Rotating crop cultivars with different resistance genes could slow the evolution of virulent strains of fungal pathogens, but could also produce highly virulent pathogen strains. We present a new model that links polycyclic pathogen epidemiology and population genetics in order to predict how different strategies of rotating cultivars with different resistances will affect the evolution of pathogen virulence and the breakdown of crop resistance. We modelled a situation where there were four different resistance genes that can be deployed within each crop cultivar, and four virulence genes that may be present within the pathogen. We simulated four different rotational management strategies: (i) no rotation; (ii) a different gene every year; (iii) a different gene every 5 years; and (iv) a different combination of two stacked genes each year. Results indicate that rotating cultivars can lead to longer periods of disease suppression but also to the selection of highly virulent strains. The efficacy and relative advantage of different resistant cultivar rotation strategies depended on the fitness penalties, initial virulence allele frequencies, and ability of non-virulent pathogen genotypes to grow and reproduce on resistant cultivars. By capturing the essential processes involved, our model provides a useful new tool for investigating the evolutionary dynamics of pathogen virulence and crop resistance breakdown.

We consider a spatio-temporal 1 model to describe the spread of apple scab within an orchard composed of several plots. The model is defined on a regular lattice and evolves in continuous time. Based on ordinal categorical data observed only at some discrete instants we adopt a continuous time approach and apply a Bayesian method for estimating unknown parameters.

Plant pathogenic fungi cause severe damage, widespread losses, and are challenging to manage. Control strategies rely on fungicides, deep tillage of the crop residues, use of resistant cultivars, and crop management (specific sowing period, crop rotations). Farmers must yearly allocate fields to different crops and choose among these crop management options. Far from being obvious, these decisions are critical because they modify farm productivity and profitability in the short and long run. We built a new model specifically to address the issues described above. The first version of the model describes the population dynamics of a fungal pathogen over a large agronomic region comprising a number of fields in which both susceptible and neutral (non-susceptible) crops are grown. We compared different rates of rotations to see what rotation strategies were optimal in maximising non-infected susceptible crop area and minimising infected crop area. Then we adapted the model to investigate the case where three different crops can be used in the landscape, one non-susceptible crop, one susceptible host crop with low resistance and one susceptible host crop with high resistance. Our results showed that for a wide majority of cases, the configuration where we rotated infested fields into neutral fields at a faster rate than we rotated neutral fields back into susceptible crop gave better yield overall by reducing fungal incidence.