The chaos in calibrating crop models

Calibration, the estimation of model parameters based on fitting the model to experimental data, is among the first steps in many applications of system models and has an important impact on simulated values. Here we propose and illustrate a novel method of developing guidelines for calibration of system models. Our example is calibration of the phenology component of crop models. The approach is based on a multi-model study, where all teams are provided with the same data and asked to return simulations for the same conditions. All teams are asked to document in detail their calibration approach, including choices with respect to criteria for best parameters, choice of parameters to estimate and software. Based on an analysis of the advantages and disadvantages of the various choices, we propose calibration recommendations that cover a comprehensive list of decisions and that are based on actual practices.HighlightsWe propose a new approach to deriving calibration recommendations for system modelsApproach is based on analyzing calibration in multi-model simulation exercisesResulting recommendations are holistic and anchored in actual practiceWe apply the approach to calibration of crop models used to simulate phenologyRecommendations concern: objective function, parameters to estimate, software usedCompeting Interest StatementThe authors have declared no competing interest

Effects of Infection Time by Fusarium Graminearum on Ear Blight, Deoxynivalenol and Zearalenone Production in Wheat

Although it is generally agreed that most Fusarium head blight infection takes place during the wheatflowering period, very rainy conditions at the end of the plant growth, such as occurred in France in 2007,raise the question of the possibility of late infections on the development of the disease and the production oftoxins. Such infections are not taken into account by predictive models. To explore the effect of infection timeon disease severity, Fusarium-damaged kernels (FDK), desoxynivalenol (DON) and zearalenone (ZON), anexperiment was set up in 2009 on two varieties. The experiment had a split-plot design. Plots were inoculatedby spraying Fusarium graminearum conidia at different stage, from heading to ripening. Inoculation time hada significant effect on disease severity, FDK, DON and ZON levels (P<0.0001), as well as interaction betweenvariety and inoculation time. The results of this trial have shown no significant difference between infection atheading, anthesis and post-anthesis until 15 days for disease severity, FDK and mycotoxins levels. Nevertheless, this trial has suggested different behaviour between the two varieties according to infection time andtoxin accumulation. The period of high susceptibility to Fusarium graminearum has appeared unstable between varieties, ranging from closed to flowering to a large period from heading to several days after flowering

Santé des plantes dans un réseau expérimental sur des variétés de blé d’hiver rustiques : analyses de risque

