceae, genus: Pyricularia. Host range: P. oryzae has the ability to infect a wide range of Poaceae. It is structured into different host-specialized lineages that are each associated with a few host plant genera. The fungus is best known to cause tremendous damage to rice crops, but it can also attack other economically important crops such as wheat, maize, barley, and finger millet. Disease symptoms: P. oryzae can cause necrotic lesions or bleaching on all aerial parts of its host plants, including leaf blades, sheaths, and inflorescences (panicles, spikes, and seeds). Characteristic symptoms on leaves are diamond-shaped silver lesions that often have a brown margin and whose appearance is influenced by numerous factors such as the plant genotype and environmental conditions.

Soil silicon enhances rice defenses against a range of biotic stresses. However, the magnitude of these effects can depend on the nature of the rice variety. We conducted a series of greenhouse experiments to examine the effects of silicon on planthoppers (Nilaparvata lugens [BPH] and Sogatella furcifera [WBPH]), a leafhopper (Nephotettix virescens [GLH]), blast disease (Magnaporthe grisea) and bacterial blight (Xanthomonas oryzae) in susceptible and resistant rice. We added powdered silica gel (SiO2) to paddy soil at equivalent to 0.25, 1.0, and 4.0 t ha−1. Added silicon reduced BPH nymph settling, but the effect was negligible under high nitrogen. In a choice experiment, BPH egg-laying was lower than untreated controls under all silicon treatments regardless of nitrogen or variety, whereas, in a no-choice experiment, silicon reduced egg-laying on the susceptible but not the resistant (BPH32 gene) variety. Stronger effects in choice experiments suggest that silicon mainly enhanced antixenosis defenses. We found no effects of silicon on WBPH or GLH. Silicon reduced blast damage to susceptible and resistant (Piz, Piz-5 and Pi9 genes) rice. Silicon reduced damage from a virulent strain of bacterial blight but had little effect on a less virulent strain in susceptible and resistant (Xa4, Xa7 and Xa4 + Xa7 genes) varieties. When combined with resistance, silicon had an additive effect in reducing biomass losses to plants infested with bacterial blight (resistance up to 50%; silicon 20%). We discuss how silicon-containing soil amendments can be combined with host resistance to reduce biotic stresses in rice.

Wild species of the genus Oryza are excellent gene pools for improvement of agronomic traits of Asian cultivated rice. The blast resistance gene Pi57(t) in the introgression line IL-E1454 derived from Oryza longistaminata was previously mapped on rice chromosome 12. Inoculation with 322 Magnaporthe oryzae isolates collected from 6 countries indicated that Pi57(t) conferred broad spectrum resistance against M. oryzae. Two mapping populations consisting of 29070 and 10375 F2 plants derived from the crosses of resistant donor IL-E1454 with susceptible parents RD23 and Lijiangxintuanheigu respectively, were used for fine mapping of Pi57(t) locus. Based on genotyping and phenotyping results of recombinants screened from the two crosses, Pi57(t) was finally mapped to a 51.7-kb region flanked by two molecular markers (STS57-320 and STS57-372) on the short arm and close to the centromere of chromosome 12. Six candidate resistance genes were predicted in the target region according to the reference sequence of Nipponbare. These results could facilitate both marker-assisted selection for disease-resistant breeding and gene cloning.

The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791. A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.

Wild species of the genus Oryza are excellent gene pools for improvement of agronomic traits of Asian cultivated rice. The blast resistance gene Pi57(t) in the introgression line IL-E1454 derived from Oryza longistaminata was previously mapped on rice chromosome 12. Inoculation with 322 Magnaporthe oryzae isolates collected from 6 countries indicated that Pi57(t) conferred broad spectrum resistance against M. oryzae. Two mapping populations consisting of 29070 and 10375 F2 plants derived from the crosses of resistant donor IL-E1454 with susceptible parents RD23 and Lijiangxintuanheigu respectively, were used for fine mapping of Pi57(t) locus. Based on genotyping and phenotyping results of recombinants screened from the two crosses, Pi57(t) was finally mapped to a 51.7-kb region flanked by two molecular markers (STS57-320 and STS57-372) on the short arm and close to the centromere of chromosome 12. Six candidate resistance genes were predicted in the target region according to the reference sequence of Nipponbare. These results could facilitate both marker-assisted selection for disease-resistant breeding and gene cloning.

The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791. A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.

Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e. the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant-pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

La pyriculariose du riz est la principale maladie fongique la plus destructive de cette culture au Burkina Faso et au Togo. Afin d'élaborer une méthode de gestion durable de cette maladie, la connaissance de la diversité de l'agent pathogène s'avère nécessaire. L'objectif est d'acquérir des données sur la structure génétique des isolats de M. oryzae collecté entre 2013 et 2015 au Burkina Faso et au Togo. Treize (13) marqueurs microsatellites ont été utilisés pour caractériser 220 isolats selon la méthode décrite par Adreit et al. (2007). Les résultats révèlent un niveau de polymorphisme très élevé entre les isolats. Les valeurs moyennes de la diversité (He) et des allèles par marqueur sont respectivement 0.55 et 9.36. Sur la base de la taille des séquences génotypes, 86 génotypes multilocus (MLGs) ont été identifiés. Ces résultats sont la conséquence probable de la diversité variétale du riz et de l'action environnementale sur l'expression des gènes chez le pathogène. Des MLGs sont partagés entre les deux pays et les pays voisins. Ce qui est probablement la conséquence directe des échanges de matériel végétal infecté entre ces pays. Ainsi, ces données couplées à la pathogénie de chaque génotype multilocus permettront l'amélioration des résistances de riz à la pyriculariose et les diverses relations identifiées nous inspirent des réflexions sur les stratégies de lutte contre M. oryzae excluant toute spécificité d'action dans la gestion de l'agent pathogène à l'intérieur d'un même pays.

Understanding how fungi specialize on their plant host is crucial for developing sustainable disease control. A traditional, centuries-old rice agro-system of the Yuanyang terraces was used as a model to show that virulence effectors of the rice blast fungus Magnaporthe oryzaeh play a key role in its specialization on locally grown indica or japonica local rice subspecies. Our results have indicated that major differences in several components of basal immunity and effector-triggered immunity of the japonica and indica rice varieties are associated with specialization of M. oryzae. These differences thus play a key role in determining M. oryzae host specificity and may limit the spread of the pathogen within the Yuanyang agro-system. Specifically, the AVR-Pia effector has been identified as a possible determinant of the specialization of M. oryzae to local japonica rice.

