Search

We review interactions between crop protection practices (developed to control plant pathogens and invertebrate pests) and human fungal infectious diseases. Unlike viral, bacterial and parasitic infections, fungal infections in humans are usually only superficial in healthy individuals, but can become invasive and pose serious risks to immunosuppressed individuals. Although their global impact is less than that of other infectious diseases, human fungal infections still pose serious public health issues. For instance, the use of synthetic agricultural fungicides, particularly the azole class, under conventional intensive, or efficiency improvement-based crop protection practices, is at risk as far as antimicrobial resistance is concerned, due to cases of cross-resistance to clinical azoles used to treat pulmonary aspergillosis, candidiasis and cryptococcocis. In this respect, the One Health approach, originally designed for other types of human pathogens, looks relevant for human pathogenic fungi. Additionally, some entomopathogenic fungi used as biocontrol products against crop pests in a substitution-based approach, may be potentially pathogenic to humans. Very few examples of redesign-based practices (i.e. Agroecological Crop Protection) emerged from our analysis on human fungal diseases. However, discontinuing agricultural azole fungicides (as practiced on organic farms, and which may to some extent be related to the redesign strategy) appears to be the best way to reduce selection pressure and hence the level of azole-resistant human pathogenic fungal strains in the environment.

BackgroundThe behavior of rice varieties under natural environments in fields often differs from the expected one. For developing varieties, breeders give then a particular importance to multi-local field screening to confirm the resistance of their germplasm. We assembled 81 accessions e.g. blast differential, traditional and improved varieties and tested them for resistance to blast (Pyricularia grisea) in eight African hot spots under different ecologies. We thus expected to identify accessions and genes or gene pyramids that provide durable resistance locally or across sites.Methods81 accessions (e.g. blast differential, traditional and improved varieties were tested in hot spots in Benin, Burkina Faso, Côte d'Ivoire, Madagascar, Mali, Rwanda, Togo and Uganda for resistance to leaf and neck blast. An Alpha design (randomized incomplete block) with four replications was used. Correlation between leaf blast and neck blast severity and between incidence and severity were analyzed.Results:From 2013 to 2016, multi-local screening tests were conducted at yje selected sites. Among the 81 rice accessions tested, seven accessions were consistently susceptible while 12 were resistant across locations and seasons. Interestingly, effective individual resistance genes (R genes) or gene pyramids efficient across the sites were identified. In addition, we noticed on some sites, changes in the responses of some rice accessions to the disease from one season to the other. Responses of some accessions also showed great variations from one site to another. In addition, several accessions sharing the same resistance genes exhibited different responses to blast. Regarding the neck blast, only fewer accessions could be assessed as very susceptible ones died at early stages. Although differential responses were observed in the four sites considered for the analysis, several accessions consistently resisted. In addition, results showed that leaf and neck blast resistances were correlated.ConclusionsResults obtained provide useful information on the tested germplasm resistance. In addition, it was possible to identify resistant accessions and sometimes the R genes associated which were effective locally or across sites. Results also showed shifts in pathogenicity of the pathogen populations over seasons and sites. Finally, breeders can now use this valuable information for sustainable blast resistance breeding.

International audience; Cereal-legume intercropping has gained increased interest in Europe. Nevertheless, performance and especially the percentage of each species at harvest are often considered highly variable. Nitrogen (N) fertilisation can be a relevant driving factor affecting the percentage of each species at harvest. Soil N availability influences competition for light and nitrogen in cereal-legume intercrops. However, management of N fertilisation still remains unclear for intercrops. Few references on the effects of a range of strategies of N fertilisation are available to guide farmers with relevant decision rules considering their expectations. Here, a modelling approach was proposed to simulate interactions between light and N acquisition of a pea-wheat intercrop and to test different scenarios for the management of such intercrops. A model (Azodyn-IC) was built resulting from the combination of two existing individual-crop models (AZODYN and AFISOL) and by applying rules of light and soil inorganic nitrogen sharing between the intercropped pea and wheat. Evaluation of the model outputs with experimental data showed satisfactory predictions of the studied variables (N accumulation, LAI, and crop dry weight). The model validated both resource sharing and light-N interactions. Furthermore, the model was able to respond to increases in inorganic N availability based upon straightforward formalisms. Simulating unmeasured variables, such as root growth and light interception and use by each species, improved our understanding of the relative dominance of each species for acquiring resources. Eventually, the model was used to simulate different scenarios of N fertilisation over 26 years of climatic data to account for climatic variability. We demonstrated the interest of such a modelling approach to design decision rules of N fertilisation according to farmers’ expectations.