Un vaste réseau d'expérimentations au champ a été conduit pendant plusieurs années à travers la France pour identifier les combinaisons de variétés cultivées de blé d'hiver et d’itinéraires techniques en vue d’atteindre le double objectif de durabilité écologique et de viabilité économique. Cet objectif implique notamment un processus d’extensification chimique, au travers duquel les intrants chimiques, dont les fongicides, sont réduits pour optimiser les performances, notamment économiques, de la production végétale. Peu d’informations sont disponibles pour documenter, dans ce réseau, la variation des niveaux de maladie multiples. Le contrôle des niveaux de maladies constitue pourtant une étape nécessaire à un processus d’extensification chimique. Cet article fournit une description des intensités des maladies du blé dans un ensemble de 101 expérimentations totalisant 3525 parcelles individuelles de blé, pendant huit années successives (2003-2010). Les maladies considérées sont la rouille brune (BR, Puccinia triticina), la rouille jaune (YR, Puccinia striiformis), la fusariose des épis (FHB, Fusarium graminearum, F. culmorum, et F. avenaceum), l’oïdium (PM, Blumeria graminis), et la septoriose (STB, Zymoseptoria tritici). Les intensités de maladies ont été représentées par des variables binaires (épidémie ou non-épidémie). Trois syndromes de maladies ont été identifiés, qui correspondent à des profils de niveau de maladie distincts. Trois groupes de variétés ont également été identifiés, qui se distinguent par leurs réponses aux maladies. Les résultats indiquent que les années climatiques, les variétés de blé et les itinéraires techniques, dans cet ordre décroissant, définissent le risque d’épidémie dans le pathosystème multiple des maladies du blé en France. Des variables synthétiques prenant en compte le climat au printemps et au début de l’été ont été construites. Les associations entre variables climatiques et risques d’épidémies identifiées sont en accord avec les connaissances sur les effets du climat sur les composants de ce pathosystème multiple. Cet article met en avant la valeur de jeux de données à grande échelle pour l’évaluation de la santé végétale et l’utilité d’une démarche analytique permettant d’identifier les facteurs de risques pour les décisions tactiques et stratégiques, pour la gestion de la santé végétale.A large network of field experiments has been conducted over several years across France to identify combinations of winter wheat cultivars and management leading to achieve the double objective of ecological sustainability and economic viability. Little information is available to document the variation in multiple disease levels, a necessary step towards a chemical extensification process, in wheat networked experiments. This article provides a description of disease intensities in a set of 101 experiments totalling 3525 individual wheat plots over eight successive years (2003–2010). The diseases considered are brown rust (BR, Puccinia triticina), yellow rust (YR, Puccinia striiformis), fusarium head blight (FHB, Fusarium graminearum, F. culmorum, and F. avenaceum), powdery mildew (PM, Blumeria graminis), and septoria tritici blotch (STB, Zymoseptoria tritici). Disease intensities were represented by binary variables (epidemic vs non-epidemic), and three disease syndromes were identified, which correspond to different disease profiles. Three variety groups were also identified, according to their responses to diseases. The results indicate that climatic years, wheat varieties, and crop management, in this decreasing order, define disease epidemic risk in the multiple wheat-diseases pathosystem. The associations between climate variables and epidemic risks identified here conform to disease-specific knowledge of climate effects on the components of the pathosystem. This report emphasises the value of large scale data in crop health assessment and the usefulness of a risk factor approach for both tactical and strategic decisions for crop health management

Contamination of durum wheat by cadmium : lessons from the field

Contamination of food crops by cadmium (Cd) is a major concern, particularly for durum wheat, which is widely consumed and which accumulates this toxic metal to a greater extent than bread wheat. Following the assessment of the risks to human health related to the presence of cadmium in foodstuffs, the European Commission intended to reduce the maximum content of Cd in wheat from 0.2 to 0.1 mg/kg grain. France is in the top 5 of European countries for the production of durum wheat and the project of a lower regulation limit for Cd stressed the urgent need i) to characterize the risk that harvests could exceed the new limit, ii) to identify, in the field, the major factors controlling the level of contamination. For that purpose, a specific project 'Cadur' was conducted between 2011 and 2014 in France. Samples of grains were collected in 2011, 2012 and 2013 among farmers of the different areas of production. The median value of Cd in durum wheat grain was 0.07 mg/kg with less than 5% of samples above the 0.2 mg/kg limit but 25% above 0.1 mg/kg (n=244). However, there were strong variations depending on the geographical areas and for some of them, up to 60% of the samples exceeded 0.1 mg Cd /kg. In order to understand the source of these variations, trials crossing cultivars and the areas of production were investigated. The cultivars were estimated to be responsible of 10-25% of the variation of the grain Cd concentration against 60-70% for the location of the culture. The effect of the location was mainly due to the concentration of Cd in the soil and to the soil pH. A statistical model with these two explanatory variables was able to explain 57% of the variability of the Cd concentration in the grains. Some of the durum wheat cultivars commonly grown in France were assessed with respect to their ability to accumulate Cd. It was found that the high:low ratio for the Cd content in grains was around 1.5 when cultivars were grown on the same soils. Contrary to Canadian cultivars, in France, no specific genetic selection has yet been performed to lower the contamination by Cd. Nitrogen fertilization was shown to have a significant effect, both by the dose and by the timing of application, presumably by modifying the mobility of Cd in the soil. Increasing N supply from 200 to 250 kg N/ha increased the Cd in grains by 20% and by 25% if the total N reached 300 kg N/ha. However, if the additional N was applied as two applications including a late one instead of a single dose, the increase in the grain contamination was not significant for a total of 250 kg N/ha. These studies confirm that both the soil conditions (Cd content, pH) and the cultivars are key points for controlling the contamination of durum wheat by Cd. French cultivars have the potential to be genetically selected to improve their ability to exclude Cd from the grain. They also have to be carefully chosen depending on the local bioavailability of Cd in soil, which can be in part, managed by controlling the pH and the nitrogen fertilisation. Funded by the projects 'Cadur', Arvalis-Inra and ANR-15-CE21-0001-04 'Cadon