A. Le riz constitue l'aliment de base de la population à Madagascar. La culture du riz pluvial s'est développée sur les versants des collines des Hautes Terres malgaches, pour répondre à une forte demande et faire face à la saturation des terres inondées permettant la riziculture irriguée. Actuellement, le riz pluvial fait partie intégrante du paysage et devient même par endroit dominant dans les systèmes de culture pluviaux. Cette rapide extension de la riziculture pluviale est le résultat de la diffusion de variétés adaptées à l'altitude, développées dans le cadre du programme d'amélioration génétique mène en partenariat par le Centre National de Recherche Appliquée au Développement Rural malgache (FOFIFA) et le Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) depuis le milieu des années 1980. Malheureusement, la plupart de ces premières variétés se sont révélées sensibles à la pyriculariose entrainant des épidémies importantes dès le début des années 2000. La pyriculariose, causée par Magnaporthe oryzae est la maladie fongique la plus dévastatrice du riz, en particulier pour la riziculture pluviale. Cette maladie représente une menace et un frein à la diffusion des systèmes de culture à base de riziculture pluviale à Madagascar. La principale méthode de lutte contre la pyriculariose est la sélection et l'utilisation de variétés résistantes. Cependant les échecs des variétés résistantes, du fait du contournement des résistances par les populations de l'agent pathogène, sont très nombreux. Dans le contexte d'une agriculture de subsistance et de petit paysannat sur les Hautes Terres centrales, il est crucial de développer des méthodes de lutte pouvant réduire la pression de la maladie sans recourir aux pesticides et améliorer la durée de l'efficacité des résistances variétales. Les associations ou mélanges de variétés de riz pourraient permettre de réduire les épidémies de pyriculariose. Le projet GIPyri (Gestion Intégrée d

Background: Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers. Results: The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance. Conclusions: It was possible to identify three chromosoma

The order Magnaporthales comprises about 200 species and includes the economically and scientifically important rice blast fungus and the take-all pathogen of cereals, as well as saprotrophs and endophytes. Recent advances in phylogenetic analyses of these fungi resulted in taxonomic revisions. In this paper we list the 28 currently accepted genera in Magnaporthales with their type species and available gene and genome resources. The polyphyletic Magnaporthe 1972 is proposed for suppression, and Pyricularia 1880 and Nakataea 1939 are recommended for protection as the generic names for the rice blast fungus and the rice stem rot fungus, respectively. The rationale for the recommended names is also provided. These recommendations are made by the Pyricularia/Magnaporthe Working Group established under the auspices of the International Commission on the Taxonomy of Fungi (ICTF).

Background Receptor-like kinases are well-known to play key roles in disease resistance. Among them, the Wall-associated kinases (WAKs) have been shown to be positive regulators of fungal disease resistance in several plant species. WAK genes are often transcriptionally regulated during infection but the pathways involved in this regulation are not known. In rice, the OsWAK gene family is significantly amplified compared to Arabidopsis. The possibility that several WAKs participate in different ways to basal defense has not been addressed. Moreover, the direct requirement of rice OSWAK genes in regulating defense has not been explored. Results Here we show using rice (Oryza sativa) loss-of-function mutants of four selected OsWAK genes, that individual OsWAKs are required for quantitative resistance to the rice blast fungus, Magnaporthe oryzae. While OsWAK14, OsWAK91 and OsWAK92 positively regulate quantitative resistance, OsWAK112d is a negative regulator of blast resistance. In addition, we show that the very early transcriptional regulation of the rice OsWAK genes is triggered by chitin and is partially under the control of the chitin receptor CEBiP. Finally, we show that OsWAK91 is required for H2O2 production and sufficient to enhance defense gene expression during infection. Conclusions We conclude that the rice OsWAK genes studied are part of basal defense response, potentially mediated by chitin from fungal cell walls. This work also shows that some OsWAKs, like OsWAK112d, may act as negative regulators of disease resistance.

La pyriculariose du riz est la principale maladie fongique la plus destructive de cette culture au Burkina Faso et au Togo. Afin d'élaborer une méthode de gestion durable de cette maladie, la connaissance de la diversité de l'agent pathogène s'avère nécessaire. L'objectif est d'acquérir des données sur la structure génétique des isolats de M. oryzae collecté entre 2013 et 2015 au Burkina Faso et au Togo. Treize (13) marqueurs microsatellites ont été utilisés pour caractériser 220 isolats selon la méthode décrite par Adreit et al. (2007). Les résultats révèlent un niveau de polymorphisme très élevé entre les isolats. Les valeurs moyennes de la diversité (He) et des allèles par marqueur sont respectivement 0.55 et 9.36. Sur la base de la taille des séquences génotypes, 86 génotypes multilocus (MLGs) ont été identifiés. Ces résultats sont la conséquence probable de la diversité variétale du riz et de l'action environnementale sur l'expression des gènes chez le pathogène. Des MLGs sont partagés entre les deux pays et les pays voisins. Ce qui est probablement la conséquence directe des échanges de matériel végétal infecté entre ces pays. Ainsi, ces données couplées à la pathogénie de chaque génotype multilocus permettront l'amélioration des résistances de riz à la pyriculariose et les diverses relations identifiées nous inspirent des réflexions sur les stratégies de lutte contre M. oryzae excluant toute spécificité d'action dans la gestion de l'agent pathogène à l'intérieur d'un même pays.

Understanding how fungi specialize on their plant host is crucial for developing sustainable disease control. A traditional, centuries-old rice agro-system of the Yuanyang terraces was used as a model to show that virulence effectors of the rice blast fungus Magnaporthe oryzaeh play a key role in its specialization on locally grown indica or japonica local rice subspecies. Our results have indicated that major differences in several components of basal immunity and effector-triggered immunity of the japonica and indica rice varieties are associated with specialization of M. oryzae. These differences thus play a key role in determining M. oryzae host specificity and may limit the spread of the pathogen within the Yuanyang agro-system. Specifically, the AVR-Pia effector has been identified as a possible determinant of the specialization of M. oryzae to local japonica rice.

A. Le riz constitue l'aliment de base de la population à Madagascar. La culture du riz pluvial s'est développée sur les versants des collines des Hautes Terres malgaches, pour répondre à une forte demande et faire face à la saturation des terres inondées permettant la riziculture irriguée. Actuellement, le riz pluvial fait partie intégrante du paysage et devient même par endroit dominant dans les systèmes de culture pluviaux. Cette rapide extension de la riziculture pluviale est le résultat de la diffusion de variétés adaptées à l'altitude, développées dans le cadre du programme d'amélioration génétique mène en partenariat par le Centre National de Recherche Appliquée au Développement Rural malgache (FOFIFA) et le Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) depuis le milieu des années 1980. Malheureusement, la plupart de ces premières variétés se sont révélées sensibles à la pyriculariose entrainant des épidémies importantes dès le début des années 2000. La pyriculariose, causée par Magnaporthe oryzae est la maladie fongique la plus dévastatrice du riz, en particulier pour la riziculture pluviale. Cette maladie représente une menace et un frein à la diffusion des systèmes de culture à base de riziculture pluviale à Madagascar. La principale méthode de lutte contre la pyriculariose est la sélection et l'utilisation de variétés résistantes. Cependant les échecs des variétés résistantes, du fait du contournement des résistances par les populations de l'agent pathogène, sont très nombreux. Dans le contexte d'une agriculture de subsistance et de petit paysannat sur les Hautes Terres centrales, il est crucial de développer des méthodes de lutte pouvant réduire la pression de la maladie sans recourir aux pesticides et améliorer la durée de l'efficacité des résistances variétales. Les associations ou mélanges de variétés de riz pourraient permettre de réduire les épidémies de pyriculariose. Le projet GIPyri (Gestion Intégrée d