International audience; Revealing belowground-aboveground relationships (BAR) is essential to drive ecological processes to address agriculture dysfunctions, especially in the management of aboveground plant diseases. Earthworms are one of the most important soil organisms involved in BAR, and silicon (Si) has been identified as a crucial element regulating aboveground plant health. How earthworm-Si interactions induce BAR in poor- and rich-nutrient soil contexts is still poorly understood, despite a growing interest in agricultural sustainability. We investigated the potential of BAR induced by the earthworm-silicon interaction to control the severity of rice blast disease in a Ferralsol in Madagascar, with or without NPK fertilization. We conducted a greenhouse microcosm experiment in which we manipulated the presence of the endogeic earthworm Pontoscolex corethrurus and the fungus Pyricularia oryzae in a Ferralsol supplied or not with Si and fertilized with macronutrients (nitrogen, phosphorus and potassium, i.e., NPK). After eight weeks of growth, plant biomass, nutrition and disease severity were measured. Our results validated the hypothesis that a dual treatment of earthworm inoculation and Si fertilization in a nutrient-poor tropical soil confers a higher tolerance of rainfed rice to P. oryzae, in comparison with treatments with only earthworms or Si, providing the optimal agronomic balance between a gain in biomass (and nutrition) and a reduction in disease severity. The supply of macronutrients altered this positive BAR by favouring the phenomenon of N-induced susceptibility. The aboveground plant C:N ratio of 15 is a threshold below which any increase in N per C unit likely enhances blast disease. The role of belowground interactions to counteract agricultural dysfunctions is supported by our study. To accomplish ecological intensification and provision of ecosystem services such as disease regulation, our findings recommend replacing excessive use of macronutrient fertilizer with sustained agricultural practices promoting the development of earthworm populations, such as organic matter inputs, superficial or no tillage, and the use of cover crops or conservation agriculture.

Magnaporthe oryzae is the fungal plant pathogen that causes rice blast. The sources of primary inoculum and overwintering mode of the fungus remain largely unknown. The effect of rice residues on the onset of blast epidemics and the potential for survival of M. oryzae in the residues were studied in upland conditions in Madagascar. Blast disease was observed in a 3-year field experiment in three treatments: with either infected or uninfected rice residues on the soil surface, or without rice residues. Leaf blast incidence was significantly higher in the treatment with infected rice residues than in the two other treatments at the early stages of the epidemic. In a second set of trials, the survival of M. oryzae on rice residues was monitored. Infected rice stems were placed by lots in three places: on the mulch of rice residues, under the mulch, and buried at a depth of 10 cm in the soil. Each month, samples were taken from the field and tested for sporulation. The survival of the blast fungus decreased rapidly on the stems buried in the soil but remained high for the other conditions. Sporulation of the fungus was observed on stems left on the mulch for up to 18 months. It is concluded that under field conditions, the presence of infected rice residues could initiate an epidemic of blast. The results of this study may help in designing effective management strategies for rice residues infected by M. oryzae. (Resume d'auteur)

In the central highlands of Madagascar, blast, a serious fungal disease of rice caused by Magnaporthe oryzae, was shown to be less severe in conservation agriculture (CA) than in conventional tillage (CT) cropping systems. To assess the effects of CA cropping systems on rice susceptibility to blast and to understand the mechanisms involved, an experiment was conducted over three growing seasons in two sites (at high and mid-altitude). Two fertilization treatments, one with mineral nitrogen (N) fertilizer, and one without, were studied in interaction with two different cropping systems (CA/CT) and two rice varieties that differ in their susceptibility to blast. The performances of the two cropping systems were assessed, and results showed that yields were no higher in the CA or were lower than in CT cropping systems. The effects of the treatments on upland rice crop growth were measured by leaf N content as an indicator of N crop status, and leaf area index (LAI) as an indicator of canopy density. In all years at both sites, leaf N content during early growth stages was higher in the CT than in the CA cropping system. The LAI was lower in the CA than in the CT cropping system at the high altitude site in all three years, and in two out of three seasons at the middle altitude site. Overall, when the level of blast was high, blast was less severe in the CA cropping system and with no N fertilizer. Leaf N content and LAI were used as intermediate explanatory variables in the statistical analyses, and one or the other or both always masked the effect of the cropping system or of N fertilization. Our results show that leaf N content during early growth stages masks the effect of the cropping system on leaf blast severity. When the LAI is strongly affected by the cropping system, it also masks the effect of the cropping system on the severity of leaf and panicle blast. Very often both variables masked the effects of the cropping system and of N fertilization. These findings should help improve disease management by modifying fertilization practices and crop nutrition in conservation agriculture cropping systems.

International audience; In the densely populated highlands of Madagascar, growing upland rice offers the opportunity to increase the total rice cropping area and to improve food security. However, rice blast was a major constraint for the first cultivars released in the 1990s and consequently limited the extension of upland rice. However, blast epidemics are much less intense in the region of Betafo, where the composition of the soil, an Andosol developed from volcanic rock, is different from the classical Ferralsol of the highlands. A 3-year field experiment (2009-2011) was conducted near Antsirabe to compare blast epidemics on rice grown in Ferralsol vs. an Andosol. Leaf and panicle blast development were monitored and the yield components of upland rice plants growing on the two different soil orders were measured. In 2009 and 2011, leaf and panicle blast development were significantly lower for plants grown on the Andosol compared to those grown on the Ferralsol (final panicle blast reduced by 40% in 2009 and 20% in 2011). The severity of blast was shown to be related to the concentrations of mineral elements in the plant, and the Si content was significantly higher in plants growing on the Andosol. In 2010, the differences of blast incidence between the two soils were less marked (14% reduction of panicle blast at the last scoring date). AUDPC were lower in the Andosol compared to the Ferralsol each year, for leaf and panicle blast. The yield components 1000 full grain weight, dry straw weight and the yield were higher in the Andosol compared to the Ferralsol in 2009 and 2010 but were not significantly different in 2011. These results clearly document that blast development may be impacted by the soil order in which rice is grown, and future agronomic management of blast should focus on improved soil mineral composition such as silicon.

