Crop diseases affect crop yield and quality and cause significant losses of total food production worldwide. With the ever‐increasing world population and decreasing land and water resources, there is a need not only to produce more food but also to reduce agricultural greenhouse gas (GHG) emissions to mitigate climate change and avoid land use change and biodiversity loss. Thus, alternative climate‐smart farming systems need to adapt to produce more food per hectare in a more sustainable way than conventional high‐input farming systems. In addition to breeding new high‐yielding cultivars adapted to future climates, there is a need to deploy Integrated Crop Management (ICM) strategies, relying less on synthetic inputs for fertilization and crop protection and less on fossil fuel‐powered machinery to decrease yield losses due to pest and pathogens and guarantee food security. In this review, we compare some low‐input farming systems to conventional agricultural systems with a focus on ICM solutions being developed to reduce synthetic inputs; these include crop genetic resistance to pathogens, intercropping, canopy architecture manipulation, and crop rotation. These techniques have potential to decrease crop disease frequency and severity by decreasing amounts and dispersal of pathogen inoculum and by producing microclimates that are less favourable for pathogen development, while decreasing GHG emissions and improving environmental sustainability. More research is needed to determine the best deployment of these ICM strategies in various cropping systems to maximize yield, crop protection, and other ecosystem services to address trade‐offs between climate change and food security.

To reduce the use of pesticides, innovative studies have been developed to introduce the plant as the centre of the crop protection system. The aim of this paper is to explain how architectural traits of plants and canopies induce a more or less severe epidemic and how they may be modified in order to reduce disease development. In particular, it focuses on three key questions: i) which processes linked to epidemics can be influenced by architecture ii) how can architecture be characterized relative to these modes of action, and iii) how can these effects be explored and exploited? The roles of plant/canopy architecture on inoculum interception, on epidemic development via the microclimate and on tissue receptivity are discussed. In addition, the concepts of disease avoidance, canopy porosity and an ideotype unfavourable for disease development are described. This paper shows that many advances have already been made, but progress is still required in four main fields: microclimatology, mathematical modelling of plants, molecular genetics and ideotype conception.

Surveillance investigations for pathogenic and toxigenic fungi are important to refine our understanding of their epidemiology and help in predicting their outbreaks. During 2019, 198 samples of wheat grains were collected from 25 wheat-growing governorates in Egypt to detect and identify seed-borne mycoflora in vitro. Forty-four fungal species belonging to 20 genera were identified. Molecular data for these fungi were analyzed to construct a phylogenetic tree. Occurrence and biodiversity indicators were calculated. Two prevalent pathogens (average incidence > 40%) were Alternaria alternata and Cladosporium spp. Ustilago tritici was present in only seven of the 25 governorates, and less abundant than Tilletia tritici, the causal agent of stinking smut. Sinai governorate recorded the greatest species diversity, while the greatest species richness was in Qena and Sohag governorates. Canonical correspondence analysis of data for 20 fungal genera with temperature, relative humidity, precipitation, wind speed or solar radiation revealed that relative humidity was the most influential weather variable. It showed that occurrence and distribution of the 20 genera corresponded well with three out of four Egyptian climatic regions: Mediterranean, semi-arid, and arid. Knowing pathogen occurrence and distribution in Egypt is the first step to developing future disease management strategies to limit yield losses and improve food security. Despite this study being conducted on the wheat-growing areas in Egypt, our findings are useful for other wheat-growing countries that share the same climatic conditions. The correlation between a given fungus and the climatic variables can be useful in other ecosystems.