BGRI 2025 Technical Workshop

Abstract:
An overview of the current status of wheat disease surveillance and early warning will be outlined. Key highlights of work in East Africa and South Asia will be the focus. The current operational early warning system for globally important wheat diseases (wheat rusts, wheat blast, FHB) will be described. The success of the system in detecting emerging new threats to wheat production will be outlined, along with new advances in diagnostics, forecasting and risk assessment. Current knowledge on the emergence and interchange of pathogens between different geographical regions will be highlighted.

Abstract:
Wheat diseases pose recurring threats to food security due to factors including climate change, land use change, and emerging virulent strains. Rapid response to a wheat disease outbreak requires a timely and accurate estimate of disease risk. Building on a century of literature, over a decade of research, and years of development in pilot studies, a Wheat Disease Early Warning and Advisory System (DEWAS) is now in operation for eight countries in Africa and South Asia. One component of the interconnected and collaborative DEWAS project is the risk forecasting of wheat diseases, including the wheat rusts and wheat blast. At the core of the forecasting system are components for meteorologically driven aerobiological spore release and dispersal from known sites of infection, environmental suitability conditions for infection for stem, stripe and leaf rust and an integrated epidemiological model for stem rust. Near real-time ground surveys are uploaded automatically by trained personnel as input to initiate the models and accessed via the Wheat Rust Toolbox. State-of-the-art seven-day weather forecasts for target countries are provided by the UK Met Office, from which daily forecasts of wheat rust risks are calculated. Forecasting is also expanding to include wheat blast in Africa. Key to making the system sustainable and adaptable are capacity building through training and modular software development. Evaluation shows that integrating near real-time surveys and modelling long-distance spore dispersal improves prediction accuracy. The flexible framework can also be applied to other airborne plant diseases.

About the Speaker:
Jacob Smith is a postdoctoral research associate in the Epidemiology & Modelling Group led by Prof Chris Gilligan at the Department of Plant Sciences, University of Cambridge in the United Kingdom. With a background in climate science, he is interested in the interactions of plant disease and climate, particularly aerial dispersal.

Abstract:
Ethiopia, the largest wheat producer in Sub-Saharan Africa, encounters considerable challenges from wheat diseases that threaten food security and agricultural sustainability. Wheat serves as a critical staple crop in Ethiopia, playing a significant role in food security and the national economy. However, its production is often affected by several diseases, such as rusts, fusarium head blight, and septoria. Research efforts in Ethiopia have made notable progress in understanding, managing, and mitigating these challenges. Key advancements encompass the release of over 115 bread wheat and 47 durum wheat varieties via breeding programs, with a particular focus on managing rust diseases, which are the most destructive. Collaborative initiatives among Ethiopian research institutions and international organizations, including CIMMYT and ICARDA, have accelerated the advancement of high-yielding, disease-resistant cultivars. Furthermore, research on disease epidemiology has enhanced the Wheat Rust Early Warning System (EWS), enabling timely interventions. The system has been providing an automatic seven-day forecast risk map along with weekly advisories and alerts. Integrated disease management strategies that incorporate resistant varieties, cultural practices, and fungicide applications have been promoted to enhance sustainable wheat production. Despite these achievements, challenges persist, including the emergence of new pathogen strains (stem rust and yellow rust races), re-emerging diseases such as fusarium head blight, limited access to improved seeds for smallholder farmers, and weakness in extension services. Ongoing research emphasizes the need for continuous surveillance, developing multi-disease resistant wheat varieties, farmer education, and investment in modern technologies to ensure long-term resilience against wheat diseases in Ethiopia.

