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.

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.

The Rlm7 gene in Brassica napus is an important source of resistance for control of phoma stem canker on oilseed rape caused by the fungus Leptosphaeria maculans . This study shows the first report of L. maculans isolates virulent against Rlm7 in the UK . Leptosphaeria maculans isolates virulent against Rlm7 represented 3% of the pathogen population when cultivars with the Rlm7 gene represented 5% of the UK oilseed rape area in 2012/13. However, the Rlm7 gene has been widely used since then, representing >15% of the UK oilseed rape area in 2015/16. Winter oilseed rape field experiments included cultivars with the Rlm7 gene, with the Rlm4 gene or without Rlm genes and took place at five sites in the UK over four cropping seasons. An increase in phoma leaf spotting severity on Rlm7 cultivars in successive seasons was observed. Major resistance genes played a role in preventing severe phoma leaf spotting at the beginning of the cropping season and, in addition, quantitative resistance ( QR ) in the cultivars examined made an important contribution to control of phoma stem canker development at the end of the cropping season. Deployment of the Rlm7 resistance gene against L. maculans in cultivars with QR in combination with sustainable disease management practices will prolong the use of this gene for effective control of phoma stem canker epidemics.

Minnesota and North Dakota combined contain 55% of the sugar beet production area in the United States, contributing to 49% of the nation’s sugar beet production in 2018. Fusarium diseases caused by Fusarium oxysporum f. betae and F. secorum on sugar beet can cause significant reduction in both root yield and sucrose concentration and purity. The objective of this research was to identify an alternative artificial inoculation method to induce Fusarium diseases on sugar beet leaves and roots caused by both Fusarium spp. in greenhouse conditions to better aid in research efforts. We tested four inoculation methods, including barley to seed, barley to root, drenching, and cutting. and compared them with the conventional root-dipping inoculation method. The inoculation method of placing Fusarium-colonized barley seed close to sugar beet seed (barley to seed) caused levels of symptom severities on both leaves and roots similar to the root-dipping method. Because the traditional root-dipping method involves a laborious transplant process, use of infected barley seed as inoculum may serve as an alternative method in the evaluation of host resistance and pathogen virulence among Fusarium diseases by Fusarium spp. on sugar beet at the seed or seedling stage.

Studies of the biodiversity of plant pathogenic and toxigenic fungi are attracting great attention to improve the predictability of their epidemics and the development of their control programs. Two hundred maize grain samples were gathered from 25 maize-growing governorates in Egypt and 189 samples were processed for the isolation and identification of seed-borne fungal microbiome. Twenty-six fungal genera comprising 42 species were identified according to their morphological characteristics and ITS DNA sequence analysis. Occurrence and biodiversity indicators of these fungal species were calculated. Ustilago maydis, Alternaria alternata, Aspergillus flavus, A. niger, Penicillium spp., Cladosporium spp. and Fusarium verticillioides were the highly frequent (>90% for each), recording the highest relative abundance (˃50%). Al-Menia governorate showed the highest species diversity and richness, followed by Sohag, Al-Nobaria and New Valley governorates. Correlations of 18 fungal species with temperature, relative humidity, precipitation, wind speed, and solar radiation were analyzed using canonical correspondence analysis. Results showed that relative humidity, temperature, and wind speed, respectively, were the most impactful weather variables. However, the occurrence and distribution of these fungi were not clearly grouped into the distinctive climatic regions in which maize crops are grown. Monitoring the occurrence and distribution of the fungal pathogens of maize grains in Egypt will play an important role in predicting their outbreaks and developing appropriate future management strategies. The findings in this study may be useful to other maize-growing countries that have similar climatic conditions.

Pyrenopeziza brassicae , cause of light leaf spot (LLS), is an important pathogen of oilseed rape and vegetable brassicas and has a wide geographic distribution. Exploitation of host resistance remains the most sustainable and economically viable solution for disease management. This study evaluated 18 oilseed rape cultivars or breeding lines for host resistance against P . brassicae in glasshouse experiments. Selected cultivars/lines were inoculated with eight single‐spore isolates of the pathogen obtained from three different regions in England. Analysis of P . brassicae infection‐related changes on host plants identified leaf deformation as a characteristic feature associated with P . brassicae infection, this showed poor correlation to LLS severity measured as the amount of pathogen sporulation on infected plants. Resistant host phenotypes were identified by limitation of P . brassicae sporulation, with or without the presence of a necrotic response (black flecking phenotype). Investigation of this pathosystem revealed significant differences between cultivars/lines, between isolates, and significant cultivar/line‐by‐isolate interactions. In total, 37 resistant and 16 moderately resistant interactions were identified from 144 cultivar/line‐by‐isolate interactions using statistical methods. Most of the resistant/moderately resistant interactions identified in this study appeared to be nonspecific towards the isolates tested. Our results suggested the presence of isolate‐specific resistant interactions for some cultivars. Several sources of resistance have been identified that are valuable for oilseed rape breeding programmes.