Stopping sweetpotato pathogens

Taking virus detection out of labs and into farmer fields in Africa

Pests and diseases cost the global agricultural sector an estimated USD 540 billion annually, and in developing countries, they cause potato and sweetpotato farmers to lose up to 60% of their yields.

Viruses can hinder the adoption of orange-fleshed sweetpotato varieties, which the International Potato Center (CIP) promotes as a sustainable source of vitamin A for families in Africa. Spread by whiteflies and aphids, those pathogens also pass from one crop generation to the next in planting material, diminishing the yields of each successive harvest.

As viruses accumulate in plants, and yields decline, farmers may stop growing a nutritious sweetpotato variety, leaving their families at risk of vitamin A deficiency and the many health problems it causes.

Finding ways to manage sweetpotato viruses is thus a priority at CIP, where virologist Jan Kreuze has made recent scientific breakthroughs to develop technologies that could revolutionize disease control in Africa.

“That this variety, which is resistant to the two most common sweetpotato viruses, could suffer that much damage from a third, underlines how much we need to learn,” Kreuze said. 

Stopping sweetpotato pathogens

Taking virus detection out of labs
and into farmer fields in Africa

Pests and diseases cost the global agricultural sector an estimated USD 540 billion annually, and in developing countries, they cause potato and sweetpotato farmers to lose up to 60% of their yields.

Viruses can hinder the adoption of orange-fleshed sweetpotato varieties, which the International Potato Center (CIP) promotes as a sustainable source of vitamin A for families in Africa. Spread by whiteflies and aphids, those pathogens also pass from one crop generation to the next in planting material, diminishing the yields of each successive harvest.

As viruses accumulate in plants, and yields decline, farmers may stop growing a nutritious sweetpotato variety, leaving their families at risk of vitamin A deficiency and the many health problems it causes.

Finding ways to manage sweetpotato viruses is thus a priority at CIP, where virologist Jan Kreuze has made recent scientific breakthroughs to develop technologies that could revolutionize disease control in Africa.

Deciphering viruses

Whereas human immune systems create antibodies to destroy viruses, plants have simpler defense responses that chop up a virus’s genetic material—ribonucleic acid (RNA)—when it enters a cell, slowing its ability to cause damage.

Kreuze pioneered the use of genetic sequencing and reassembly of RNA fragments from a plant’s anti-viral response to identify the sweetpotato viruses that infect it. He led a field study that analyzed tissue samples from 1,168 sweetpotato plants in farmer fields across 11 African countries, identifying more than 15 viruses, some previously unknown.

The team then used the data to develop models to predict where specific viruses are likely to be found and how climate change will affect their distribution. They also identified genetic markers to develop a diagnostic field test for three common sweetpotato viruses using a technology known as a LAMP. The LAMP assay is vital because some infected plants are asymptomatic—like many people with COVID-19—which complicates detection.

The LAMP assay, which is faster and cheaper than laboratory-based methods, was tested at four different sites in Kenya and was 100% accurate. Though deployment was delayed by COVID-19, scientists expect the tool to be available soon in Kenya, allowing for the removal of infected planting material from seed systems and faster identification of virus-resistant varieties for farmers.

Diagnosis by phone

With the help of the assay, scientists are using photos of infected plants to develop the artificial intelligence to enable the smartphone app Nuru (“Light” in Swahili) to provide farmers with a real-time diagnosis of sweetpotato virus infections via their phones. Developed by CGIAR and Penn State University scientists, the app is part of a platform called Plant Village that also provides instructions on managing pests and diseases. Nuru has been used since 2018 to diagnose cassava and maize pests and diseases. Sweetpotato is one of a growing number of crops that it will provide diagnoses and advice for.

Both the app and LAMP assay are expected to help identify and control the most common viruses. But more work is needed to understand some previously unknown threats identified by Kreuze’s team.  In field trials they discovered that a group of common but asymptomatic viruses, known as begomoviruses, reduced yields of a popular orange-fleshed variety — widely considered virus resistant — by 40%.

“That this variety, which is resistant to the two most common sweetpotato viruses, could suffer that much damage from a third, underlines how much we need to learn,” Kreuze said.

“By better understanding viruses, and improving diagnostic tools, we can help increase crop yields,” he added. “This will put more nutritious food on the tables, and income in the pockets, of some of the world’s most vulnerable families.”

Funders: Bill & Melinda Gates Foundation; Biotechnology and Biological Sciences Research Council; European Union; The Howard G. Buffett Foundation; International Centre for Genetic Engineering and Biotechnology, The World Academy of Sciences and United Nations Educational, Scientific and Cultural Organization; National Science Foundation (US).