Abstract:
Wheat blast, caused by Magnaporthe oryzae pathotype Triticum (MoT), is an emerging and highly destructive disease in global wheat production. Previously confined to South America—especially Brazil, Paraguay, and Bolivia—MoT had not been reported in Uruguay until the 2023 season. That year, unusually favorable weather conditions in northwestern Uruguay, similar to those associated with outbreaks in Brazil, triggered intensive disease surveillance. Seventeen wheat spike samples showing blast-like symptoms were collected from 11 fields; nine tested positive for M. oryzae based on morphological traits. Four monosporic isolates were recovered, and three underwent molecular and genomic analyses. PCR confirmed their identity as MoT, and pathogenicity assays showed that all could infect both leaves and spikes of susceptible wheat genotypes. Whole-genome sequencing and phylogenetic analysis of 57 M. oryzae strains—spanning Triticum, Lolium, and Eleusine hosts—revealed that the Uruguayan strains are closely related to some Brazilian MoT isolates but genetically distinct from the B71 lineage implicated in Asia and Africa. Notably, isolates PyrUy10.1 and PyrUy14.1 shared 99.9% of SNPs, while PyrUy11.1 showed only 73% similarity, suggesting multiple introductions and the coexistence of genetically distinct lineages. These findings confirm the first detection of MoT in Uruguay and underscore the risk of cross-border pathogen movement. The presence of diverse MoT lineages presents new challenges for disease management and highlights the urgent need for ongoing monitoring in areas with favorable conditions for wheat blast development.

Abstract:
Authors: Diane G.O. Saunders, David P. Hodson and all DEWAS project partners

Wheat production is under constant threat from rapidly evolving, transboundary fungal diseases, with rust and blast diseases among the biggest concerns. Wheat rusts have ravaged wheat cultivation ever since the dawn of agriculture about 10,000 years ago, with new variants continually emerging and spreading rapidly on a global scale. In contrast, wheat blast is a recently emergent disease that can cause complete crop loss under favourable conditions, although, it remains more limited in geographical distribution. In both cases rapid and accurate diagnostics is essential to inform effective disease management decisions. To address this, within the DEWAS programme we have developed and deployed advanced genomic-based diagnostic methods across South Asia, South-Central and East Africa. This includes further development and deployment of the Mobile And Real-time PLant disEase (MARPLE) diagnostics platform, that has reduced the speed of strain-level diagnostics for yellow and stem rust to just 48 hours. This new rapid diagnostic system is now situated in multiple countries across East Africa and South Asia to keep track of the changing landscape of wheat rust populations. We also further developed and trialled a new point-of-care real-time diagnostic method for wheat blast to provide accurate and timely diagnostics in South Asia and South-Central Africa. This is further complemented by detailed genetic analysis using the T-Plex genotyping platform that provides genomic-based insight into the distribution of specific lineages of the wheat blast pathogen worldwide. Together, these advances are helping rapidly detect changes in rust and blast populations to ensure timely deployment of intervention strategies.

Abstract:
Stripe rust (Puccinia striiformis f. sp. Tritici; YR) and stem rust (Puccinia graminis f. sp. Tritici; SR) remain major threats to global wheat production due to evolving virulences and emerging races. This study reports the spread of the PstS16 stripe rust race (virulence: 1,2,3,(4),-,6,7,8,9,-,-,17,-,25,27,32,-,AvS,-) in Kenya, breaking resistance in previously resistant varieties. Race-typing and monitoring across major wheat-growing regions confirmed its spread, emphasizing the need for improved breeding strategies. To address this challenge, a genome-wide association study (GWAS) using a linear mixed model was conducted on 829 elite parental wheat lines from CIMMYT’s breeding program. The panel was field-phenotyped in Njoro, Kenya, over two years, where stripe rust data showed a 70% correlation, and stem rust showed a 60% correlation, indicating consistent disease responses. Genotyping with the 40K XT SNP array identified significant markers for stem rust resistance on chromosomes 1A.1 (88 Mb), 1A.2 (585 Mb), 1B (650 Mb), 1D.1 (10-12 Mb), 1D.2 (410-418 Mb), 2A (3-6 Mb), 2B (531 Mb), 2D (2.5 Mb), 3A (22-25 Mb), 3B (690 Mb), 3D (165 Mb), 4A.1 (2 Mb), 4A.2 (690-700 Mb), 4B.1 (66 Mb), 4B.2 (620 Mb),5A (687 Mb), 5B (538 Mb) 6A.1 (2 Mb), 6A.2 (615 Mb), 6B (618-620 Mb), 7A (697 Mb), 7B (621 Mb) and 7D (330 Mb) with several regions overlapping known SR genes (Sr8, Sr9h, Sr13, Sr22, Sr25, Sr38, Sr50, Sr58). For YR resistance, significant SNPs were identified on  chromosomes 1A (580-592 Mb), 1B (682 Mb), 2A (744 Mb), 2B (26.8 Mb), 3B (23 Mb), 4B (670-672 Mb), 6A (7 Mb), 6B (98 Mb), 6D (8.6 Mb), and 7B (99 Mb) aligning with some of the known resistance genes; Yr29, Yr78, and Yr81. Candidate genes were identified within most QTL regions, providing valuable targets for marker-assisted selection. Further studies are underway to characterize these genomic regions.