Background: Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers. Results: The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance. Conclusions: It was possible to identify three chromosoma

The order Magnaporthales comprises about 200 species and includes the economically and scientifically important rice blast fungus and the take-all pathogen of cereals, as well as saprotrophs and endophytes. Recent advances in phylogenetic analyses of these fungi resulted in taxonomic revisions. In this paper we list the 28 currently accepted genera in Magnaporthales with their type species and available gene and genome resources. The polyphyletic Magnaporthe 1972 is proposed for suppression, and Pyricularia 1880 and Nakataea 1939 are recommended for protection as the generic names for the rice blast fungus and the rice stem rot fungus, respectively. The rationale for the recommended names is also provided. These recommendations are made by the Pyricularia/Magnaporthe Working Group established under the auspices of the International Commission on the Taxonomy of Fungi (ICTF).

Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e. the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant-pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

Background Receptor-like kinases are well-known to play key roles in disease resistance. Among them, the Wall-associated kinases (WAKs) have been shown to be positive regulators of fungal disease resistance in several plant species. WAK genes are often transcriptionally regulated during infection but the pathways involved in this regulation are not known. In rice, the OsWAK gene family is significantly amplified compared to Arabidopsis. The possibility that several WAKs participate in different ways to basal defense has not been addressed. Moreover, the direct requirement of rice OSWAK genes in regulating defense has not been explored. Results Here we show using rice (Oryza sativa) loss-of-function mutants of four selected OsWAK genes, that individual OsWAKs are required for quantitative resistance to the rice blast fungus, Magnaporthe oryzae. While OsWAK14, OsWAK91 and OsWAK92 positively regulate quantitative resistance, OsWAK112d is a negative regulator of blast resistance. In addition, we show that the very early transcriptional regulation of the rice OsWAK genes is triggered by chitin and is partially under the control of the chitin receptor CEBiP. Finally, we show that OsWAK91 is required for H2O2 production and sufficient to enhance defense gene expression during infection. Conclusions We conclude that the rice OsWAK genes studied are part of basal defense response, potentially mediated by chitin from fungal cell walls. This work also shows that some OsWAKs, like OsWAK112d, may act as negative regulators of disease resistance.

Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g; flowering and floral organ identity), as well as in stress-related developmental processes such as abscission, fruit ripening and senescence. Over-expression of the OsMADS26 gene in rice (Oryza sativa) has revealed a possible function related to stress response (Lee et al., 2008b). Here we show that OsMADS26 down-regulated plants exhibit enhanced resistance against two major rice pathogens, Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26 down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed both in controlled and field conditions. Interestingly, alteration of OsMADS26 expression has no strong impact on plant development. Gene expression profiling revealed that a majority of genes miss-regulated in over-expresser and down-regulated OsMADS26 lines compared to control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby as a hub to modulate the response to various stresses in the rice plant.

Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).

El brusone del trigo causado por Magnaporthe grisea (T.T. Hebert) M.E. Barr (anamorfo Pyricularia griseaSacc.), tuvo su primera epidemia en Paraguay en 2002, causando pérdidas de más del 70% en campos sembrados en la primera quincena de abril. Este hongo presenta una amplia gama de hospederos entre los cuales se destacan el arroz y el trigo, así como otras gramíneas cultivadas, nativas y malezas. Hasta el momento no se conocen los hospederos alternativos de este hongo en Paraguay o la importancia del inóculo procedente de los mismos para el cultivo del trigo. El objetivo de este estudio es identificar los posibles hospederos alternativos de Magnaporthe grisea en el Centro de Investigación Capitán Miranda, Itapúa, y en el Campo Experimental Yhovy, Canindeyú, durante los ciclos 2013 y 2014. Para ello, muestras de malezas, con síntomas característicos del ataque del hongo, fueron recolectadas en ambas localidades. Estas muestras fueron puestas en cámara húmeda y sembradas sobre medio de cultivo PDA, e incubadas durante 5 días a 25ºC en el laboratorio de Fitopatología del Centro de Investigación Hernando Bertoni, Caacupé. Posteriormente se realizó la identificación del hongo mediante observación al estereoscopio y microscopio. De las 21 especies recolectadas se constató la presencia del hongo en: Bromus catharticus, Brachiaria sp., Chloris gayana, Cyperus diffusus, Digitaria horizontalis y Lolium multiflorum. Así también se realizaron pruebas de patogenicidad con los aislados de Bromus catharticus, Digitaria horizontalis y Lolium multiflorum las cuales confirmaron la patogenicidad de dichos aislados sobre trigo.

El brusone del trigo causado por Magnaporthe grisea (T.T. Hebert) M.E. Barr (anamorfo Pyricularia griseaSacc.), tuvo su primera epidemia en Paraguay en 2002, causando pérdidas de más del 70% en campos sembrados en la primera quincena de abril. Este hongo presenta una amplia gama de hospederos entre los cuales se destacan el arroz y el trigo, así como otras gramíneas cultivadas, nativas y malezas. Hasta el momento no se conocen los hospederos alternativos de este hongo en Paraguay o la importancia del inóculo procedente de los mismos para el cultivo del trigo. El objetivo de este estudio es identificar los posibles hospederos alternativos de Magnaporthe grisea en el Centro de Investigación Capitán Miranda, Itapúa, y en el Campo Experimental Yhovy, Canindeyú, durante los ciclos 2013 y 2014. Para ello, muestras de malezas, con síntomas característicos del ataque del hongo, fueron recolectadas en ambas localidades. Estas muestras fueron puestas en cámara húmeda y sembradas sobre medio de cultivo PDA, e incubadas durante 5 días a 25ºC en el laboratorio de Fitopatología del Centro de Investigación Hernando Bertoni, Caacupé. Posteriormente se realizó la identificación del hongo mediante observación al estereoscopio y microscopio. De las 21 especies recolectadas se constató la presencia del hongo en: Bromus catharticus, Brachiaria sp., Chloris gayana, Cyperus diffusus, Digitaria horizontalis y Lolium multiflorum. Así también se realizaron pruebas de patogenicidad con los aislados de Bromus catharticus, Digitaria horizontalis y Lolium multiflorum las cuales confirmaron la patogenicidad de dichos aislados sobre trigo.

Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g; flowering and floral organ identity), as well as in stress-related developmental processes such as abscission, fruit ripening and senescence. Over-expression of the OsMADS26 gene in rice (Oryza sativa) has revealed a possible function related to stress response (Lee et al., 2008b). Here we show that OsMADS26 down-regulated plants exhibit enhanced resistance against two major rice pathogens, Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26 down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed both in controlled and field conditions. Interestingly, alteration of OsMADS26 expression has no strong impact on plant development. Gene expression profiling revealed that a majority of genes miss-regulated in over-expresser and down-regulated OsMADS26 lines compared to control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby as a hub to modulate the response to various stresses in the rice plant.

Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).

Species of Pyricularia (magnaporthe-like sexual morphs) are responsible for major diseases on grasses. Pyricularia oryzae (sexual morph Magnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, while Pyricularia grisea (sexual morph Magnaporthe grisea) is responsible for foliar diseases of Digitaria. Magnaporthe salvinii, M. poae and M. rhizophila produce asexual spores that differ from those of Pyricularia sensu stricto that has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation. Magnaporthe salvinii was recently allocated to Nakataea, while M. poae and M. rhizophila were placed in Magnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species of Pyricularia s. str. belong to a monophyletic clade that includes all P. oryzae/P. grisea isolates tested, defining the Pyriculariaceae, which is sister to the Ophioceraceae, representing two novel families. These clades are clearly distinct from species belonging to the Gaeumannomyces pro parte/Magnaporthiopsis/Nakataea generic complex that are monophyletic and define the Magnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated to Magnaporthaceae and Pyriculariaceae. Pyricularia oryzae/P. grisea isolates cluster into two related clades. Host plants such as Eleusine, Oryza, Setaria or Triticum were exclusively infected by isolates from P. oryzae, while some host plant such as Cenchrus, Echinochloa, Lolium, Pennisetum or Zingiber were infected by different Pyricularia species. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate coni

Frequent and devastating epidemics of parasites are one of the major issues encountered by modern agriculture. To manage the impact of pathogens, resistant plant varieties have been selected. However, resistances are overcome by parasites requiring the use of pesticides and causing new economical and food safety issues. A promising strategy to maintain the epidemic at a low level and hamper pathogen's adaptation to varietal resistance is the use of mixtures of varieties such that the mix will form a heterogeneous environment for the parasite. A way to find the good combination of varieties that will actually constitute a heterogeneous environment for pathogens is to look for genotype × genotype (G × G) interactions between pathogens and plant varieties. A pattern in which pathogens have a high fitness on one variety and a poor fitness on other varieties guarantees the efficiency of the mixture strategy. In the present article, we inoculated 18 different genotypes of the fungus Magnaporthe oryzae on three rice plant varieties showing different levels of partial resistance in order to find a variety combination compatible with the requirements of the variety mixture strategy, i.e., showing appropriate G × G interactions. We estimated the success of each plant-fungus interaction by measuring fungal fitness and three fungal life history traits: infection success, within-host growth, sporulation capacity. Our results show the existence of G × G interactions between the two varieties Ariete and CO39 on all measured traits and fungal fitness. We also observed that these varieties have different resistance mechanisms; Ariete is good at controlling infection success of the parasite but is not able to control its growth when inside the leaf, while CO39 shows the opposite pattern. We also found that Maratelli's resistance has been eroded. Finally, correlation analyses demonstrated that not all infectious traits are positively correlated.

Magnaporthe oryzae, the rice blast pathogen, causes significant annual yield loss of rice worldwide. Currently, the most effective disease control approach is deployment of host resistance through introduction of resistance (R) genes into elite cultivars. The function of each R gene relies on the specific recognition of an avirulence (AVR) gene of the pathogen. However, the introduced resistance can be broken down within a few years, due to mutation of the AVR genes in the field populations. It is known from a few case studies that AVR mutation patterns are different from one to another. Therefore, knowledge of AVR genes sequence diversity serves as fundamental background in introducing new resistance to control rice blast. In this study, we focused on a newly identified AVR gene AvrPiz-t. We PCR amplified open reading frames (ORFs) of AvrPiz-t as well as promoter regions to detect size variation at this locus in 711 isolates of M. oryzae collected from 38 countries and regions. Through sequencing and Southern hybridization of the amplified locus, strains with polymorphisms in the ORF were classified into groups based on mutation type and site. Natural selection intensity on this gene was calculated and pathogenicity assays were applied to evaluate the association between AvrPiz-t ORF/promoter polymorphism and virulence. In conclusion, sequences at the AvrPiz-t locus were revealed to contain variations at both promoter and ORF regions. This locus is undergoing a relatively strong positive selection. The diversity in coding sequence and the insertions of transposable elements in the promoter region enable M. oryzae to evade recognition by the cognate Piz-t R gene in the host.

Magnaporthe oryzae, the rice blast pathogen, causes significant annual yield loss of rice worldwide. Currently, the most effective disease control approach is deployment of host resistance through introduction of resistance (R) genes into elite cultivars. The function of each R gene relies on the specific recognition of an avirulence (AVR) gene of the pathogen. However, the introduced resistance can be broken down within a few years, due to mutation of the AVR genes in the field populations. It is known from a few case studies that AVR mutation patterns are different from one to another. Therefore, knowledge of AVR genes sequence diversity serves as fundamental background in introducing new resistance to control rice blast. In this study, we focused on a newly identified AVR gene AvrPiz-t. We PCR amplified open reading frames (ORFs) of AvrPiz-t as well as promoter regions to detect size variation at this locus in 711 isolates of M. oryzae collected from 38 countries and regions. Through sequencing and Southern hybridization of the amplified locus, strains with polymorphisms in the ORF were classified into groups based on mutation type and site. Natural selection intensity on this gene was calculated and pathogenicity assays were applied to evaluate the association between AvrPiz-t ORF/promoter polymorphism and virulence. In conclusion, sequences at the AvrPiz-t locus were revealed to contain variations at both promoter and ORF regions. This locus is undergoing a relatively strong positive selection. The diversity in coding sequence and the insertions of transposable elements in the promoter region enable M. oryzae to evade recognition by the cognate Piz-t R gene in the host.

Species of Pyricularia (magnaporthe-like sexual morphs) are responsible for major diseases on grasses. Pyricularia oryzae (sexual morph Magnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, while Pyricularia grisea (sexual morph Magnaporthe grisea) is responsible for foliar diseases of Digitaria. Magnaporthe salvinii, M. poae and M. rhizophila produce asexual spores that differ from those of Pyricularia sensu stricto that has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation. Magnaporthe salvinii was recently allocated to Nakataea, while M. poae and M. rhizophila were placed in Magnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species of Pyricularia s. str. belong to a monophyletic clade that includes all P. oryzae/P. grisea isolates tested, defining the Pyriculariaceae, which is sister to the Ophioceraceae, representing two novel families. These clades are clearly distinct from species belonging to the Gaeumannomyces pro parte/Magnaporthiopsis/Nakataea generic complex that are monophyletic and define the Magnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated to Magnaporthaceae and Pyriculariaceae. Pyricularia oryzae/P. grisea isolates cluster into two related clades. Host plants such as Eleusine, Oryza, Setaria or Triticum were exclusively infected by isolates from P. oryzae, while some host plant such as Cenchrus, Echinochloa, Lolium, Pennisetum or Zingiber were infected by different Pyricularia species. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate coni

