Indicators to assess temporal genetic diversity in the French Catalogue: no losses for maize and peas

International audienceThe aim of this study, led by the GEVES (Research and Control Group for Varieties and Seeds), was to suggest indicators to assess the diversity available to farmers since the French Official Catalogue for Plant Varieties and Species was initiated. The largest datasets of 1990 inbred maize lines and 578 pea lines from the last 50 years were analysed using morphological and enzymatic parameters. Lines were grouped into three to five periods. Genetic diversity was estimated in each period from morphological and enzymatic markers by computing numerous indices, such as the number of classes of scores for each characteristic, allelic richness or genetic diversity index (H (e) ). Population differentiation parameters (G(ST), G(ST)', F-ST, Q(ST)) were also estimated between periods. While genetic diversity computed from distinction, uniformity, stability traits was more marked for maize (0.66) than for garden peas (0.35) or feed peas (0.29), the opposite trend was observed with enzymes, resulting in a genetic diversity of 0.43, 0.35 and 0.22 for garden peas, feed peas and maize, respectively. However, no significant changes in genetic diversity were observed over time, and genetic differentiation was slight between periods. All our results demonstrated that no significant reduction in the diversity available to farmers had been observed since initiation of the French Catalogue. The H (e) was a good indicator providing a quantitative estimate of genetic diversity, but it should be interpreted alongside a more precise indicator such as allelic richness or the number of classes for morphological characteristic

Comparison of Multispectral imaging and Near infrared Reflectance Spectroscopy methods for phenotyping resistance of cereals to Fusarium Head Blight (FHB) and Deoxynivalenol (DON)

To encourage development of cereal varieties resistant to Fusarium Head Blight and mycotoxins for the National List, two new methods of phenotyping were developed by GEVES on winterwheat. They are more reliable and faster than in-field visual assessment and cheaper than LCMS-MS for measuring DON content. Multispectral imaging is being developed to predict /quantify damage from diseases on several species. Near-Infrared Spectroscopy is an efficient and non-destructive method for seed quality analysis. The aim was to assess the potential of these technologies for quantifying Fusarium graminearum damage, compared to visual assessment and DON content in kernels. i) With Multispectral imaging (VideometerR), the algorithm “Fusa-spectrale wheat”, was developed to evaluate the percentage of Fusarium Damaged Kernels (FDK) at maturity for varietal classification using Canonical Discriminant Analysis between kernels infected/not infected, on three years at several sites. FDK is strongly correlated with percentage of scabbed spikelets assessed by visual scorings (R>0.87) and with DON content (R>0.88). Correlation between FDK and Fusarium graminearum biomass assessed by real-time PCR was stronger in trials with only F. graminearum (R=0.97) than trials with a complex Fusarium-Microdochium. For durum wheat and triticale, studies are ongoing. ii) NIR calibration was developed from a sample set of varieties produced in two locations over two crop years. Calibration models (visual scoring, DON content) were developed using Partial Least Square Regression (PLS). Each model was checked by internal cross validation. Their performance was assessed by the coefficient of determination in calibration (R2cal) and standard error in cross validation. The R2cal observed was 0.90 for “DON content” model and 0.79 for “visual scoring” model.[br/] These two technologies show potential to evaluate FHB and DON resistance on cereals. The NIRS models require additional data to include geographical, genotyping and years effects. With multipectral and hyperspectral imaging, research is ongoing to quantify Microdochium spp

Comparaison des méthodes de détection des mosaïques des blés (Bymovirus et Furovirus) par marquage moléculaire et par détection sérologique