We tested the ability of root-adhering soils (RAS) from eight rice cultivars to attract a bacterivorous nematode (Acrobeloides sp.) living in a poor-nutrient soil in Madagascar. We showed that the ability of rice to attract bacterivorous nematodes in its rhizosphere is variable among cultivars. FOFIFA 172 was the cultivar with the highest attraction value, the lowest root biomass (RB) and the highest RAS:RB ratio and RAS respiration. In contrast, nematodes exhibited strong repellent response to W880 RAS. Also, nematode attractancy was not related to rice resistance against pests (blast rice disease and Striga asiatica) neither to cultivar ability to grow at specific altitude. Our results suggest a trade-off in carbon allocation between plant biomass and root exudation driving nematode attractancy and raise questions about the impact of plant breeding on cultivar ability to interact with soil mutualists such as bacterivorous nematodes. Further investigations are required into (i) variation in root exudate quantity and composition among the eight cultivars and (ii) the response of rice cultivars to bacterivorous nematode inoculation.

Rice is the staple crop and food in Madagascar. Since the 1980s, a joint breeding program conducted by CIRAD and Fofifa, has led to the creation of new varieties adapted to the high altitude and at the same time to rainfed cropping environment (Raboin et al., 2014). But the first released varieties rapidly became susceptible to rice blast, a fungal disease caused by Magnaporthe oryzae, and had to be abandoned. In the 2000 and 2010s, new varieties tolerant to blast were proposed to farmers. Upland rice cropping system has become an important complement to irrigated rice, and a way to improve self-sufficiency in rice and food security. Rice blast, a fungal disease caused by Magnaporthe oryzae, is a major constraint for rice particularly in upland cropping conditions. In developing countries like in Madagascar, no chemical solution can be considered, so there is a crucial importance to find out agroecological solutions to limit the risk of epidemics. The interactions between upland rice and blast epidemics have then been studied in a multidisciplinary team in the highlands of Madagascar for more than 10 years. Conservation agriculture cropping systems were studied (Sester et al., 2014, Dusserre et al., in press) and showed an interesting impact on rice susceptibility to blast. Complementary field experiments showed that rice susceptibility was affected by soil origin and crop density and that infested crop residues appeared as sources of primary inoculum (Raveloson et al., 2013). Experiments on cultivar mixtures showed promising results to control blast epidemics (Raboin et al., 2012). These data were measured in field experiments and integrated together in a simulation model at the landscape scale (Sester et al., 2016).

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 de la Pyriculariose du Riz pluvial) mis en oeuvre dans le cadre de PArtenariat et Recherche dans le secteur RURal (PARRUR), finance par le Fonds de Solidarité Prioritaire (FSP) du Service de Coopération et d'Action Culturelle de l'Ambassade de France, a pour objectif d'optimiser l'utilisation de la diversité génétique des résistances du riz pluvial pour contrôler la pyriculariose sur les Hautes Terres de Madagascar. Ce projet comporte trois volets : • L'étude des populations de l'agent pathogène et la caractérisation des résistances du riz vis-à-vis de ces différentes populations nécessitant la mise au point d'une technique d'inoculation artificielle au sein de laboratoire de phytopathologie de la station régionale de recherche du FOFIFA Antsirabe. Des analyses des réactions de variétés différentielles et de variétés du riz pluvial par inoculation avec des souches collectées dans la région du Vakinankaratra, ont été menées. Les résultats ont permis d'identifier les gènes de résistance qui pourraient être contournes et de voir les réponses de variétés du riz pluvial vis-à-vis des souches testées. Les informations obtenues aideront beaucoup à l'amélioration des stratégies de lutte contre la pyriculariose. • La construction de stratégies de déploiement des résistances a la pyriculariose à l'échelle de la parcelle cultivée : étude et optimisation de l'effet des mélanges variétaux sur le contrôle des épidémies de pyriculariose. Plusieurs tests de mélanges variétaux ont été conduits durant les trois campagnes de 2011-2014 en associant des variétés sensibles avec des variétés tolérantes ou des variétés résistantes à la maladie. Les résultats de tous les essais montrent l'atténuation de l'attaque de pyriculariose dans les parcelles cultivées en mélange par rapport aux parcelles cultivées en pure. • La validation de l'efficacité des mélanges de variétés en conditions paysannes avec l'aide de partenaires intervenant dans le développement agricole. Durant les campagnes 2011-2013, l'efficacité de mélange variétal compare à la culture pure, a été confirmée dans les dispositifs mis en place en milieu paysan. Les mélanges variétaux pourraient permettre de continuer à cultiver des variétés devenues sensibles par leur utilisation en mélange avec des variétés résistantes ou dans des mélanges constitues de variétés possédant des gènes de résistance différents. Ils constituent un des moyens pour réduire le risque d'une épidémie forte engendrée par le déploiement massif d'une variété tolérante par les agriculteurs en cas de contournement de sa résistance par des souches plus virulentes.