Abstract:
Of the many constraints of wheat production, pests and diseases are important biotic constraints. Pest and diseases surveillance is one of the key activities carried out by National Plant Protection Organizations (NPPO’s). It helps to them gain knowledge of the prevalence of pests and diseases. Despite on-going efforts, however, gathering timely and quality-controlled data has been a challenge for many NPPO’s in developing countries.
Wilkinson et.al. (2016) argues for an urgent need of improving the infrastructure to support the reuse of scholarly data. They coined an acronym called FAIR data. FAIR data is data that meets the FAIR principles. These are Fundability, Accessibility, Interoperability and Reusability. Nonetheless, abiding to FAIR principles is not only limited by willingness to share data but the investment required to ensure acquisition and storage of quality data in a sustainable platform. This calls for affordable platforms that can be used by NPPO’s.

This paper reviews surveillance systems implemented by different organizations. It also discusses the power of Free and Open-source (FOSS) tools that are available but largely overlooked. FOSS is an application that is available for free, and its source code is available for review or further development. The paper also shares experience from the key wheat diseases surveillance activity in the Disease Early Warning and Advisory System (DEWAS) project that employed the Open Data Kit (ODK). The use of the ODK helped the collection of near-real time data to ensure timely information and made sample tracking possible.

Abstract:
Authors: Huw R. Davis, Tansy Chia, Hayley Rhodes, Clare M. Lewis, Andrey Korolev, Lesley Boyd, Diane G.O. Saunders, Charlotte F. Nellist and Kostya Kanyuka

The United Kingdom Cereal Pathogen Virulence Survey (UKCPVS) was established in 1967 following a major yellow rust outbreak on the previously resistant wheat variety Rothwell Perdix. Since then, Puccinia striiformis f. sp. tritici (Pst), the causal agent of yellow rust, has been routinely monitored across the UK wheat growing regions.

In spring 2025, unusually high levels of yellow rust were observed by the Niab Northern trials team on wheat varieties rated as highly resistant at both the seedling and the adult plant stages. Similar reports and samples were received from across the industry. Pathotyping of three of these early-season isolates on a wheat differential line set confirmed that all three carried virulence to Yr15 – a major, broad-spectrum, all-stage resistance gene first identified in the 1980s and widely deployed worldwide. Genotyping using KASP markers revealed that Yr15 is present in many UK AHDB Recommended List varieties previously classified as resistant at the young plant stage. Collectively these account for at least 58.7% of the UK certified seed market, excluding farm-saved seed. MARPLE diagnostics genotyping performed on two of the early isolates (from varieties Champion and KWS Dawsum) indicate that the new virulent pathotype likely represent a locally evolved variant of the European PstS10 (Warrior -) lineage, rather than a recent exotic incursion. The widespread cultivation of Yr15-carrying varieties has likely exerted strong selection pressure on the pathogen population, facilitating the emergence of virulence in the current season. Ongoing work includes transcriptome and whole genome sequencing of these isolates to investigate the underlying genetic changes associated with the breakdown of resistance.