La revue Innovations agronomiques s'adresse à l'ensemble des acteurs de la chaîne de valeur agronomique, aux services institutionnels, aux chercheurs, enseignants et apprenants et à la société civile intéressés par les sujets de l’agriculture, de l’alimentation et de l’environnement. Elle reprend et complète les thèmes abordés lors des CIAg ainsi que des synthèses de résultats de programmes de recherche sur ces champs thématiques.National audienceThe mosaic viruses of cereals, Soil-Borne Cereal Mosaic (SBCMV) and Wheat Spindle Streak Mosaic Virus (WSSMV) are RNA viruses transmitted by a soil microorganism: Polymyxa graminis. Wheat cropsare increasingly affected by the virus, resulting in large yield losses and up to now, only the varietal resistance makes it possible to fight against these mosaics. Currently, serological tests (ELISA) areperformed to support visual scores in order to confirm varietal resistance in the context of varieties registration in the National Catalogue by GEVES and as part of post registration tests by ARVALIS PlantInstitute. But since 2009, questions have been raised concerning the stability of sera performance depending on the supplier. The objective of this study was to define a reliable reference method toconfirm the resistance of wheat varieties to WSSMV (bymovirus) and to SBCMV (furovirus), depending on the reproducibility, sensitivity, and cost of methods. In 2009-2010, the laboratories optimized amethod for molecular detection by RT-PCR, by choosing primer pairs of Vaïanopoulos (2006) c2F/c1R for WSSMV and FURO2-F / R for SBCMV, (2009) optimized by BioGEVES in 2010, followed byagarose gel electrophoresis. In 2010-2011, ring tests showed a very good reproducibility of RT-PCR tests (> 95%), with rare cases of false positives, and a good reproducibility of ELISA tests (> = 89%),with some cases of false negatives, in connection with the sensitivity of each method. A simplified RTPCR protocol, “Jus GES”, was not retained, due to a lower sensitivity than ELISA tests, despite its lowercost than RT-PCR. For the registration of wheat varieties to the French catalogue, the detection reference method remains the DAS-ELISA test, conducted by GEVES. This method has proven itsrobustness with a good concordance with the visual scores, a sufficient sensitivity and a cost eight times lower than RT-PCR. But in case of defective sera, it will now be possible to use a test by RT-PCR; thisservice is now offered to the whole seed supply chain by GEVES. For the varieties in post-registration, the method used is the molecular method by RT-PCR.Le virus de la mosaïque des céréales, Soil-Borne Cereal Mosaic (SBCMV) et le Virus des stries en fuseau du blé, Wheat Spindle Streak Mosaic Virus (WSSMV) sont des virus à ARN transmis par un micro-organisme du sol : Polymyxa graminis. Les cultures de blé sont de plus en plus touchées par ces virus, entraînant d’importantes pertes de rendement et seules les résistances variétales permettent actuellement de lutter contre ces mosaïques. Actuellement, des tests sérologiques (ELISA) sont réalisés en appui des notations visuelles pour confirmer la résistance variétale, dans le cadre de l’inscription des variétés de blé au Catalogue national par le GEVES et de la post inscription par ARVALIS Institut du Végétal. Mais depuis 2009, des interrogations ont été soulevées sur les performances durables des sérums selon le fournisseur. L’objectif de cette étude est de définir une méthode de détection de référence fiable pour confirmer la résistance des variétés de blé au WSSMV (bymovirus) et au SBCMV (furovirus), en fonction de la reproductibilité, de la sensibilité, et du coût des méthodes. En 2009-2010, les laboratoires ont optimisé une méthode de détection moléculaire par RT-PCR, en choisissant les couples d’amorces de Vaïanopoulos, (2006) c2F/c1R pour le WSSMV et FURO2-F/R (2009) pour le SBCMV, optimisée en 2010 par BioGEVES, suivi d’une lecture par gel d’agarose. En 2010-2011, des ring tests ont montré une très bonne reproductibilité des tests RT-PCR (>95%), avec de rares cas de faux positifs, et une bonne reproductibilité des tests ELISA (>=89%), avec quelque cas de faux négatifs, en lien avec la sensibilité de chaque méthode. Une méthode RT-PCR simplifiée, Jus GES, n’a pas été retenue, en raison d’une sensibilité inférieure aux tests ELISA, malgré son coût inférieur à la RT-PCR. Pour l’inscription des variétés de blé au Catalogue, la méthode de détection de référence reste le test DASELISA, mené par le GEVES. Cette méthode a prouvé sa robustesse avec une bonne avec une bonne concordance avec les notations visuelles, une sensibilité suffisante et un coût huit fois moins élevé que la RT-PCR. Mais en cas de sérums défectueux, il sera à présent possible de recourir à un test par RT-PCR ; cette prestation étant maintenant proposée à toute la filière par le GEVES. Pour les variétés en postinscription, la méthode retenue est la méthode moléculaire par RT-PCR

La fusariose des épis des céréales à paille : synthèse de 10 années de recherche pour une meilleure gestion intégrée de la maladie.