The effect of two-component rice cultivar mixtures on the control of rice blast disease was studied in three different experiments under rainfed upland conditions in the Madagascar Highlands. The mixtures involved a susceptible cultivar (either susceptible or very susceptible) and a resistant cultivar in different mixture arrangements (random or row mixtures) and with different proportions of the susceptible cultivar (50, 20 and 16AE7%),which were compared to the susceptible cultivar grown in a pure stand. The effect of these mixtures on the incidence and severity of leaf and panicle blast was measured weekly, and on yield and yield components at harvest time. The mixture effect was more efficient in reducing disease with a proportion of 16AE7% susceptible component than with a proportion of 50%. Blast epidemic was significantly reduced in all three experiments. However, under high blast pressure, there was no reduction in the disease by the end of the epidemic and yields of the susceptible cultivar were almost zero whatever the mixture. In two other experiments performed under lower blast pressure, disease incidence and severity were significantly lower in mixtures, and yields of the susceptible cultivars grown in mixtures were higher than those of their respective pure stands. Cultivar mixtures are a promising strategy that could contribute to a more sustainable cultivation of rice under upland conditions in the context of subsistence agriculture in Madagascar, where all cropping operations are manual. (Resume d'auteur)

A weedy form of the genus Beta, i.e. Beta vulgaris ssp. vulgaris (hence ''weed beet'') frequently found in sugar beet is impossible to eliminate with herbicides because of its genetic proximity to the crop. It is presumed to be the progeny of accidental hybrids between sugar beet (ssp. vulgaris) and wild beet (ssp. maritima), or of sugar beet varieties sensitive to vernalization and sown early in years with late cold spells. In this context, genetically modified (GM) sugar beet varieties tolerant to non-selective herbicides would be interesting to manage weed beet. However, because of the proximity of the weed to the crop, it is highly probable that the herbicide-tolerance transgene would be transmitted to the weed. To evaluate the likelihood of gene flow from GM varieties to weed beet and to propose cropping systems that reduce this likelihood, a model of the effects of cropping systems on population dynamics and gene flow in weed beet was developed, based on the existing spatio-temporal framework GENESYS and on field experiments for parametrising the life-cycle of weed beet. The resulting GENESYS-Beet model consists in simulating every year the life-cycle of weed and crop beet in each field of a given region. During flowering, the various life-cycles connect, leading to pollen exchanges which depend on field areas, shapes and distances. The life-cycle consists of a succession of life-stages for which both densities and genotype proportions are calculated. The relationships between the various stages depend on the crop grown in the field, the stage and genotype of the modelled crop relative, as well as the cultivation techniques (tillage tools and dates, sowing date and density, herbicides,mechanical and manual weeding, harvest date) used to manage the crop. Simulations of GM spread in different farms and regions and of the effects of weed management on the advent of GM beet were carried out to illustrate the possible uses of the model and the consequences of co-existing GM and non-GM crops. (Résumé d'auteur)

National audience; Evaluating cropping systems depends on the perspective and scale considered. An agronomic point of view is often considered with the assessment of the impacts of the cropping system at the field scale, or an economic point of view with the consequences of implementing a cropping system on the farm. Tools have been developed to enable a more integrative assessment of cropping systems. This is the case of the MASC (R) model which, using multicriteria evaluation, estimates the sustainability of cropping systems from environmental, economic and social perspectives. MASC-Mada was developed specifically for upland cropping systems in Madagascar. It has been used to compare conservation agriculture cropping systems with conventional cropping systems. The results, confronted to the opinion of farmers, show that conservation agriculture systems are generally more sustainable than conventional systems but a mixed system combining the use of cover crops and less frequent tillage would better take social and economic aspects into account.; L’évaluation des systèmes de culture de´pend du point de vue et de l’échelle envisagés. Un point de vue agronomique est souvent adopté avec l’évaluation des impacts de différents systèmes à l’échelle de la parcelle, ou un point de vue économique avec les conséquences d’un système de culture sur le fonctionnement de l’exploitation agricole. Des outils ont néanmoins été développés pour permettre une évaluation plus intégrative des systèmes de culture. C’est le cas du modèle MASC1 qui permet, par une approche multicritère, d’évaluer la durabilité des systèmes de culture à la fois d’un point de vue environnemental, économique et social. MASC-Mada, développe pour les systèmes de culture pluviaux à Madagascar, a été utilisé pour comparer des systèmes en agriculture de conservation avec des systèmes conventionnels. Les résultats des évaluations, confrontés aux points de vue des agriculteurs, révèlent que les systèmes en agriculture de conservation sont globalement plus durables que les systèmes traditionnels, mais qu’un système mixte alliant utilisation de plantes de couverture et des labours moins fréquents prendrait mieux en compte les aspects sociaux et économiques.

