Abstract: Agricultural systems models are complex and tend to be over-parameterized with respect to observational datasets. Practical identifiability analysis based on local sensitivity analysis has proved effective in investigating identifiable parameter sets in environmental models, but has not been applied to agricultural systems models. Here, we demonstrate that identifiability analysis improves experimental design to ensure independent parameter estimation for yield and quality outputs of a complex grassland model. The Pasture Simulation model (PaSim) was used to demonstrate the effectiveness of practical identifiability analysis in designing experiments and measurement protocols within phe-notyping experiments with perennial ryegrass. Virtual experiments were designed combining three factors: frequency of measurements, duration of the experiment. and location of trials. Our results demonstrate that (i) PaSim provides sufficient detail in terms of simulating biomass yield and quality of perennial ryegrass for use in breeding, (ii) typical breeding trials are insufficient to parameterize all influential parameters, (iii) the frequency of measurements is more important than the number of growing seasons to improve the identifiability of PaSim parameters, and (iv) identifiability analysis provides a sound approach for optimizing the design of multi-location trials. Practical identifiability analysis can play an important role in ensuring proper exploitation of phenotypic data and cost-effective multi-location experimental designs. Considering the growing importance of simulation models, this study supports the design of experiments and measurement protocols in the phenotyping networks that have recently been organized.

Abstract: Crop growth simulation models can differ greatly in their treatment of key processes and hence in their response to environmental conditions. Here, we used an ensemble of 26 process-based wheat models applied at sites across a European transect to compare their sensitivity to changes in temperature (-2 to +9 degrees C) and precipitation (-50 to +50%). Model results were analysed by plotting them as impact response surfaces (IRSs), classifying the IRS patterns of individual model simulations, describing these classes and analysing factors that may explain the major differences in model responses. The model ensemble was used to simulate yields of winter and spring wheat at four sites in Finland, Germany and Spain. Results were plotted as IRSs that show changes in yields relative to the baseline with respect to temperature and precipitation. IRSs of 30-year means and selected extreme years were classified using two approaches describing their pattern. The expert diagnostic approach (EDA) combines two aspects of IRS patterns: location of the maximum yield (nine classes) and strength of the yield response with respect to climate (four classes), resulting in a total of 36 combined classes defined using criteria pre-specified by experts. The statistical diagnostic approach (SDA) groups IRSs by comparing their pattern and magnitude, without attempting to interpret these features. It applies a hierarchical clustering method, grouping response patterns using a distance metric that combines the spatial correlation and Euclidian distance between IRS pairs. The two approaches were used to investigate whether different patterns of yield response could be related to different properties of the crop models, specifically their genealogy, calibration and process description. Although no single model property across a large model ensemble was found to explain the integrated yield response to temperature and precipitation perturbations, the application of the EDA and SDA approaches revealed their capability to distinguish: (i) stronger yield responses to precipitation for winter wheat than spring wheat; (ii) differing strengths of response to climate changes for years with anomalous weather conditions compared to period-average conditions; (iii) the influence of site conditions on yield patterns; (iv) similarities in IRS patterns among models with related genealogy; (v) similarities in IRS patterns for models with simpler process descriptions of root growth and water uptake compared to those with more complex descriptions; and (vi) a closer correspondence of IRS patterns in models using partitioning schemes to represent yield formation than in those using a harvest index. Such results can inform future crop modelling studies that seek to exploit the diversity of multi-model ensembles, by distinguishing ensemble members that span a wide range of responses as well as those that display implausible behaviour or strong mutual similarities.

Abstract: Fusarium spp. belong to the division Ascomycota and cause important plant diseases; these fungi may contaminate food products with mycotoxins, endangering human and animal health. Several Fusarium spp. have been associated with potato dry rot. The most frequent and devastating of these species are F. sambucinum, F. solani and F. oxysporum, depending on the geographic location and the season. Samples of potato tubers with dry rot symptoms were collected, and their putative fungal isolates were identified as Fusarium species using partial nucleotide sequences of the internal transcribed spacer, translation elongation factor 1-α and β-tubulin genes. Among 149 isolates, 12 species were identified. F. oxysporum was the most frequent (45 % of the isolates), followed by F. avenaceum (12.1 %), F. solani (10.7 %) and F. sambucinum (7.4 %). Phylogenetic analyses confirmed the species identifications and revealed a high diversity of F. solani and a low diversity of F. oxysporum. Potential producers of zearalenone and trichothecenes were identified within the obtained isolates using PCR markers. Isolates that were pathogenic to potatoes in laboratory tests were found in four species: F. sambucinum, F. avenaceum, F. culmorum, and F. graminearum. The effects of increased temperature and mixed inoculum on the pathogenicities of chosen species were evaluated. This study adds 434 potato-derived Fusarium sequences to the NCBI GenBank database and demonstrates that the list of Fusarium species and mycotoxins present in potato tubers may be richer than previously believed, regardless of whether these species cause dry rot or live as saprophytes.