International audienceFusarium head blight (FHB) is a cereal disease caused by a complex of plant pathogenic fungal species of the genera Fusarium andMicrodochium, with different epidemiological characteristics and producing or not different toxins. The FHB causes significant yieldlosses, health issues and technological quality concerns in all temperate areas worldwide. The composition of the species complexis different according to the cereal, depending on the climate of the year and the agronomic practices. These species may havedifferent susceptibilities to the fungicides used and different behaviors towards genetic resistance. Thus, investigating thesecharacteristics is required to implement integrated pest management strategies adapted to this disease. For more than 10 years,several research programs have led to significant progress in this area. Tools have been developed to more accurately characterizefungal populations and their interactions. Models have been developed to predict the risk and to adapt control measures. Themolecular mechanisms involved in the interaction between plant genes and the pathogenicity of fungal species are beginning to bedeciphered. Phenotyping methods are being developed to help in the characterization of varietal susceptibility and direct controlmethods using biocontrol products are under investigation. The goal of this paper is to review the main results obtained in thecontext of integrated management of fusarium head blight.La fusariose de l’épi (FHB) est une maladie des céréales causée par un complexe d’espèces de champignons phytopathogènes desgenres Fusarium et Microdochium, ayant des caractéristiques épidémiologiques différentes et productrices ou non de différentestoxines. Le FHB entraîne d’importantes pertes de rendement et des problèmes de qualité sanitaire et technologique dans toutes lesrégions tempérées du globe. La composition du complexe d’espèces est différente selon les céréales, très dépendante du climat del’année et de l’itinéraire technique. Ces espèces peuvent avoir des sensibilités différentes aux fongicides utilisés et descomportements différents vis à vis des résistances présentes dans les variétés. Ainsi, il est essentiel de connaître ces caractéristiquespour mettre en œuvre les méthodes de lutte intégrée adaptées à cette maladie. Depuis plus de 10 ans, plusieurs programmes derecherche ont permis des avancées significatives sur cette thématique. Des outils ont été développés et ont permis de caractériserplus précisément les populations fongiques selon les céréales et leurs interactions. Des modèles ont été développés pour prédire lerisque et adapter les moyens de lutte. Les mécanismes moléculaires impliqués dans l’interaction entre les gènes de la plante et lapathogénicité des espèces fongiques commencent à être décryptés. Des méthodes de phénotypage se développent pour aider à lacaractérisation de la sensibilité variétale et des méthodes de lutte directe utilisant des produits de biocontrôle sont endéveloppement. L’objectif de cet article est de synthétiser les principaux résultats acquis dans l’objectif d’une protection intégréevis‐à‐vis de la fusariose des épis des céréales

IRIGAM - Identification de résistances à l’infection des grains par Fusarium graminearum et à l’accumulation des mycotoxines au sein des variétés de blé françaises grâce à la mise en place de nouvelles technologies de phénotypage

Kernels contamination by mycotoxins and especially deoxynivaneol (DON) represents a major sanitarythreat for the cereals. Here, we compared a set of different methodologies to evaluate Fusarium damagedkernels and DON contaminated flours. This will allow to routinely assessing these traits in breedingprograms. Thanks to these methodologies, we identified seven wheat genomic regions involved inresistance to DON accumulation. Molecular markers associated with these regions are now available tobreed for varieties with improved resistance, a high priority of the grain sector.La contamination des grains par les mycotoxines et notamment le deoxynivalenol (DON) est un problèmesanitaire majeur chez les céréales. Cette étude a permis de comparer un ensemble exhaustif deméthodologies pour évaluer le taux de grains symptomatiques suite à une attaque de Fusariumgraminearum et la contamination des farines par le DON pour permettre une évaluation en routine de cescaractères dans les programmes de sélection. Grace à ces nouvelles méthodologies, le projet aégalement mis en avant sept régions du génome de blé impliquées dans la résistance aux DON ainsi quedes marqueurs moléculaires utilisables en sélection pour construire des variétés plus résistantes, unenjeu prioritaire pour la filière céréalièr