Summary Weed beet populations growing in each crop of the arable rotation could be a relay for the gene flow from adjacent transgenic herbicide-resistant sugarbeet. In this study, weed beet growth and reproduction were assessed under several conditions which could be found in the rotation: various weed beet densities (ranging from 1 to 120 plants m−2) and various crops (winter wheat, spring barley, spring pea, sugarbeet, maize, ryegrass). Measurements were carried out both on life-cycle dynamics (bolting time, time to flowering onset, dynamics of flower opening) and on other quantitative data (survival rate, bolting rate and pollen, flower and seed production). Increasing weed beet density resulted in decreases in bolting rate and flower and seed production per plant. In cereals, weed beet establishment and reproduction were strongly reduced, compared with bare ground as a control situation. In pea, there was no effect on establishment, but the early harvest limited seed set. In the other crops, flower and seed production were reduced to a lesser extent. Parameters of the fitted equations on the bolting and flowering progress were modified by the weed beet density and by the crop. Our data may be used in a model predicting weed beet demographic evolution according to cropping system, and in assessing gene flow.

In response to the extensive development of upland rice on the hillsides of the Madagascan highlands, alternative cropping systems based on conservation agriculture have been recommended to halt declining soil fertility and to limit erosion. To assess the efficiency of these cropping systems in limiting rice blast disease and to measure their yield performance, an experiment was set up in 2003 at Andranomanelatra (1640 m a.s.l.) in the Madagascan highlands. The rice crop was planted every second year following oat (Avena sativa) after common bean (Phaseolus vulgaris), with both conventional tillage and no tillage. For each cropping system, two levels of fertilization were used: (i) organic and (ii) organic + mineral fertilization. The level of blast epidemic was measured on two different cultivars over a 5-year period. Disease severity was significantly lower in the no-tillage cropping system than in the conventional tillage system. Mineral fertilization increased the level of blast. A significant interaction between cropping system and fertilization indicated that the impact of fertilization differed with the cropping system. When the level of blast was low, yield was higher in the conventional cropping system but as soon as blast level increased, yield was better in the no-tillage cropping system. Possible interactions between cropping system and blast epidemics are explained and the problem of high performance but risky cropping systems is discussed. (Resume d'auteur)

International audience; Weed beet cannot be controlled by herbicides in sugar beet (except via height-selective applicators) as it is a crop relative, descending from accidentally flowering sugar beet (Beta vulgaris) crop plants either because of vernalization during cold springs, or presence of a dominant bolting allele in sugar beet seed lots due to cross-pollination by annual wild beet (B. vulgaris ssp. maritima) in seed production areas. A second, minor source of weed beet are crop roots lost during harvest. These roots ("groundkeepers") can reproduce in the year after sugar beet and potentially contribute to weed beet dynamics and gene flow. Bolting, flowering and seed production timing and potential of groundkeepers were measured in field experiments. Bolting and flowering were faster in groundkeepers vs. weed beet; flower and seed production was lower in groundkeepers but the latter were less sensitive to competitive crops. The measured parameters were used to introduce a ground-keeper life-cycle into the GENESYS-BEET model which quantifies the effects of cropping systems on weed beet in landscapes. Simulations over several years showed weed beet dynamics to be more sensitive to groundkeeper parameter values than to root loss at sugar beet harvest. Groundkeepers were identified as a key source of weed beet populations and of gene escape from novel sugar beet varieties (e.g. genetically-modified herbicide-tolerant varieties) in the absence of crop bolters. The control of the latter, either by manual weeding or by genetic improvement of sugar beet varieties, was shown to be essential for controlling weed beet populations and avoid the advent of herbicide-tolerant weed beet

International audience; Cropping system is an essential aspect to take into account to manage blast disease (caused by the fungus Magnaporthe oryzae). In addition to the selection of resistant cultivars, studies report opportunities to limit blast incidence by managing mineral amendment (N, Si, P, etc.), cultivar mixtures or other cropping system adaptations. In Madagascar, rice is the staple crop and food. Farmers traditionally grow irrigated or rainfed lowland rice wherever possible. In the mid-1980s, CIRAD and FOFIFA launched a research program for the highlands to extend upland rice growing areas in high elevation areas of the tropics. This program was consolidated with research on cropping practices that ensure the sustainability of upland rice based cropping systems in this poor and fragile environment. New varieties where obtained, adapted for rainfed cropping up to 1800 m altitude (Dzido et al., 2004). However, farmers had to face attacks of blast disease. Due to the small genetic basis of these varieties, the fungus quickly overcame resistant or tolerant lines selected by breeders. The ways of management of blast disease are very limited in a country like Madagascar where efficient solutions are often not suitable for farmers. Observations of blast epidemics in different regions made us consider the soil as a key factor for rice susceptibility. In a first experiment, we measured the potential of our very susceptible varieties to tolerate blast when cropped in different soil conditions. During two years, we transported volcanic soil from a very fertile area close to the experimentation site and where blast pressure is much lower. We observed a decrease of blast symptoms on rice cropped on that soil compared to the soil of the experimental site, both on leaves and panicles. That decrease was bound to a significant yield increase, demonstrating the importance of plant nutrition on blast incidence. Such results confirm those obtained in 1981 by Seguy et al. Our aim was then to develop cropping systems that could influence blast incidence through an improvement of soil functions. Direct seeded mulch based (DSMB) cropping systems were first used in Madagascar to limit erosion in upland areas. During 4 years, we compared blast epidemics between a traditional cropping system with ploughing each year and a DSMB cropping system, on a midsusceptible variety specific of the highlands conditions. Two fertilisation levels were also tested in these systems: zebu manure only and manure plus additional mineral fertiliser. A significant difference between the two systems was observed, both at leaf and panicle stage. Blast incidence was reduced in DSMB cropping system and, on the contrary to the traditional cropping system, the mineral fertilisation had no effect on blast in DSMB. N fertilisation is known for a long time as an essential factor in blast management. The fact that DSMB cropping system reduced the effect of N-fertilisation made us consider N as the determinant factor of the interaction between cropping system and blast incidence. The determinants of this interaction must then be explained to enable new and durable cropping systems to be developed to manage blast epidemics, in addition to cultivar improvement. This is the objectives of the starting project GARP (ANR-Systerra) which is conducted in Bolivia, Brazil, France, and Madagascar. Its aim is to quantify the interactions between cropping system, N-nutrition and blast resistance in upland rice. Hypotheses and preliminary results of the project will be presented.