Frequent and devastating epidemics of parasites are one of the major issues encountered by modern agriculture. To manage the impact of pathogens, resistant plant varieties have been selected. However, resistances are overcome by parasites requiring the use of pesticides and causing new economical and food safety issues. A promising strategy to maintain the epidemic at a low level and hamper pathogen's adaptation to varietal resistance is the use of mixtures of varieties such that the mix will form a heterogeneous environment for the parasite. A way to find the good combination of varieties that will actually constitute a heterogeneous environment for pathogens is to look for genotype × genotype (G × G) interactions between pathogens and plant varieties. A pattern in which pathogens have a high fitness on one variety and a poor fitness on other varieties guarantees the efficiency of the mixture strategy. In the present article, we inoculated 18 different genotypes of the fungus Magnaporthe oryzae on three rice plant varieties showing different levels of partial resistance in order to find a variety combination compatible with the requirements of the variety mixture strategy, i.e., showing appropriate G × G interactions. We estimated the success of each plant-fungus interaction by measuring fungal fitness and three fungal life history traits: infection success, within-host growth, sporulation capacity. Our results show the existence of G × G interactions between the two varieties Ariete and CO39 on all measured traits and fungal fitness. We also observed that these varieties have different resistance mechanisms; Ariete is good at controlling infection success of the parasite but is not able to control its growth when inside the leaf, while CO39 shows the opposite pattern. We also found that Maratelli's resistance has been eroded. Finally, correlation analyses demonstrated that not all infectious traits are positively correlated.

With the aim of identifying novel regulators of host and nonhost resistance to fungi in rice, we carried out a systematic mutant screen of mutagenized lines. Two mutant wrky22 knockout lines revealed clear-cut enhanced susceptibility to both virulent and avirulent Magnaporthe oryzae strains and altered cellular responses to nonhost Magnaporthe grisea and Blumeria graminis fungi. In addition, the analysis of the pathogen responses of 24 overexpressor OsWRKY22 lines revealed enhanced resistance phenotypes on infection with virulent M. oryzae strain, confirming that OsWRKY22 is involved in rice resistance to blast. Bioinformatic analyses determined that the OsWRKY22 gene belongs to a well-defined cluster of monocotspecific WRKYs. The co-regulatory analysis revealed no significant co-regulation of OsWRKY22 with a representative panel of OsWRKYs, supporting its unique role in a series of transcriptional responses. In contrast, inquiring a subset of biotic stress-related Affymetrix data, a large number of resistance and defencerelated genes were found to be putatively co-expressed with OsWRKY22. Taken together, all gathered experimental evidence places the monocot-specific OsWRKY22 gene at the convergence point of signal transduction circuits in response to both host and nonhost fungi encountering rice plants.

Background: Sexual reproduction is common in eukaryotic microorganisms, with few species reproducing exclusively asexually. However, in some organisms, such as fungi, asexual reproduction alternates with episodic sexual reproduction events. Fungi are thus appropriate organisms for studies of the reasons for the selection of sexuality or clonality and of the mechanisms underlying this selection. Magnaporthe oryzae, an Ascomycete causing blast disease on rice, reproduces mostly asexually in natura. Sexual reproduction is possible in vitro and requires (i) two strains of opposite mating types including (ii) at least one female-fertile strain (i.e. a strain able to produce perithecia, the female organs in which meiosis occurs). Female-fertile strains are found only in limited areas of Asia, in which evidence for contemporary recombination has recently been obtained. We induced the forced evolution of four Chinese female-fertile strains in vitro by the weekly transfer of asexual spores (conidia) between Petri dishes. We aimed to determine whether female fertility was rapidly lost in the absence of sexual reproduction and whether this loss was controlled genetically or epigenetically. Results: All the strains became female-sterile after 10 to 19 rounds of selection under asexual conditions. As no single-spore isolation was carried out, the observed decrease in the production of perithecia reflected the emergence and the invasion of female-sterile mutants. The female-sterile phenotype segregated in the offspring of crosses between female-sterile evolved strains and female-fertile wild-type strains. This segregation was maintained in the second generation in backcrosses. Female-sterile evolved strains were subjected to several stresses, but none induced the restoration of female fertility. This loss of fertility was therefore probably due to genetic rather than epigenetic mechanisms. In competition experiments, female-sterile mutants produced similar numbers of viable conid

With the aim of identifying novel regulators of host and nonhost resistance to fungi in rice, we carried out a systematic mutant screen of mutagenized lines. Two mutant wrky22 knockout lines revealed clear-cut enhanced susceptibility to both virulent and avirulent Magnaporthe oryzae strains and altered cellular responses to nonhost Magnaporthe grisea and Blumeria graminis fungi. In addition, the analysis of the pathogen responses of 24 overexpressor OsWRKY22 lines revealed enhanced resistance phenotypes on infection with virulent M. oryzae strain, confirming that OsWRKY22 is involved in rice resistance to blast. Bioinformatic analyses determined that the OsWRKY22 gene belongs to a well-defined cluster of monocotspecific WRKYs. The co-regulatory analysis revealed no significant co-regulation of OsWRKY22 with a representative panel of OsWRKYs, supporting its unique role in a series of transcriptional responses. In contrast, inquiring a subset of biotic stress-related Affymetrix data, a large number of resistance and defencerelated genes were found to be putatively co-expressed with OsWRKY22. Taken together, all gathered experimental evidence places the monocot-specific OsWRKY22 gene at the convergence point of signal transduction circuits in response to both host and nonhost fungi encountering rice plants.

Background: Sexual reproduction is common in eukaryotic microorganisms, with few species reproducing exclusively asexually. However, in some organisms, such as fungi, asexual reproduction alternates with episodic sexual reproduction events. Fungi are thus appropriate organisms for studies of the reasons for the selection of sexuality or clonality and of the mechanisms underlying this selection. Magnaporthe oryzae, an Ascomycete causing blast disease on rice, reproduces mostly asexually in natura. Sexual reproduction is possible in vitro and requires (i) two strains of opposite mating types including (ii) at least one female-fertile strain (i.e. a strain able to produce perithecia, the female organs in which meiosis occurs). Female-fertile strains are found only in limited areas of Asia, in which evidence for contemporary recombination has recently been obtained. We induced the forced evolution of four Chinese female-fertile strains in vitro by the weekly transfer of asexual spores (conidia) between Petri dishes. We aimed to determine whether female fertility was rapidly lost in the absence of sexual reproduction and whether this loss was controlled genetically or epigenetically. Results: All the strains became female-sterile after 10 to 19 rounds of selection under asexual conditions. As no single-spore isolation was carried out, the observed decrease in the production of perithecia reflected the emergence and the invasion of female-sterile mutants. The female-sterile phenotype segregated in the offspring of crosses between female-sterile evolved strains and female-fertile wild-type strains. This segregation was maintained in the second generation in backcrosses. Female-sterile evolved strains were subjected to several stresses, but none induced the restoration of female fertility. This loss of fertility was therefore probably due to genetic rather than epigenetic mechanisms. In competition experiments, female-sterile mutants produced similar numbers of viable conid

