Disease Early

Warning And
Advisory Systems
– The Case of
Wheat Rusts
Dave Hodson
d.hodson@cgiar.org
Thanks to a Global Community
 An Increasing Threat –
Transboundary Pathogens & Pests
• Rate of spread, appearance in new areas, and
detection of new pathogen races (new diseases)
is increasing
– Drivers: globalization (trade, travel), climate change,
selection pressure (uniform cropping systems)

Wheat Blast Fall Army Worm

Stem Rust Maize Lethal Necrosis
Yellow Rust

Pathogen Surveillance & Monitoring Systems increasingly needed

Wheat Rusts: Combating Cereal Killers
Highly mobile pathogens, extremely destructive and constantly changing!

Stem (Black) Rust Stripe (Yellow) Rust

• Most destructive disease on wheat, historically the most
• Significant increase in spread since 1960
feared disease
• Est. 5.47 million tonnes loss/yr (US$979
• Under favourable conditions, capable of causing 100%
million / yr)
crop loss within weeks Source: Beddow et al 2015 Nature Plants
• Re-emerging as a disease of concern

Wheat crop killed by stem Yellow rust epidemic,

rust, Ethiopia Nov 2013 Ethiopia
 Rust Surveillance History

Ug99 – A call to action

●1998: Anomalous results from
a nursery in Uganda

● 1999:Confirmation of loss of
important Sr genes (Sr31, Sr38
+++) “Ug99” [TTKSK]

● 2005: “Sounding the Alarm on

Global Stem Rust”. Formation of
the (Borlaug) Global Rust Initiative
● ?’s – Susceptibility? Where next? How soon?....

● Clear need for effective monitoring & surveillance

 Pathogen Surveillance

Wheat Rusts
• Since 2008
• 63,000+ survey records
• 19,000+ samples
• Covers 43 countries: large % of developing world wheat
• Most comprehensive, operational monitoring system
Large-scale for major crop diseases

surveillance networks
 Wheat Rust Toolbox

• The wheat rust toolbox -

core data management
system
• One of the most
comprehensive crop
disease data resources
• 63,000+ geo ref. survey
records from 43 countries
• 19,000+ sample records
• Data-driven display /
analytical tools
 Rust Pathotyping Lab Network

Canada
Canada Denmark Turkey
AAFC Morden Global Rust Reference Center Central Field Crops Research Inst + Pakistan
ICARDA, Regional Rust Research Center PARC, Crop Diseases Res. Inst, Murree

India
DWR Flowerdale, Shimla
Iran
SPII
USA

USDA-ARS Cereals Disease Lab

Ethiopia

EIAR, Ambo PPRC

Kenya
KALRO, Njoro Research Center

Australia
PBI, University of Sydney

South Africa
University of the Free State
 Evolution and Spread of
Races Belonging to the Ug99
Lineage of the Stem (Black)
Rust Fungus
2005 2008 2010 2021

• Ug99 is mutating and migrating

• Seventeen (+) Ug99 races now known. Presence in 14 countries confirmed
• 80-90% wheat varieties/germplasm susceptible or with inadequate resistance in 2006
• Launch of Borlaug Global Rust Initiative in 2005 (DRRW project in 2008)
• Global stem rust threats now extend beyond Ug99
 Stem Rust: Recent Developments
Europe: Sweden – 1st outbreak in 60 years
Stem rust continues to re-emerge Sexual population (Barberry)
• 2020 – Ireland
• 2021 – Belgium
W Siberia / N Kazakhstan
• 2022 - UK
Sexual population (Barberry)
• All Non Ug99 races
Outbreak on 3 million ha

Spain – Unique races – sexual

population from Barberry
Race TKHBK Iraq
Vir: Sr31, Sr33, Sr53 and Sr59 • 2019: Ug99 Race
Sr31 virulence (non-Ug99) TTKTT first detection
Olivera et al 2022 Plant Pathology

Kenya
Ug99 New variants continue to emerge
• Kenya (2019) : Race TTKTT +Sr8155B1
(14th Ug99 variant)
• Kenya (2020) : Race TTHTT (15th Ug99
variant)
• Kenya (2020): Race PTKTT (16th Ug99
variant)
• Kenya (2020): Race PTKTK (17th Ug99
variant?)
Ethiopia
• Ug99 Race TTKTT
increasing in frequency
• TTKTT +Sr8155B1 (1st
detection 2021)
• Stem Rust is re-emerging as a disease of concern
• Non Ug99 races spreading e.g., TKKTF, TKTTF,
TTRTF…
• New Ug99 variants emerging + spreading

University of
Minnesota
 Pathogens without Borders-
Recent Yellow Rust
• New race (PstS16) –
Afghanistan/Pakistan
(2018) – Ethiopia 2015