La durabilité de la culture continue à long terme dans les programmes rizicoles irrigués est toujours incertaine. Les effets de 18 années de culture continue du riz de bas-fond irrigué sur les sols et les rendements ont été étudiés dans deux expérimentations de fertilité à long terme (EFLT) dans le delta et dans la moyenne vallée du fleuve Sénégal (VFS) en Afrique de l'Ouest. Le riz a été planté deux fois dans l'année - pendant la saison sèche et chaude (SSC) et pendant la saison humide (SH) avec différents traitements d'engrais. Le carbone organique du sol (COS) en jachère variait de 7,1 g kg-1 dans la moyenne vallée à 11 g kg-1 dans le delta. La culture du riz a maintenu et augmenté le COS à Ndiaye et Fanaye, respectivement et les traitements d'engrais n'ont pas affecté le COS. Le faible taux de P du sol extractible en condition de jachère (4 à 5 mg P kg-1) a doublé avec la riziculture avec les applications de l'engrais NPK. Sans engrais, les rendements de riz ont varié pendant la saison humide de 3,9 à 7,3 Mg ha-1 dans le delta et de 2,2 à 8 Mg ha-1 dans la moyenne vallée. Sans engrais, les rendements ont baissé de 60 kg ha-1 (1,5 %) et 115 kg ha-1 (3 %) à Fanaye et Ndiaye, respectivement. Les baisses annuelles de rendements les plus élevées de 268 kg ha-1 (3,6 %) et 277 kg ha-1 (4,1 %) ont été observées dans les parcelles sans P et K à Fanaye et Ndiaye, respectivement. Les rendements de riz étaient maintenus seulement avec l'application de l'engrais NPK d'au moins 60 kg de N, 26 kg de P et 50 kg de K ha-1. Il a été conclu que la double culture du riz irrigué ne fait pas baisser le COS, et que les applications saisonnières de l'engrais NPK ont permis de maintenir les rendements de riz pendant plus de 18 ans.(Texte intégral)

National audience; Les variétés de betteraves sucrières génétiquement modifiées (GM) résistantes à un herbicide sont, a priori, intéressantes dans des champs fortement infestés par la betterave adventice. Cependant, la montée à fleurs de ces betteraves GM peut entraîner l’apparition d’individus résistants, via la dispersion de pollen. Nous avons développé et utilisé le modèle GENESYS-Betterave pour simuler, à l’échelle d’une petite région agricole, l’impact des pratiques culturales sur la dispersion du transgène. Il permet d'identifier des stratégies pour contrôler les adventices et limiter l'apparition de populations résistantes en zone de production de betterave sucrière. L’utilisation de variétés GM dont le transgène est d’origine paternelle, l'augmentation du temps de retour de la betterave dans la rotation, l'introduction de cultures pérennes et l'arrachage systématique des montées sont des mesures efficaces et souvent essentielles.

International audience; Weed beet (Beta vulgaris) is a serious problem in sugar beet fields in many European countries and in the USA. This weed is the progeny either of accidental hybrids between sugar beet (ssp. vulgaris) and wild beet (ssp. maritima), or of bolted sugar beet plants in the case of varieties with low bolting resistance. Because of its proximity to the crop, the weed cannot be eradicated by herbicides in sugar beet crops. With the advent of genetically modified (GM) sugar beet varieties tolerant to non-selective herbicides, weed beet could also become tolerant to these herbicides because the sugar beet and weed beet are interfertile. It is therefore crucial to evaluate and develop cropping systems for managing weed beet. Consequently, we need models quantifying the effects of cropping systems on weed beet dynamics. Because of the seed longevity, the seed bank of weed beet constitutes a key step for these dynamics. The objective of the present work was to develop a model quantifying the effects of tillage, in interaction with soil climate and structure, on the seed bank dynamics and the emergence of weed beet. The model was based on sub-models predicting (a) soil environment (climate, structure) resulting from the cropping system and weather, (b) vertical soil seed distribution after tillage, depending on the tool, the characteristics of the tillage implement and the soil structure; and (c) seed mortality, dormancy, germination and pre-emergent growth depending on season, soil environment, seed depth and age. Seed mortality occurs only during autumn; seed dormancy increases during summer and autumn and decreases during winter; it also increases with seed depth. Germination is triggered by rain or tillage and driven by hydrothermal time; pre-emergent shoot elongation increases with thermal time; pre-emergent seedling mortality increases with soil clod size and seed depth. The sub-models for soil environment and seed movements were based on existing models; the weed beet sub-model was developed from our previously published studies and completed here with additional experiments. Simulations were carried out to show how crop rotation and tillage influence weed beet seed bank and emergence in different crops.