Assessing plant health in a network of experiments on hardy winter wheat varieties in France: patterns of disease-climate associations

International audienceA data set generated by a multi-year (2003 – 2010) and multi-site network of experiments on winter wheat varieties grown at different levels of crop manage- ment is analysed in order to assess the importance of climate on the variability of wheat health. Wheat health is represented by the multiple pathosystem involving five components: leaf rust, yellow rust, fusarium head blight, powdery mildew, and septoria tritici blotch. An overall framework of associations between multiple diseases and climate variables is developed. This framework involves disease levels in a binary form (i.e. epidemic vs. non- epidemic) and synthesis variables accounting for climate over spring and early summer. The multiple disease- climate pattern of associations of this framework con- forms to disease-specific kn owledge of climate effects on the components of the pathosystem. It also concurs with a (climate-based) risk factor approach to wheat diseases. This report emphasizes the value of large scale data in crop health assessment and the usefulness of a risk factor approach for both tactical and s trategic decisions for crop health management

Assessing plant health in a network of experiments on hardy winter wheat varieties in France: multivariate and risk factor analyses

International audienceA large network of field experiments has been conducted over several years across France to identify combinations of winter wheat cultivars and management practices in which partial resistances under limited chemical protection would achieve adequate disease management, while leading to satisfactory yield performance, and so achieve the double objective of ecological sustainability and economic viability. Little information is available to document the variation in multiple disease levels, a n ecessary step towards a chemical extensification process, in wheat networked experiments. This article provides a description of dis- ease intensities in a set of 101 experiments totalling 3525 individual wheat plots over eight successive years (2003 – 2010). The diseases considered are brown rust (BR, Puccinia triticina ), yellow rust (YR, Puccinia striiformis ), fusarium head blight (FHB, Fusarium graminearum , F. culmorum ,and F. avenaceum ), pow- dery mildew (PM, Blumeria graminis ), and septoria tritici blotch (STB, Zymoseptoria tritici ). Hierarchical cluster analysis led to the identification of three variety groups associated with (1) moderate-low disease levels in general, except for YR (moderate levels) – 16 varie- ties; (2) moderate-low BR, YR, and FHB levels, and moderate PM and STB levels – 12 varieties; (3) com- paratively higher BR, YR, FHB, and STB levels, and moderate PM levels – 17 varieties. The association of disease levels represented as binary categories (i.e., epidemics vs. non-epidemics) with climatic years corresponded to chi-square values ( χ 2 =87.0 – 1402) that were one to two orders of magnitude larger than the values corresponding to the associations of diseases with variety groups ( χ 2 =6.41 – 321) or with levels of crop management ( χ 2 =21.2 – 82.1). Multivariate non parametric analyses indicated the existence of three disease syndromes, two of which being dominated by BR or STB, and a third associated with diverse diseases and frequent FHB. This suggests that STB and BR might each be considered as key-stone species dominat- ing specific wheat disease syndromes. Multiple corre- spondence analysis highlighted the linkages between multiple epidemic occurrence and the three character- ized variety groups. Risk factors analyses conducted through logistic regressions provided quantitative estimates of the contribution of climatic years, variety groups, and crop management, to the likelihood of epidemic occurrence for each of the five diseases considered. The results indicate that climatic years, wheat varieties, and crop management, in this decreasing order, define disease epidemic risk in the multiple wheat-diseases pathosystem

