François Bussière

An overview of the crop model stics

Abstract stics is a model that has been developed at INRA (France) since 1996. It simulates crop growth as well as soil water and nitrogen balances driven by daily climatic data. It calculates both agricultural variables (yield, input consumption) and environmental variables (water and nitrogen losses). From a conceptual point of view, stics relies essentially on well-known relationships or on simplifications of existing models. One of the key elements of stics is its adaptability to various crops. This is achieved by the use of generic parameters relevant for most crops and on options in the model formalisations concerning both physiology and management, that have to be chosen for each crop. All the users of the model form a group that participates in making the model and the software evolve, because stics is not a fixed model but rather an interactive modelling platform. This article presents version 5.0 by giving details on the model formalisations concerning shoot ecophysiology, soil functioning in interaction with roots, and relationships between crop management and the soil–crop system. The data required to run the model relate to climate, soil (water and nitrogen initial profiles and permanent soil features) and crop management. The species and varietal parameters are provided by the specialists of each species. The data required to validate the model relate to the agronomic or environmental outputs at the end of the cropping season. Some examples of validation and application are given, demonstrating the generality of the stics model and its ability to adapt to a wide range of agro-environmental issues. Finally, the conceptual limits of the model are discussed.

Modification of the soil temperature and water content regimes by a crop residue mulch: experiment and modelling

Abstract Unchopped crop residues are widely used in the tropics for reducing erosion or soil temperature and for soil water conservation. Quantitative estimation of the mulch influence on the mass and energy exchanges between the soil and the atmosphere is necessary for assessing the positive or negative mulch effects. A mechanistic model of heat and water transfer at hourly time intervals in a soil-mulch system was developed. Soil temperature and water content changes were simulated with a coupled heat and mass transfer model. Radiative and convective exchanges in the mulch were simulated as in plant canopies. The model also deals with rain interception processes. An experiment was performed to estimate how the mulch changes the soil conditions and to validate this model. Soil temperature, water content, and energy fluxes were measured over a mulched and unmulched plot. Experimental results showed that the mulch reduced soil evaporation, and soil temperature (average and amplitude). The model was calibrated by fitting only one mulch parameter. This allowed a correct simulation of the thermal exchanges in the soil. More accurate simulation of diffusive transfers through the mulch would need further investigations. Simulations are made to study the influence of the mulch leaf area index (LAI) on soil water content and temperature. An LAI of 4.0 limits more evaporation but intercepts more rainfall than an LAI of 1.0 which is consequently more efficient for soil water conservation. On the other hand, the mulch with the highest LAI has better insulating properties and is more useful to prevent soil heating.

Modelling evapotranspiration partitioning in a shrub/grass alley crop

Improving intercropping requires a thorough understanding of resource, particularly water, between the plant species. Evaporative demand was modelled for the soil and the components of a shrub/grass intercrop planted in rows, by determining the energy balance of each component and by distinguishing between sunlit and shaded foliage. Modelling was based on a light partitioning model and micrometeorological data from the canopy. Stomatal conductance, necessary for estimating transpiration, was modelled as a function of photosynthetically active radiation (PAR). This enabled the validation of the model with evapotranspiration measurements in the field, during 10 days. There was a good agreement between the measured and estimated fluxes, for both the soil/grass layer and shrubs (r2 = 0.95). The difference, less than 10% at a daily scale, between the measurements and the model was due to the difficulty in estimating the flux transfer resistances, ie stomatal and aerodynamic. The model enables the analysis of the influence of microclimate changes due to shrub development on grass transpiration.

Direct Splash Dispersal Prevails over Indirect and Subsequent Spread during Rains in Colletotrichum gloeosporioides Infecting Yams

Plant pathogens have evolved many dispersal mechanisms, using biotic or abiotic vectors or a combination of the two. Rain splash dispersal is known from a variety of fungi, and can be an efficient driver of crop epidemics, with infectious strains propagating rapidly among often genetically homogenous neighboring plants. Splashing is nevertheless a local dispersal process and spores taking the droplet ride seldom move farther than a few decimeters. In this study, we assessed rain splash dispersal of conidia of the yam anthracnose agent, Colletotrichum gloeosporioides, in an experimental setting using a rain simulator, with emphasis on the impact of soil contamination (i.e., effect of re-splashing events). Spores dispersed up to 50 cm from yam leaf inoculum sources, though with an exponential decrease with increasing distance. While few spores were dispersed via re-splash from spore-contaminated soil, the proportion deposited via this mechanism increased with increasing distance from the initial source. We found no soil contamination carryover from previous rains, suggesting that contamination via re-splashing from contaminated soils mainly occurred within single rains. We conclude that most dispersal occurs from direct splashing, with a weaker contribution of indirect dispersal via re-splash.

Varietal Dynamics and Yam Agro-Diversity Demonstrate Complex Trajectories Intersecting Farmers’ Strategies, Networks, and Disease Experience

Loss of varietal diversity is a worldwide challenge to crop species at risk for genetic erosion, while the loss of biological resources may hinder future breeding objectives. Loss of varieties has been mostly investigated in traditional agricultural systems where variety numbers are dramatically high, or for most economically important crop species for which comparison between pre-intensive and modern agriculture was possible. Varietal dynamics, i.e., turnover, or gains and losses of varieties by farmers, is nevertheless more rarely studied and while we currently have good estimates of genetic or varietal diversity for most crop species, we have less information as to how on farm agro-diversity changes and what cause its dynamics. We therefore investigated varietal dynamics in the agricultural yam system in the Caribbean island of Guadeloupe. We interviewed producers about varieties they cultivated in the past compared to their current varieties, in addition to characterizing yam cropping characteristics and both farm level and producers socio-economic features. We then used regression tree analyses to investigate the components of yam agro-diversity, varietal dynamics and impact of anthracnose on varieties. Our data demonstrated that no dramatic loss of varieties occurred within the last decades. Cultivation changes mostly affected widespread cultivars while frequency of uncommon varieties stayed relatively stable. Varietal dynamics nevertheless followed sub-regional patterns, and socio-economic influences such as producer age or farm crop diversity. Recurrent anthracnose epidemics since the 1970s did not alter varietal dynamics strongly, but sometimes translated into transition from Dioscorea alata to less susceptible species or into a decrease of yam cultivation. Factors affecting changes in agro-diversity were not relating to agronomy in our study, and surprisingly there were different processes delineating short term from long term varietal dynamics, independently of disease risk. Our results highlighted the importance of understanding varietal dynamics, an often overlooked component of agriculture sustainability, in addition to evolutionary forces shaping agro-diversity and genetic diversity distribution within crops. It is also crucial to understand how processes involved do scale up worldwide and for different crop species, so as not to mislead on-farm conservation efforts and efficacy of agro-diversity preservation.

Data on microsatellite markers in Colletotrichum gloeosporioides s.l., polymorphism levels and diversity range

Colletotrichum gloeosporioides is a species complex of fungi belonging to the Glomerellaceae family (Ascomycota). It has a global worldwide occurrence and while sometimes described as a plant endophytic commensal, it also often demonstrates pathogenicity on crops and is responsible for anthracnose disease in many cultivated species. Thirty-nine polymorphic microsatellites were isolated and their polymorphism levels were determined in 95 strains from Guadeloupe (Lesser Antilles), mostly isolated from Water Yam (Dioscorea alata). The average allele number per polymorphic locus was 12.3 (decreasing to 4.3 at 5% frequency threshold, indicative of dramatic amounts of rare polymorphisms), with a range of 2–29 alleles. The microsatellite markers data will facilitate genetic diversity analyses and population genetics studies for the species complex.