International audience; Weed beet is an important weed of sugar beet crops. Weed and cropped beets can cross easily and the management of weed beet is therefore crucial in the case of the advent of GM sugar beet, especially herbicide-tolerant cultivars, in order to ensure the co-existence of GM and non-GM crops and to avoid the appearance of herbicide-resistant weed beet. The inability of weed beet to compete in most other crops of the rotation makes the seed bank evolution a crucial stage of the life-cycle because in the rotation, sugar beet is at the most cultivated only every 3 years. The present study used seed burial experiments and laboratory analyses to characterise each step of the evolution of the weed beet seed bank and the external factors that could modify seed persistence in the soil. A monthly seed mortality of 10% was observed between October and December, while mortality was nil during the other seasons. Equations were then developed to describe the observed seasonal variations in seed survival. Seed dormancy also varied with season: the proportion of non-dormant seeds increased during winter (appearance of secondary dormancy) and decreased during the remaining seasons (loss of dormancy). In addition, the germinating seeds decreased with seed age and seed depth, while the presence of light stimulated germination. These observations were also translated into equations. Last, the pre-emergence hypocotyl growth and its variability were studied according to seed age, but no significant effect was observed. The results confirm the importance of the effects of cropping system on the evolution of the weed seed bank, especially the effect of soil tillage, which determines the date and conditions of seed burial, seed excavation and germination stimulation.

National audience; Simulations were carried out with the GeneSys sugar beet model to assess the impact of introduction of GM herbicide-tolerant beet varieties into actual European cropping systems. Problems related to the appearance of HT weed beet and related practices were identified and further evaluated. As final step, the efficiency of different mitigation measures applied by the GM crop farmer to reduce the content of GM seeds with tolerance to herbicide in the seed bank of the neighbouring non-GM fields was compared.

The process of introgression between a transgenic crop modified for better agronomic characters and a wild relative could lead potentially to increased weediness and adaptation to the environment of the wild species. However, the formation of hybrid and hybrid progeny could be associated with functional imbalance and low fitness, which reduces the risk of gene escape and establishment of the wild species in the field. Our work compares the fitness components of parents and different types of backcross in the sixth generation of hybrids between transgenic oilseed rape (Brassica napus, AACC, 2n = 38) resistant to the herbicide glufosinate and wild radish (Raphanus raphanistrum, RrRr, 2n = 18). The backcross with oilseed rape cytoplasm (OBC) has a fitness value 100 times lower than that of the backcross with wild radish cytoplasm (RBC). The herbicide-resistant RBC has similar growth to the susceptible RBC, but final male and female fitness values are two times lower. In turn, susceptible RBC exhibit similar fitness to the control wild radishes. The relative fitnesses of the different types are the same whether or not they grow under competitive conditions. The consequence on fitness of the chromosome location of the transgene conferring resistance and the relevance of these results to the impact of gene flow on the environment are discussed.

