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Wheat is one of the high value important major crops of the globe. However, wheat stem rust is considered one of the determinant threats to wheat production in Ethiopia and the globe. So this study was conducted with the objective to assess disease intensity, seasonal distribution dynamics, and genetic variability and to determine virulence spectrum of stem rust in the irrigated wheat areas of Ethiopia. A total of 137 wheat farms were evaluated from 2014/15 - 2019/20 in six districts of Awash River basin. Farm plots were assessed every 5 - 10 km interval with ‘X’ fashion, and data on disease incidence, severity, and healthy plants were scored with diseased wheat plant samples collection for stem rust race analysis. The seasonal trend of wheat stem rust disease was also compared to see the future importance of the diseases. The result revealed that the prevalence, incidence, and severity of stem rust were significantly varied among the different districts and seasons in the two regions. The survey results also indicated that about 71.7% of the wheat fields were affected by stem rust during the 2018/19 growing season. The overall incidence and mean severity of the disease during the same season were 49.02% and 29.27%, respectively. During 2019/20 about 63.7% of the wheat fields were affected by stem rust, which, however, the incidence (30.97%) and severity (17.22%) were lower than the previous season. Although the seasonal disease distribution was decreased, its spatial distribution was expanding into Lower Awash. The physiological and the genetic race analysis identified four dominant races (TTTTF, TKTTF TKKTF, and TTKTF) during 2018/19 and additional race (TKPTF) during 2019/20. Thus races are highly virulent and affect most of the Sr genes except Sr – 31 and Sr – 24. TTTTF and TKKTF are the widest virulence spectrum which affects 90% of the Sr genes. Thus, it can be concluded that the spatial and seasonal distribution of the disease was expanding. Moreover, most of the races were similar with rain-fed production, and thus care must be given for effective management of the diseases to both agro-ecologies. Therefore, these findings provide inputs or insight for breeders to think about the breeding programs in their crossing lines and wheat producers to reduce the damage of the disease in the irrigated ecologies.ETHICAL STATEMENTThus, surveys were conducted with the lateral aim of rust epidemics early warning and monitoring support program in the Awash River basin. Samples for this study were collected from farmers’ fields of the irrigated production areas in the Awash River basin. The disease was an air-borne disease that is difficult to contain. Still, we give maximum care during surveying through spore-free through self-sanitation after Pgt infested field observation to minimize induced disease dissemination to the communities in the production areas that no specific permissions were required for these locations. Field sites are on public access, and P. graminis f. sp. tritici is already an air-born pathogen that doesn’t need special protection kinds. This work was our study experience in the endeavor in irrigated wheat technology dissemination.

Wheat is one of the high-value major crops in the world. However, wheat stem rust is considered one of the determinant threats to wheat production in Ethiopia and the world. So this study was conducted to assess the disease intensity, seasonal distribution dynamics pattern, the genetic variability of Puccinia graminis f. sp. tritici, and to determine the virulence spectrum in the irrigated ecology of the Awash River Basin. Totally 137 wheat farms were evaluated, from 2014/15–2019/20 in six districts representing the Upper, Middle, and Lower Awash River Basin. Farm plots were assessed, in every 5–10 km intervals, with ’X’ fashion, and data on disease incidence, severity, healthy plants were counted and recorded. Diseased samples were collected from the diseased wheat stem by Puccinia graminis physiological and genetic race analysis. The seasonal trend of stem rust disease progress showed its importance to infer the future progresses of the disease for the country’s potential production plan of irrigated wheat. The result revealed that the disease prevalence, disease incidence, and severity were significantly varied; among the different districts and seasons in the two regions. The survey results also indicated that about 71.7% of the wheat fields were affected by stem rust during the 2018/19 growing period. The disease’s overall incidence and mean severity during the same season were 49.02% and 29.27%, respectively. In 2019/20, about 63.7% of the wheat fields were affected by stem rust, disease incidence 30.97%, and severity 17.22% were lower than the previous season. In 2019/20, even though seasonal disease distribution decreased, the spatial distribution was expanding in Afambo and Dubti districts. Four, stem rust dominant races were identified (TTTTF, TKTTF TKKTF, and TTKTF) by physiological and genetic race analysis during 2018/19 and one additional race (TKPTF) in 2019/20, production year. The result indicated that the races are highly virulent and affect most Sr genes except Sr31 and Sr24. From the race analysis result, TTTTF, and TKKTF have the broadest virulence spectrum race, which affects 90% of the Sr genes. Generally, we can conclude that the spatial and seasonal distribution of the disease is expanding. Most of the races in the irrigated areas in the Basin were similar to that of rain-fed wheat production belts in Ethiopia, so care must be given, to effective management of the diseases, in both production ecologies towards controlling the spore pressure than race variability. Therefore, these findings provide inputs for wheat producers to reduce the spread and disease’ damage in the irrigated ecologies of Ethiopia. Also, it gives an insight for breeders to think about the breeding program in their crossing lines.