Determining if recombination occurs is of uttermost importance, particularly in pathogenic species, since it impacts the adaptive potential of populations. This might be strenuous in fungi, where sex can be cryptic or facultative. Magnaporthe oryzae is the heterothallic fungus responsible for rice blast. Its sexual cycle was never observed in the field and the worldwide population genetic structure is consistent with asexual reproduction. However, previous scattered data suggested that recombination could occur in limited areas of South Asia. Here we provide biological and population genetics evidences that M. oryzae reproduces sexually in some localities in China. In one population, almost all strains were female fertile, whereas this phenotype required for sexual reproduction is rare or absent in most populations. Strains from complementary mating types were also present in equal frequencies and underwent normal sexual cycle in vitro. Population genetics parameters fitted a recombinant population. Computer simulations confirmed that this genetic structure could not be observed without recombination. An in vitro evolution experiment showed the loss of female fertility after few clonal reproduction cycles. The wild phenotype was not restored by various stresses. The loss of female fertility segregated in progenies of crosses between evolved strains and wild ones, indicating a putative genetic basis. (Texte intégral)

Determining if recombination occurs is of uttermost importance, particularly in pathogenic species, since it impacts the adaptive potential of populations. This might be strenuous in fungi, where sex can be cryptic or facultative. Magnaporthe oryzae is the heterothallic fungus responsible for rice blast. Its sexual cycle was never observed in the field and the worldwide population genetic structure is consistent with asexual reproduction. However, previous scattered data suggested that recombination could occur in limited areas of South Asia. Here we provide biological and population genetics evidences that M. oryzae reproduces sexually in some localities in China. In one population, almost all strains were female fertile, whereas this phenotype required for sexual reproduction is rare or absent in most populations. Strains from complementary mating types were also present in equal frequencies and underwent normal sexual cycle in vitro. Population genetics parameters fitted a recombinant population. Computer simulations confirmed that this genetic structure could not be observed without recombination. An in vitro evolution experiment showed the loss of female fertility after few clonal reproduction cycles. The wild phenotype was not restored by various stresses. The loss of female fertility segregated in progenies of crosses between evolved strains and wild ones, indicating a putative genetic basis. (Texte intégral)

Les organismes vivants puisent leurs ressources de l'environnement pour les allouer aux différentes fonctions biologiques assurant leur développement (croissance, survie, reproduction). La quantité de ressources disponibles dans un environnement étant finie voire limitante, les individus doivent faire des compromis lors de l'allocation de ces ressources à leurs différentes fonctions biologiques. Ces compromis contraignent le développement des individus et entraînent l'apparition d'autres compromis entre leurs traits d'histoire de vie (âge et taille à maturité, nombre de descendants), conditionnant ainsi les capacités d'adaptation des individus à leur environnement. Au cours de cette thèse, nous avons étudié l'évolution de traits d'histoire de vie des pathogènes relatifs à la virulence, par une approche de modélisation. Nous avons centré notre approche sur l'étude des stratégies d'allocation des ressources entre la croissance (ou multiplication intra-hôte) et la production de spores au cours d'une infection par un unique génotype pathogène. Nous avons déterminé, les stratégies optimales d'allocation des ressources ponctionnées à l'hôte, entre la multiplication intra-hôte et la production de spores dans différentes conditions écologiques. Le résultat principal de ces travaux de modélisation est qu'il n'est jamais optimal d'allouer un pourcentage fixe des ressources exploitées à la croissance et à la production de spores tout au long de l'infection. Au contraire, la stratégie optimale comporte généralement une période de latence, c'est-à-dire un temps au cours duquel toute l'énergie est investie dans la croissance et où aucune spore n'est produite. Après la période de latence, toutes les ressources consommées sont utilisées pour la production de spores si le pathogène a un accès limité aux ressources de l'hôte. Au contraire, si le pathogène a un accès illimité aux ressources de l'hôte, une partie fixe des ressources consommées est réservée pour la maintenance des forme

Background: Partial resistance to plant pathogens is extensively used in breeding programs since it could contribute to resistance durability. Partial resistance often builds up during plant development and confers quantitative and usually broad-spectrum resistance. However, very little is known on the mechanisms underlying partial resistance. Partial resistance is often explained by poorly effective induction of plant defense systems. By exploring rice natural diversity, we asked whether expression of defense systems before infection could explain partial resistance towards the major fungal pathogen Magnaporthe oryzae. The constitutive expression of 21 defense-related genes belonging to the defense system was monitored in 23 randomly sampled rice cultivars for which partial resistance was measured. Results: We identified a strong correlation between the expression of defense-related genes before infection and partial resistance. Only a weak correlation was found between the induction of defense genes and partial resistance. Increasing constitutive expression of defense-related genes also correlated with the establishment of partial resistance during plant development. Some rice genetic sub-groups displayed a particular pattern of constitutive expression, suggesting a strong natural polymorphism for constitutive expression of defense. Constitutive levels of hormones like salicylic acid and ethylene cannot explain constitutive expression of defense. We could identify an area of the genome that contributes to explain both preformed defense and partial resistance. Conclusion: These results indicate that constitutive expression of defense-related genes is likely responsible for a large part of partial resistance in rice. The finding of this preformed defense system should help guide future breeding programs and open the possibility to identify the molecular mechanisms behind partial resistance.

Les organismes vivants puisent leurs ressources de l'environnement pour les allouer aux différentes fonctions biologiques assurant leur développement (croissance, survie, reproduction). La quantité de ressources disponibles dans un environnement étant finie voire limitante, les individus doivent faire des compromis lors de l'allocation de ces ressources à leurs différentes fonctions biologiques. Ces compromis contraignent le développement des individus et entraînent l'apparition d'autres compromis entre leurs traits d'histoire de vie (âge et taille à maturité, nombre de descendants), conditionnant ainsi les capacités d'adaptation des individus à leur environnement. Au cours de cette thèse, nous avons étudié l'évolution de traits d'histoire de vie des pathogènes relatifs à la virulence, par une approche de modélisation. Nous avons centré notre approche sur l'étude des stratégies d'allocation des ressources entre la croissance (ou multiplication intra-hôte) et la production de spores au cours d'une infection par un unique génotype pathogène. Nous avons déterminé, les stratégies optimales d'allocation des ressources ponctionnées à l'hôte, entre la multiplication intra-hôte et la production de spores dans différentes conditions écologiques. Le résultat principal de ces travaux de modélisation est qu'il n'est jamais optimal d'allouer un pourcentage fixe des ressources exploitées à la croissance et à la production de spores tout au long de l'infection. Au contraire, la stratégie optimale comporte généralement une période de latence, c'est-à-dire un temps au cours duquel toute l'énergie est investie dans la croissance et où aucune spore n'est produite. Après la période de latence, toutes les ressources consommées sont utilisées pour la production de spores si le pathogène a un accès limité aux ressources de l'hôte. Au contraire, si le pathogène a un accès illimité aux ressources de l'hôte, une partie fixe des ressources consommées est réservée pour la maintenance des forme