Barley soil borne mosaic viruses: Identification of predominant viruses affecting yield and malting quality, in order to orientate breeding towards a sustainable resistance

Genetic resistance is the only way to control mosaic damage in winter barley. At least 18 resistance genes are known, but until recently, rym4 was the most used by breeders to control Barley yellow mosaic virus-1 (BaYMV-1), predominant in France and Barley mild mosaic virus (BaMMV). However, since 2009, new significant damage has been observed in malting barley in a widening production area, indicating possible overcoming of resistance, with the development of BaYMV-2. The objectives of the Mosa-hordeum project were to: identify new viruses or pathotypes; develop new detection tools; confirm cultivar resistance observed in field using MB tools; confirm efficiency of resistance genes cited in literary reviews; quantify impact on yield and malting quality. A complete viral inventory was carried out 2013- 2016 on affected barley crops in 108 sites using: real-time PCR; Sanger sequencing; Next-Generation Sequencing; and serological tests. A new tool, based on derived Cleaved Amplified Polymorphic Sequences (dCAPS), developed to investigate BaYMV-1 and 2 distributions, demonstrated that BaYMV-2 is predominant (> 95%) in diseased samples. BaYMV-1 and BaMMV were also identified in co-infection with BaYMV-2 on susceptible cultivars. Comparison of yield components, malting and beer quality obtained on healthy/contaminated plots with couples of cultivars revealed variation in yield losses, up to 3t/ha, reduction in number of spikes and kernels/m², smaller kernels, slight increase in protein content and decrease of malt extract. Phylogenetic analyses indicated that the rym4 resistance-breaking ability of BaYMV-2 independently evolved on multiple occasions. In limited number of trials, rym5 resistance was overcome by a variant of BaMMV. The implantation of differentials in 21 contaminated trials confirmed the efficiency of 11 resistance genes against the BaYMV-2/BaMMV complex. To monitor BaYMV and BaMMV resistance for registration in the National List real-time PCR appears more efficient than dCAPS. These findings will help breeders achieve sustainable resistance

Barley soil borne mosaic viruses: Identification of predominant viruses affecting yield and malting quality, in order to orientate breeding towards a sustainable resistance

Genetic resistance is the only way to control mosaic damage in winter barley. At least 18 resistance genes are known, but until recently, rym4 was the most used by breeders to control Barley yellow mosaic virus-1 (BaYMV-1), predominant in France and Barley mild mosaic virus (BaMMV). However, since 2009, new significant damage has been observed in malting barley in a widening production area, indicating possible overcoming of resistance, with the development of BaYMV-2. The objectives of the Mosa-hordeum project were to: identify new viruses or pathotypes; develop new detection tools; confirm cultivar resistance observed in field using MB tools; confirm efficiency of resistance genes cited in literary reviews; quantify impact on yield and malting quality. A complete viral inventory was carried out 2013- 2016 on affected barley crops in 108 sites using: real-time PCR; Sanger sequencing; Next-Generation Sequencing; and serological tests. A new tool, based on derived Cleaved Amplified Polymorphic Sequences (dCAPS), developed to investigate BaYMV-1 and 2 distributions, demonstrated that BaYMV-2 is predominant (> 95%) in diseased samples. BaYMV-1 and BaMMV were also identified in co-infection with BaYMV-2 on susceptible cultivars. Comparison of yield components, malting and beer quality obtained on healthy/contaminated plots with couples of cultivars revealed variation in yield losses, up to 3t/ha, reduction in number of spikes and kernels/m², smaller kernels, slight increase in protein content and decrease of malt extract. Phylogenetic analyses indicated that the rym4 resistance-breaking ability of BaYMV-2 independently evolved on multiple occasions. In limited number of trials, rym5 resistance was overcome by a variant of BaMMV. The implantation of differentials in 21 contaminated trials confirmed the efficiency of 11 resistance genes against the BaYMV-2/BaMMV complex. To monitor BaYMV and BaMMV resistance for registration in the National List real-time PCR appears more efficient than dCAPS. These findings will help breeders achieve sustainable resistance