Wheat rusts are the key biological constraint to wheat production in Ethiopia—one of Africa’s largest wheat producing countries. The fungal diseases cause economic losses and threaten livelihoods of smallholder farmers. While it is known that wheat rust epidemics have occurred in Ethiopia, to date no systematic long-term analysis of past outbreaks has been available. We present results from one of the most comprehensive surveillance campaigns of wheat rusts in Africa. More than 13,000 fields have been surveyed during the last 13 years. Using a combination of spatial data-analysis and visualization, statistical tools, and empirical modelling, we identify trends in the distribution of wheat stem rust (Sr), stripe rust (Yr) and leaf rust (Lr). Results show very high infection levels (mean incidence for Yr: 44%; Sr: 34%; Lr: 18%). These recurrent rust outbreaks lead to substantial economic losses, which we estimate to be of the order of 10s of millions of US-D annually. On the widely adopted wheat variety, Digalu, there is a marked increase in disease prevalence following the incursion of new rust races into Ethiopia, which indicates a pronounced boom-and-bust cycle of major gene resistance. Using spatial analyses, we identify hotspots of disease risk for all three rusts, show a linear correlation between altitude and disease prevalence, and find a pronounced north-south trend in stem rust prevalence. Temporal analyses show a sigmoidal increase in disease levels during the wheat season and strong inter-annual variations. While a simple logistic curve performs satisfactorily in predicting stem rust in some years, it cannot account for the complex outbreak patterns in other years and fails to predict the occurrence of stripe and leaf rust. The empirical insights into wheat rust epidemiology in Ethiopia presented here provide a basis for improving future surveillance and to inform the development of mechanistic models to predict disease spread.

Background Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. Results Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (Pst), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. Conclusions MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats. Electronic supplementary material The online version of this article (10.1186/s12915-019-0684-y) contains supplementary material, which is available to authorized users.

Highlights • Maize lethal necrosis (MLN) emerged as a serious threat to maize production and livelihoods of smallholders in eastern Africa since 2011. • An intensive multi-disciplinary and multi-institutional strategy is being implemented to curb the spread of MLN in sub-Saharan Africa, and mitigate the impact of the disease. • Intensive germplasm screening led to identification of MLN-resistant sources, and fast-tracked development and commercial release of 19 MLN-tolerant/resistant hybrids in eastern Africa. • Marker-assisted breeding led to successful conversion of 52 elite but MLN-susceptible inbred lines into MLN-resistant versions. • MLN/MCMV diagnostic protocols have been optimized, and personnel from relevant public and private sector institutions trained on MLN diagnostics, monitoring and surveillance., Maize lethal necrosis (MLN), a complex viral disease, emerged as a serious threat to maize production and the livelihoods of smallholders in eastern Africa since 2011, primarily due to the introduction of maize chlorotic mottle virus (MCMV). The International Maize and Wheat Improvement Center (CIMMYT), in close partnership with national and international partners, implemented a multi-disciplinary and multi-institutional strategy to curb the spread of MLN in sub-Saharan Africa, and mitigate the impact of the disease. The strategy revolved around a) intensive germplasm screening and fast-tracked development and deployment of MLN-tolerant/resistant maize hybrids in Africa-adapted genetic backgrounds; b) optimizing the diagnostic protocols for MLN-causing viruses, especially MCMV, and capacity building of relevant public and private sector institutions on MLN diagnostics and management; c) MLN monitoring and surveillance across sub-Saharan Africa in collaboration with national plant protection organizations (NPPOs); d) partnership with the private seed sector for production and exchange of MLN pathogen-free commercial maize seed; and e) awareness creation among relevant stakeholders about MLN management, including engagement with policy makers. The review concludes by highlighting the need to keep continuous vigil against MLN-causing viruses, and preventing any further spread of the disease to the major maize-growing countries that have not yet reported MLN in sub-Saharan Africa.