Deposition patterns of Fusarium graminearum ascospores and conidia within a wheat canopy

Fusarium graminearum is the most important species in the fungal complex causing Fusarium head blight of small grain cereals. The fungus produces two types of spores on crop residues (ascospores and conidia), which are dispersed to ears by air currents and rain splashes, respectively. The distribution patterns of ascospores and conidia within a wheat canopy between booting and grain maturity were assessed by using leaflike spore traps placed at 10, 30, and 60 cm height, and ear-like spore traps at 90 cm height. Maize residues were the inoculum source for both ascospores and conidia within the wheat plot. Of the total spores counted, 93 % were ascospores and 7 % were conidia. Approximately 41, 22, 19, and 18 % of the ascospores, and 77, 10, 8, and 5 % of the conidia were sampled at 10, 30, 60, and 90 cm height, respectively. Ascospore numbers did not significantly differ between those sampled on the upper or the lower sides of the leaf-like traps or among the four orientations (north, south, east, or west) of the ear-like traps. According to the index of dispersion (D), the spatial distribution of trapped ascospores was largely random (i.e., D≤1) rather than aggregated (i.e., D>1). The collective results (averaged across all traps and sampling periods) showed that the random distribution of the ascospores within the wheat canopy and at the ear level was associated with a clear vertical distribution pattern indicating an upward movement of ascospores from the maize residues on the ground

Predictive statistical modelling of cadmium content in durum wheat grain based on soil parameters

Regulatory limits on cadmium (Cd) content in food products are tending to become stricter, especially in cereals, which are a major contributor to dietary intake of Cd by humans. This is of particular importance for durum wheat, which accumulates more Cd than bread wheat. The contamination of durum wheat grain by Cd depends not only on the genotype but also to a large extent on soil Cd availability. Assessing the phytoavailability of Cd for durum wheat is thus crucial, and appropriate methods are required. For this purpose, we propose a statistical model to predict Cd accumulation in durum wheat grain based on soil geochemical properties related to Cd availability in French agricultural soils with low Cd contents and neutral to alkaline pH (soils commonly used to grow durum wheat). The best model is based on the concentration of total Cd in the soil solution, the pH of a soil CaCl2 extract, the cation exchange capacity (CEC), and the content of manganese oxides (Tamm's extraction) in the soil. The model variables suggest a major influence of cadmium buffering power of the soil and of Cd speciation in solution. The model successfully explains 88% of Cd variability in grains with, generally, below 0.02 mg Cd kg(-1) prediction error in wheat grain. Monte Carlo cross-validation indicated that model accuracy will suffice for the European Community project to reduce the regulatory limit from 0.2 to 0.15 mg Cd kg(-1) grain, but not for the intermediate step at 0.175 mg Cd kg(-1). The model will help farmers assess the risk that the Cd content of their durum wheat grain will exceed regulatory limits, and help food safety authorities test different regulatory thresholds to find a trade-off between food safety and the negative impact a too strict regulation could have on farmers

Blé dur : freiner l’accumulation de cadmium dans les grains

National audienceDes travaux menés par l’INRA et ARVALIS - Institut du végétal tentent de mettre en lumière les mécanismes impliqués dans le transfert du cadmium du sol jusqu’aux grains de blé dur. Ces avancées devraient aboutir à l’élaboration d’un modèle de prédiction du risque contre ce contaminant et de stratégies de réduction des contaminations à moyen terme

Blé dur : freiner l’accumulation de cadmium dans les grains

National audienceDes travaux menés par l’INRA et ARVALIS - Institut du végétal tentent de mettre en lumière les mécanismes impliqués dans le transfert du cadmium du sol jusqu’aux grains de blé dur. Ces avancées devraient aboutir à l’élaboration d’un modèle de prédiction du risque contre ce contaminant et de stratégies de réduction des contaminations à moyen terme