Background: Partial resistance to plant pathogens is extensively used in breeding programs since it could contribute to resistance durability. Partial resistance often builds up during plant development and confers quantitative and usually broad-spectrum resistance. However, very little is known on the mechanisms underlying partial resistance. Partial resistance is often explained by poorly effective induction of plant defense systems. By exploring rice natural diversity, we asked whether expression of defense systems before infection could explain partial resistance towards the major fungal pathogen Magnaporthe oryzae. The constitutive expression of 21 defense-related genes belonging to the defense system was monitored in 23 randomly sampled rice cultivars for which partial resistance was measured. Results: We identified a strong correlation between the expression of defense-related genes before infection and partial resistance. Only a weak correlation was found between the induction of defense genes and partial resistance. Increasing constitutive expression of defense-related genes also correlated with the establishment of partial resistance during plant development. Some rice genetic sub-groups displayed a particular pattern of constitutive expression, suggesting a strong natural polymorphism for constitutive expression of defense. Constitutive levels of hormones like salicylic acid and ethylene cannot explain constitutive expression of defense. We could identify an area of the genome that contributes to explain both preformed defense and partial resistance. Conclusion: These results indicate that constitutive expression of defense-related genes is likely responsible for a large part of partial resistance in rice. The finding of this preformed defense system should help guide future breeding programs and open the possibility to identify the molecular mechanisms behind partial resistance.

Keywords: Disease management, genetic diversity, rice interplanting, competition, resource complementarity, technical efficiency, production function, Magnaporthe grisea The experience on rice blast in Yunnan Province, China, is one of the most successful and widely publicized examples of genetic diversification for disease suppression in practice. The wet, cool climate of the province is highly favourable for the development of rice blast epidemics. Before 1998, farmers had to spray fungicides three to eight times per cropping season to successfully grow a crop of glutinous or sticky rice. To reduce farmers’ dependence on these harmful agrochemicals, a team of scientists from the International Rice Research Institute (IRRI) and Yunnan Agricultural University (YAU) initiated a project in Yunnan Province with the objective to explore the possibilities of using biodiversity as a means to control blast outbreaks, and through the associated increase in productivity and income, contribute to poverty alleviation. This study focuses on the effects of the developed technology, i.e., interplanting one row of high-value, but blast-susceptible glutinous rice, with four to six rows of blast-resistant hybrid indica rice varieties, on blast management and the socio-economics, i.e., productivity and farm income, as a basis for explaining its adoption. In a field experiment in Gejiu, Yunnan Province, it was shown that niche differentiation, leading to resource complementarity between the two rice varieties, was marginal and hardly increased the land productivity of the rice varietal mixtures. Prevention of lodging of glutinous rice appeared an important additional advantage of growing rice in varietal mixtures. Results of farm surveys involving both, adopters and non-adopters, showed that contact with extension workers and farmers’ perceptions of the technology-specific attributes of the rice varietal mixtures were the major factors determining adoption probability and use intensit

In Vakinankaratra , where irrigated rice has been cultivated for several hundred years, blast damages increased heavily in the newly developed upland rice. Using epidemiological records, pathogen population genetic data, and pathogenicity test, we studied blast pathogen colonization of the new upland agrosystem. Genotyping with microsattelite markers, showed a significant differentiation between upland and irrigated isolates. Comparison of populations from 3 irrigated valleys (Antsirabe, Manandona, Mangalaza) showed the first two having no differentiation while Mangalaza showed slight differentiation with the two others. That is probably due to selection by the host since Mangalaza had more diversified varieties than the 2 first locations. There is no differentiation between the early isolates causing leaf blast and those causing neck blast In upland agrosystem, differentiation was observed in Mangalaza between 2004 and 2005, and in Andranomanelatra between 2005 and 2006 isolates. Differentiation from one season to the next could be observed during the study for upland isolates. However for each location, ie in Mangalaza, in Manandona and in Antsirabe, differentiation could not be observed between the 2004 and 2005 irrigated isolates. The 99 isolates selected from different branches of the genetic dendrogram formed two distinct groups according to their pathogenicity. The first group brings together irrigated isolates. They have narrow virulence spectrum, ie they could not attack most of the upland cultivars. Even irrigated isolates collected from geographically distant areas like Antananarivo, Lac Alaotra or Vakinankaratra exhibited narrow virulence spectrum. The second gathers upland isolates of Vakinankaratra region. They have a broader virulence spectrum than the irrigated ones. Among the upland isolates, those collected in 2001 showed narrower virulence spectrum than isolates collected in 2005 or 2006, suggesting that the virulence spectrum enlarged with time.

Background: Tetraspanins are small membrane proteins that belong to a superfamily encompassing 33 members in human and mouse. These proteins act as organizers of membrane-signalling complexes. So far only two tetraspanin families have been identified in fungi. These are Pls1, which is required for pathogenicity of the plant pathogenic ascomycetes, Magnaporthe grisea, Botrytis cinerea and Colletotrichum lindemuthianum, and Tsp2, whose function is unknown. In this report, we describe a third family of tetraspanins (Tsp3) and a new family of tetraspanin-like proteins (Tpl1) in fungi. We also describe expression of some of these genes in M. grisea and a basidiomycete, Laccaria bicolor, and also their functional analysis in M. grisea. Results: The exhaustive search for tetraspanins in fungal genomes reveals that higher fungi (basidiomycetes and ascomycetes) contain three families of tetraspanins (Pls1, Tsp2 and Tsp3) with different distribution amongst phyla. Pls1 is found in ascomycetes and basidiomycetes, whereas Tsp2 is restricted to basidiomycetes and Tsp3 to ascomycetes. A unique copy of each of PLS1 and TSP3 was found in ascomycetes in contrast to TSP2, which has several paralogs in the basidiomycetes, Coprinus cinereus and Laccaria bicolor. A tetraspanin-like family (Tpl1) was also identified in ascomycetes. Transcriptional analyses in various tissues of L. bicolor and M. grisea showed that PLS1 and TSP2 are expressed in all tissues in L. bicolor and that TSP3 and TPL1 are overexpressed in the sexual fruiting bodies (perithecia) and mycelia of M. grisea, suggesting that these genes are not pseudogenes. Phenotypic analysis of gene replacementmutants tsp3 and [delta]tpl1 of M. grisea revealed a reduction of the pathogenicity only on rice, in contrast to [delta]pls1 mutants, which are completely non-pathogenic on barley and rice. Conclusion: A new tetraspanin family (Tsp3) and a tetraspanin-like protein family (Tpl1) have been identified in fungi. Functional analysis

In Vakinankaratra , where irrigated rice has been cultivated for several hundred years, blast damages increased heavily in the newly developed upland rice. Using epidemiological records, pathogen population genetic data, and pathogenicity test, we studied blast pathogen colonization of the new upland agrosystem. Genotyping with microsattelite markers, showed a significant differentiation between upland and irrigated isolates. Comparison of populations from 3 irrigated valleys (Antsirabe, Manandona, Mangalaza) showed the first two having no differentiation while Mangalaza showed slight differentiation with the two others. That is probably due to selection by the host since Mangalaza had more diversified varieties than the 2 first locations. There is no differentiation between the early isolates causing leaf blast and those causing neck blast In upland agrosystem, differentiation was observed in Mangalaza between 2004 and 2005, and in Andranomanelatra between 2005 and 2006 isolates. Differentiation from one season to the next could be observed during the study for upland isolates. However for each location, ie in Mangalaza, in Manandona and in Antsirabe, differentiation could not be observed between the 2004 and 2005 irrigated isolates. The 99 isolates selected from different branches of the genetic dendrogram formed two distinct groups according to their pathogenicity. The first group brings together irrigated isolates. They have narrow virulence spectrum, ie they could not attack most of the upland cultivars. Even irrigated isolates collected from geographically distant areas like Antananarivo, Lac Alaotra or Vakinankaratra exhibited narrow virulence spectrum. The second gathers upland isolates of Vakinankaratra region. They have a broader virulence spectrum than the irrigated ones. Among the upland isolates, those collected in 2001 showed narrower virulence spectrum than isolates collected in 2005 or 2006, suggesting that the virulence spectrum enlarged with time.

