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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.

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.

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)

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.

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.