Pest and pathogen losses jeopardise global food security and ever since the 19th century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.

Factors affecting the severity of leaf blotch on the two upper leaves of wheat plants in crops at the milky ripe growth stage (GS 73-75) were investigated using survey data from 3513 randomly selected wheat crops sampled during 1985-1996. Year-to-year variation in disease severity was greater than spatial variability at county level, although both showed significant differences. The presence of disease above a 5% severity threshold was modelled using random effects logistic regression (Generalised Linear Mixed Model), which enabled risk variables measured at the field level to be combined with meteorological variables estimated at county level. The final model included terms for the fixed effects of disease resistance rating, date of sowing, high risk septoria periods in May and June, number of fungicide sprays and number of days with frost (£ -2°C) in November. The percentage of crops above the threshold decreased with later sowing, increased number of November frost days and increased number of fungicide sprays. In contrast, high risk septoria periods (rain splash events) in May and June showed a positive correlation with the percentage of crops above the threshold. There were benefits from using resistant cultivars. The model showed that a range of risk variables were of broadly equivalent importance in determining the development of leaf blotch. These risk variables should be integrated in any scheme designed to support fungicide use decisions.

No abstract

In continuation of the annual national surveys of winter wheat, which began in 1970, samples from between 250 and 350 randomly selected wheat crops in England and Wales between 1999 to 2019 were visually assessed for disease symptoms during the milky ripe development stages (GS 73–75). Septoria tritici blotch was the most prevalent and severe foliar disease each year, although annual levels fluctuated considerably and there was no overall significant change over the two decades. Incidence of brown rust, yellow rust, take‐all, and barley yellow dwarf virus also showed no significant overall change during the survey period, whereas glume blotch, powdery mildew, eyespot, and sharp eyespot all showed significant decline. Fusarium ear blight has significantly increased in both incidence and severity, causing a serious epidemic in 2012, when 96% of crops were affected. Tan spot has been the third most prevalent foliar disease since 2009 although severity is still very low. Regional disease levels were consistent over the two decades, providing reliable baselines to measure changes in seasonal disease severity. There were significant changes in agronomic practice with a rise to predominance of minimum tillage over the use of ploughing, decreases in overall disease susceptibility of cultivars grown, a major increase in the use of oilseed rape in the rotation and a long‐term trend towards earlier sowing. Fungicide use increased considerably, with over 98% crops sprayed and an average of 3.5 applications made per crop each year since 2014. Implications of changes over the last 21 years are discussed.

Disease survey data from 4475 randomly selected crops of wheat from England and Wales during 1985-2000 showed that yellow rust was most prevalent in 1988, 1989, 1990, 1998 and 1999. Disease severity on the upper two leaves was low as >95% crops had received foliar fungicides. Factors affecting the presence or absence (incidence) of yellow rust were investigated using random effects logistic regression (general linear mixed model). This enabled crop management (risk) variables for individual crops to be combined with meteorological variables measured at the county level. Two models are presented that analysed the effect of host genotype on incidence either solely through yellow rust resistance rating (Model 1) or by including both resistance rating (fixed effect) and cultivar (fitted as a random term) (Model 2). In both models, the percentage of crops with yellow rust decreased with cultivar disease resistance ratings !3, the occurrence of severe frosts (<25°C), use of systemic seed treatment and application of foliar fungicide sprays. There were no significant effects (P < 0.05) of timing of fungicide sprays, previous cropping or summer weather. The use of risk variables associated with overwintering survival may help adjust fungicide inputs to seasonal risk.