2020
(2020), Uganda (2023) 2012
2018
• PstS10 (2017) PstS13 2016
(2018) confirmed in 2021: Paraguay 2018
2017?
1st report of YR
Australia
2022
• PstS14 Iraq (2020) PstS11 2016
• 2021 First report of YR PstS13
2021
2020
Paraguay (PstS13) PstS14
• 2021 Nepal – high PstS16
diversity (sexual PstS17 2017 2018

population?)
• 2022 PstS17 confirmed
Ethiopia
• New genotype – • New Emerging Genetic Groups of Yellow Rust
Ethiopia 2021 (from S • Spreading Extremely Quickly
Asia) • Large Scale Epidemics
 Development of
Early Warning Systems
• Advanced Spore Dispersal
Model (NAME model, UK
Met Office)
• 7 day forecast models for
dispersal and risk (daily, in-
season)
• 3 weeks’ warning to prevent
epidemics

Olivera et al Phytopathology 2015

Dispersal + Suitability → Risk

 Wheat Rust
Early Warning Advisory Systems
• Advanced, in-season,
early warning systems 7 day forecast models for
dispersal and risk
• Operational: Ethiopia, Models Weekly Advisories
Dispersal + Suitability → Risk
Nepal, Bangladesh
• Reaching 100,000’s Advisories
farmers – timely,
actionable information Survey Data 7 day forecast
(automatic) (automatic)
Alerts
Crowdsourced Phone
Surveys

Targeted SMS alerts

Central Early
Warning Unit
Field Survey (Integrated Data
hub) Reach (SHF/Extension): Target 1 million

Rapid Action
Near real-time data (ODK)
Surveillance
MinION
Near Real-time
Diagnostics Control ahead
of disease in
key areas

Wheat Rust Toolbox

Global Data Management System
Allen-Sader et al, 2019 Env Res Letters
 Early Warning Impact:
Ethiopia 2010 vs 2021
2010 No Early Warning System 2021 Operational Early Warning
Situation: Extreme high-risk rust season Situation: Extreme high-risk rust season
Outcome: Devastating yellow rust epidemic Outcome: Record wheat production
Over 600,000 ha affected, est. losses
>US$250 million

Early Warning Systems contributed to prevention of epidemic in 2021

 Early Warning South Asia
• Successful transfer meteorologically-
driven dynamic epidemiological
forecasting models for wheat rust from
Ethiopia to:
– Nepal and Bangladesh
• In-season, operational system – daily,
7-day forecasts (spore dispersal,
environmental suitability), weekly
advisories
• Reaching over 500,000 farmers in
2020/21 season (Nepal & Bangladesh)
• Regional forecasting (South Asia) now
operational + weekly regional advisories
• MARPLE + Nuru (AI) – start in Nepal
2022
 Next Steps: DEWAS Wheat Project
South Asia
• Duration: 3-year project - Nepal
Bangladesh
2023-2026 Pakistan
• Geographic Focus: East Africa+ Bhutan

& South Asia

• Diseases: Wheat Rusts +
Wheat Blast (+FHB)

East Africa+
Ethiopia
Kenya
Tanzania
Zambia
Mobile And Real-time PLant disEase (MARPLE) diagnostics

PCR
388 genes Risk Forecasting

Identify Extract Mobile Data Diagnostics > Early Warning

disease DNA sequencing analysis define strain System

2 days from sample prep to results!!

Radhakrishnan et al & Saunders (2019) BMC Biology

Slide courtesy of Dr Diane Saunders

 Wheat Blast
• Spreading globally
• Increasing geographical spread
in both Bangladesh and Zambia
• Clear need for increased
surveillance and efficient early
detection

Singh et al, 2021. Front. Plant Sci. 12:710707. doi: 10.3389/fpls.2021.710707

 Develop Rapid Diagnostics for Wheat Blast &
Monitor and Track Through Advanced Genotyping
Aim: Provide tools & build capacity to rapidly respond to wheat blast outbreaks
In situ rapid detection Multiplex amplicon sequencing Full genome sequencing

Wheat blast

Board of Trustees

MonsterPlex amplicon sequencing to

analyze 84 variable SNPs

http://getgenome.net
Latorre et al 2023 PLoSBiology https://doi.org/10.1371/journal.pbio.3002052

Slide courtesy of Diane Saunders JIC,UK

 New threats: Fusarium Head Blight
(FHB) in Ethiopia (East Africa)
Urgent action is needed in East
Africa to tackle the increasing
threat of FHB, to increase wheat
productivity, ensure food safety
• One of the most challenging wheat
diseases globally
• Yield losses of more than 50%
• Mycotoxins: Grain containing more than
5% of FHB infected kernels can contain
enough toxin to be harmful to humans and
animals
• Increasing rapidly in East Africa
• Ethiopia 2022 – over 50% of fields
Ethiopia Oct 2022 infected
• Integrated disease management, is
critically needed in Ethiopia to successfully
tackle FHB
 Thank you
for your
interest!

Photo Credits (top left to bottom right): Julia Cumes/CIMMYT, Awais

Yaqub/CIMMYT, CIMMYT archives, Marcelo Ortiz/CIMMYT, David
Hansen/University of Minnesota, CIMMYT archives, CIMMYT archives (maize),
Ranak Martin/CIMMYT, CIMMYT archives.