Background: Tetraspanins are small membrane proteins that belong to a superfamily encompassing 33 members in human and mouse. These proteins act as organizers of membrane-signalling complexes. So far only two tetraspanin families have been identified in fungi. These are Pls1, which is required for pathogenicity of the plant pathogenic ascomycetes, Magnaporthe grisea, Botrytis cinerea and Colletotrichum lindemuthianum, and Tsp2, whose function is unknown. In this report, we describe a third family of tetraspanins (Tsp3) and a new family of tetraspanin-like proteins (Tpl1) in fungi. We also describe expression of some of these genes in M. grisea and a basidiomycete, Laccaria bicolor, and also their functional analysis in M. grisea. Results: The exhaustive search for tetraspanins in fungal genomes reveals that higher fungi (basidiomycetes and ascomycetes) contain three families of tetraspanins (Pls1, Tsp2 and Tsp3) with different distribution amongst phyla. Pls1 is found in ascomycetes and basidiomycetes, whereas Tsp2 is restricted to basidiomycetes and Tsp3 to ascomycetes. A unique copy of each of PLS1 and TSP3 was found in ascomycetes in contrast to TSP2, which has several paralogs in the basidiomycetes, Coprinus cinereus and Laccaria bicolor. A tetraspanin-like family (Tpl1) was also identified in ascomycetes. Transcriptional analyses in various tissues of L. bicolor and M. grisea showed that PLS1 and TSP2 are expressed in all tissues in L. bicolor and that TSP3 and TPL1 are overexpressed in the sexual fruiting bodies (perithecia) and mycelia of M. grisea, suggesting that these genes are not pseudogenes. Phenotypic analysis of gene replacementmutants tsp3 and [delta]tpl1 of M. grisea revealed a reduction of the pathogenicity only on rice, in contrast to [delta]pls1 mutants, which are completely non-pathogenic on barley and rice. Conclusion: A new tetraspanin family (Tsp3) and a tetraspanin-like protein family (Tpl1) have been identified in fungi. Functional analysis

Polyunsaturated fatty acids can be bioactivated by two families of dioxygenases, which either contain non-heme iron (lipoxygenases) or heme (cyclooxygenases, linoleate diol synthases and α-dioxygenases). Lipoxygenases and their products play important roles in the pathophysiology of plants and fungi. The only known lipoxygenase with catalytic manganese (Mn-lipoxygenase) is secreted by a devastating root pathogen of wheat, the Take-all fungus Gaeumannomyces graminis. Its mycelia also contains linoleate diol synthase (LDS), which can oxidize linoleic acid to sporulation hormones. Mn-lipoxygenase belongs to the lipoxygenase gene family. Recombinant Mn-lipoxygenase was successfully expressed in the yeast Pichia pastoris with an expression level of 30 mg/L in fermentor culture. The tentative metal ligands of Mn-lipoxygenase were studied by site-directed mutagenesis. The results show that four residues His-274, His-278, His-462 and the C-terminal Val-602 likely coordinate manganese, as predicted by sequence alignments with Fe lipoxygenases. Mn-lipoxygenase (~100 kDa) contains an Asp-Pro peptide bond in the N-terminal region, which appears to hydrolyze during storage and in the acidic media during Pichia expression to an active enzyme of smaller size, mini-Mn-lipoxygenase (~70 kDa). The active form of Mn-lipoxygenase can oxygenate fatty acids of variable chain length, suggesting that the fatty acids enter the catalytic site with the ω-end (“tail first”). Mn-lipoxygenase is an R-lipoxygenase with a conserved Gly316 residue known as a determinant of stereospecificity in other R/S lipoxygenases. The Gly316Ala mutant showed an increased hydroperoxide isomerase activity and transformed 18:3n-3 and 17:3n-3 to epoxyalcohols. The genome of the rice blast fungus, Magnaporthe grisea, contains putative genes of lipoxygenases and LDS. Mycelia of M. grisea were found to express LDS activity. This enzyme was cloned and sequenced and showed 65% amino acid identity with LDS from G.gramini

Polyunsaturated fatty acids can be bioactivated by two families of dioxygenases, which either contain non-heme iron (lipoxygenases) or heme (cyclooxygenases, linoleate diol synthases and α-dioxygenases). Lipoxygenases and their products play important roles in the pathophysiology of plants and fungi. The only known lipoxygenase with catalytic manganese (Mn-lipoxygenase) is secreted by a devastating root pathogen of wheat, the Take-all fungus Gaeumannomyces graminis. Its mycelia also contains linoleate diol synthase (LDS), which can oxidize linoleic acid to sporulation hormones. Mn-lipoxygenase belongs to the lipoxygenase gene family. Recombinant Mn-lipoxygenase was successfully expressed in the yeast Pichia pastoris with an expression level of 30 mg/L in fermentor culture. The tentative metal ligands of Mn-lipoxygenase were studied by site-directed mutagenesis. The results show that four residues His-274, His-278, His-462 and the C-terminal Val-602 likely coordinate manganese, as predicted by sequence alignments with Fe lipoxygenases. Mn-lipoxygenase (~100 kDa) contains an Asp-Pro peptide bond in the N-terminal region, which appears to hydrolyze during storage and in the acidic media during Pichia expression to an active enzyme of smaller size, mini-Mn-lipoxygenase (~70 kDa). The active form of Mn-lipoxygenase can oxygenate fatty acids of variable chain length, suggesting that the fatty acids enter the catalytic site with the ω-end (“tail first”). Mn-lipoxygenase is an R-lipoxygenase with a conserved Gly316 residue known as a determinant of stereospecificity in other R/S lipoxygenases. The Gly316Ala mutant showed an increased hydroperoxide isomerase activity and transformed 18:3n-3 and 17:3n-3 to epoxyalcohols. The genome of the rice blast fungus, Magnaporthe grisea, contains putative genes of lipoxygenases and LDS. Mycelia of M. grisea were found to express LDS activity. This enzyme was cloned and sequenced and showed 65% amino acid identity with LDS from G.gramini