In sub-Saharan Africa (SSA), “maize is life,” due to its importance to food security and economic wellbeing. Around 40 % of Africa’s maize-growing area faces occasional drought stress, resulting in yield losses of 10–25 %. Around 25 % of the maize crop suffers frequent drought, with losses of up to half the harvest. To reduce vulnerability and improve food security, the Drought Tolerant Maize for Africa (DTMA) project has made releases of 160 drought tolerant (DT) maize varieties between 2007 and 2013. These have been tested in experimental and farmers’ fields, and disseminated to farmers in 13 African countries through national agricultural research systems and private seed companies. Yields of the new varieties are superior to those of currently available commercial maize varieties under both stress and optimum growing conditions. Although the benefits of DT maize for African farmers have been repeatedly predicted, realization of those benefits depends on farmer uptake, which has received limited empirical study. We use new plot-level data from surveys of 3,700 farm households in six countries (Ethiopia, Tanzania, Uganda, Malawi, Zambia, and Zimbabwe) to measure DT maize adoption rates and their determinants. The data reveal considerable inter-country variation in farmer uptake of DT maize, from 9 % of maize plots in Zimbabwe to 61 % in Malawi. The major barriers to adoption include unavailability of improved seed, inadequate information, lack of resources, high seed price, and perceived attributes of different varieties. Based on the results, we recommend that seed companies and agro-dealers ensure adequate supply of DT maize seed in local markets and sell seed in affordable micro-packs (1 or 2 kg). Furthermore, the DTMA project and partners should ramp up promotional efforts to ensure widespread awareness and understanding of the benefits of the new DT maize varieties.

Wheat rust diseases pose one of the greatest threats to global food security, including subsistence farmers in Ethiopia. The fungal spores transmitting wheat rust are dispersed by wind and can remain infectious after dispersal over long distances. The emergence of new strains of wheat rust has exacerbated the risks of severe crop loss. We describe the construction and deployment of a near real-time early warning system (EWS) for two major wind-dispersed diseases of wheat crops in Ethiopia that combines existing environmental research infrastructures, newly developed tools and scientific expertise across multiple organisations in Ethiopia and the UK. The EWS encompasses a sophisticated framework that integrates field and mobile phone surveillance data, spore dispersal and disease environmental suitability forecasting, as well as communication to policy-makers, advisors and smallholder farmers. The system involves daily automated data flow between two continents during the wheat season in Ethiopia. The framework utilises expertise and environmental research infrastructures from within the cross-disciplinary spectrum of biology, agronomy, meteorology, computer science and telecommunications. The EWS successfully provided timely information to assist policy makers formulate decisions about allocation of limited stock of fungicide during the 2017 and 2018 wheat seasons. Wheat rust alerts and advisories were sent by short message service and reports to 10 000 development agents and approximately 275 000 smallholder farmers in Ethiopia who rely on wheat for subsistence and livelihood security. The framework represents one of the first advanced crop disease EWSs implemented in a developing country. It provides policy-makers, extension agents and farmers with timely, actionable information on priority diseases affecting a staple food crop. The framework together with the underpinning technologies are transferable to forecast wheat rusts in other regions and can be readily adapted for other wind-dispersed pests and disease of major agricultural crops.

Background: Accurate information on the distribution of the tsetse fly is of paramount importance to better control animal trypanosomosis. Entomological and parasitological surveys were conducted in the tsetse belt of south-western Ethiopia to describe the prevalence of trypanosomosis (PoT), the abundance of tsetse flies (AT) and to evaluate the association with potential risk factors. Methods: The study was conducted between 2009 and 2012. The parasitological survey data were analysed by a random effects logistic regression model, whereas the entomological survey data were analysed by a Poisson regression model. The percentage of animals with trypanosomosis was regressed on the tsetse fly count using a random effects logistic regression model. Results: The following six risk factors were evaluated for PoT (i) altitude: significant and inverse correlation with trypanosomosis, (ii) annual variation of PoT: no significant difference between years, (iii) regional state: compared to Benishangul-Gumuz (18.0 %), the three remaining regional states showed significantly lower PoT, (iv) river system: the PoT differed significantly between the river systems, (iv) sex: male animals (11.0 %) were more affected than females (9.0 %), and finally (vi) age at sampling: no difference between the considered classes. Observed trypanosome species were T. congolense (76.0 %), T. vivax (18.1 %), T. b. brucei (3.6 %), and mixed T. congolense/vivax (2.4 %). The first four risk factors listed above were also evaluated for AT, and all have a significant effect on AT. In the multivariable model only altitude was retained with AT decreasing with increasing altitude. Four different Glossina species were identified i.e. G. tachinoides (52.0 %), G. pallidipes (26.0 %), G. morsitans submorsitans (15.0 %) and G. fuscipes fuscipes (7.0 %). Significant differences in catches/trap/day between districts were observed for each species. No association could be found between the tsetse fly counts and trypanosomosis prevalence. Conclusions: Trypanosomosis remains a constraint to livestock production in south-western Ethiopia. Four Glossina and three Trypanosoma species were observed. Altitude had a significant impact on AT and PoT. PoT is not associated with AT, which could be explained by the importance of mechanical transmission. This needs to be investigated further as it might jeopardize control strategies that target the tsetse fly population.