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola is an important disease of rice. BLS is prevalent in Asia and West Africa, where it was first reported in Nigeria and Senegal in the early 1980s (4). Recently, molecular analysis of strains from Mali (2) and Burkina Faso (5) further confirmed the presence of BLS in West Africa. In Madagascar, BLS symptoms were first reported in the 1980s by Buddenhagen but the causal agent was not unequivocally determined (1). To confirm Buddenhagen's observations using modern molecular typing tools, we surveyed several rice fields in the Antananarivo and Antsirabe districts in March 2013. BLS symptoms were observed on cultivated Oryza sativa grown under both upland and lowland conditions, with a proportion of diseased individuals varying from 30% up to 80%. Symptomatic leaves presenting water-soaked lesions that developed into translucent, yellow streaks with visible exudates at the surface were sampled. One to four centimeter long pieces of diseased leaves were ground using the Qiagen TissueLyser system at 30 rps for 30 s (Qiagen, Courtaboeuf, France). The ground tissue was then macerated in 1 ml of sterile water for 1 h at 4°C. Non-diluted and 10-fold diluted tissue macerates were plated on semi-selective PSA medium (peptone 10 g/liter, sucrose 10 g/liter, glutamic acid 1 g/liter, bacto agar 16 g/liter, actidione 50 mg/liter, cephalexin 40 mg/liter, and kasugamycin 20 mg/liter) and incubated for 3 to 7 days at 28°C. Single, yellow, Xanthomonas-like colonies were isolated on non-selective PSA medium. Diagnostic multiplex PCR was performed on single colonies for pathovar identification (3). Five strains that produced three diagnostic bands corresponding to the X. oryzae pv. oryzicola pattern were further analyzed for pathogenicity on 3-week-old O. sativa cv. Nipponbare plants. Bacteria grown on PSA plates and adjusted to 1 × 108 CFU/ml were infiltrated into rice leaves with a needleless 1-ml syringe (2 × 3 infiltrations per plant and strain). Seven days after incubation in the greenhouse (27 ± 1°C with a 12-h photoperiod), inoculated leaves showed water-soaked lesions that produced yellow exudates corresponding to those initially observed in rice fields and observed for leaves challenged with the X. oryzae pv. oryzicola reference strain BLS256. Symptomatic leaf tissues were ground and plated on non-selective PSA medium, resulting in colonies with typical Xanthomonas morphology that were confirmed as X. oryzae pv. oryzicola by multiplex PCR typing (3), thus fulfilling Koch's postulates. Finally, the five strains were subjected to gyrB sequencing upon PCR amplification using the universal primers XgyrB1F (5′-ACGAGTACAACCCGGACAA-3′) and XgyrB1R (5′-CCCATCARGGTGCTGAAGAT-3′). The 743-bp partial gyrB sequences were 100% identical to the gyrB sequence of strain BLS256. As expected, the gyrB sequence of strains KACC10331, MAFF311018, and PXO99A of the X. oryzae pv. oryzae pathovar respectively showed nine, 16, and 10 mismatches in comparison to the Malagasy strains, thus further supporting that they belong to the pathovar oryzicola. References: (1) I. W. Buddenhagen. Int. Rice Comm. Newsl. 34:74, 1985. (2) C. Gonzalez et al. Mol. Plant Microbe Interact. 20:534, 2007. (3) J. M. Lang et al. Plant Dis. 94:311, 2010. (4) D. O. Niño-Liu et al. Mol. Plant Pathol. 7:303, 2006. (5) I. Wonni et al. Plant Dis. 95:72, 2011.

International audience; In regions of sugar beet cultivation, weed beet infestations are responsible for economic losses. Weed beet belongs to the same species as the cropped plant, thus rendering herbicide control impossible in conventional sugar beet where costly practices such as manual weeding of bolters must be carried out instead. Genetically-modified herbicide-tolerant (GMHT) sugar beet varieties might provide an alternative in fields heavily infested with weed beet. However, accidental bolting of GMHT plants would result in pollen-mediated transgene flow towards weed beets. The objective of the present paper was to use a spatiotemporal simulation model for comparing three production systems with different cultural practices to evaluate the risk of herbicide-tolerant weed beet populations in a small agricultural region where GMHT and conventional sugar beet coexist. The GENESYS-Beet simulation model was used in a case study of a French sugar beet production region where three types of intensive production systems had been identified: (1) “potato grower”; (2) “beet grower”; and (3) “cereal grower”. The three production systems were successively simulated on a real 149 field map extracted from the studied region. Our simulation results show that gene flow is inevitable, both in time and in space, but that it varies considerably with the cropping system. Similar results were obtained for oilseed rape. Simulation models proved to be powerful tools for predicting the effect of alternative methods on gene flow to and from weed populations. However proposals still require economic feasibility studies.

Madagascar is one of the biggest rice producers in Africa. About 20% of the production is rainfed rice. Since the 1990's, cold tolerant cultivars adapted to high altitude have been successfully proposed to farmers and adopted in the central highlands of the country. But rice blast pressure on the hillsides is important and is the second constraint (after cold) breeders have to take into account. In the same time, hillsides were more and more put under cultivation, conservation agriculture cropping systems have been proposed to farmers (Scopel et al., 2013), to limit erosion and to ensure the sustainability of rainfed crops. In experimental studies, these conservation agriculture cropping systems were shown to limit blast epidemics (Sester et al., in press). We hypothesized that the specificities of the conservation agriculture cropping systems (no tillage, permanent soil cover and rotations) induced changes in plant nutrition and plant nutritional balance, especially nitrogen assimilation, and that it was the reason of a differential expression of tolerance to blast. To test this hypothesis, pluriannual factorial experiments were conducted in two sites to measure blast disease severity on leaves and on panicles in two cropping systems (conservation agriculture vs conventional) and three nitrogen fertilization levels. Crop development and nitrogen assimilation were measured at four stages and yield components were assessed at harvest. A mineral diagnosis was performed at booting stage on the flag leaf. A relational database has been created to manage agronomic and disease severity rating data from the project. For statistical analysis (performed using Sas) the proportion of damaged leaf area and damaged panicles were fitted to a generalized linear model. We will present the results of the respective impacts of the cropping system environment, the nitrogen fertilization and the crop density on the leaf and panicle blast level. In some particular conditions, a significant impact of the cropping system appeared in addition to the effects explained by crop density, confirming the hypothesis of a plant susceptibility modification. We present then the way these results could be used to adapt cropping systems and to improve upland rice tolerance to blast in a sustainable way.