Partners: Boyce Thomson Institute; CGIAR Research Program on Roots, Tubers and Bananas; Donald Danforth Plant Science Center; Food and Agriculture Organization of the United Nations; Food and Environment Research Agency/Fera Science Limited; Kenya Plant Health Inspectorate Service and Penn State.

Associated CGIAR Research Programs or Platforms: Roots, Tubers and Bananas.

ABOUT

CIP is a CGIAR research center with a focus on potato, sweetpotato and Andean roots and tubers. It delivers innovative science-based solutions to enhance access to affordable nutritious food, foster inclusive sustainable business and employment growth, and drive the climate resilience of root and tuber agri-food systems. Headquartered in Lima, Peru, CIP has a research presence in more than 20 countries in Africa, Asia and Latin America. www.cipotato.org

CGIAR is a global research partnership for a food-secure future. Its science is carried out by 15 research centers in close collaboration with hundreds of partners across the globe. www.cgiar.org

CIP ACHIEVEMENTS

CREDITS

Discovery to Impact
Science-based solutions for global challenges

International Potato Center | Annual Report 2019
© 2020, International Potato Center
ISSN 0256-6311
DOI: 10.4160/02566311/2018
Hecho el Depósito Legal en la Biblioteca Nacional del Perú  N° 2005-9640 

Readers are encouraged to quote or reproduce material from this report. As copyright holder, CIP requests acknowledgement and a copy of the publication where the citation or material appears. Please send this to the Communications Department at the address below. 

International Potato Center
Av. La Molina 1895, La Molina, Peru
Apartado 1558, Lima 12, Peru
cip@cgiar.org
www.cipotato.org 

Direction
James Stapleton 

Managing editor
Christopher Butler 

Writing 
David Dudenhoefer (consultant) 

Production coordinator
Cecilia Lafosse 

Multimedia productions
Sara Fajardo
Hugh Rutherford
Isabel Corthier 

Web development
Moises Rosario
Andrea Prado 

Design and infographics
José Enrique Torres 

Photo captions and credits 

Sliders:
Sweetpotato vine distribution in Mozambique (CIP/I. Corthier).
Jan Kreuze in the lab. (Credit CIP/J. Torres).
Genetic markers facilitate breeding resilient potatoes with characteristics local people want. (Credit CIP/H. Rutherford).

Sub-menus:

Discovery:
Jan Kreuze in the lab. (Credit CIP/J. Torres)

Innovation:
Ms Tirhas Woldu and her daughters, of Tigray, Ethiopia, enjoy orange-fleshed sweetpotato. (Credit CIP/A.Frezer)

Impact:
A combination of sweetpotato planting material, agronomic training and nutrition education has helped millions of rural families improve their food and nutrition security. (Credit CIP/I. Corthier)

Next-generation breeding:
Research assistant Monica Santayana works on a project to crossbreed potato and its wild relatives (Crop Trust/M. Major).

Stopping sweetpotato pathogens:
Scientist Barack Wanjawa tests the LAMP assay for sweetpotato viruses in Kenya (KALRO/A. Mulwa).

Triple advantage:
By storing sweetpotatoes in dry sand and using them to produce planting material, farmers are able to plant and harvest the nutritious crop earlier (CIP/M. Cherinet).

Potatoes for prosperity:
Farmer Doris Kagendo Gikunda, of Meru county, with the high-yielding CIP potato variety Unica (CIP/V. Atakos).

Sweet resilience:
Thousands of farmers received sweetpotato planting material to replace crops destroyed by Cyclone Idai (CIP/I. Corthier).

Asian appetites:
Nutrition education in Bangladesh (CIP/S.Quinn)

CIP at a glance:
Credit CIP/H. Rutherford

CIP in CGIAR:
Credit CIP/I. Corthier

Board of Trustees:
Credit CIP/J.Torres

July 2020 

CREDITS

Discovery to Impact
Science-based solutions for global challenges

International Potato Center | Annual Report 2019
© 2020, International Potato Center
ISSN 0256-6311
DOI: 10.4160/02566311/2018
Hecho el Depósito Legal en la Biblioteca Nacional del Perú  N° 2005-9640 

Readers are encouraged to quote or reproduce material from this report. As copyright holder, CIP requests acknowledgement and a copy of the publication where the citation or material appears. Please send this to the Communications Department at the address below. 

International Potato Center
Av. La Molina 1895, La Molina, Peru
Apartado 1558, Lima 12, Peru
cip@cgiar.org
www.cipotato.org 

Direction
James Stapleton 

Managing editor
Christopher Butler 

Writing 
David Dudenhoefer (consultant) 

Production coordinator
Cecilia Lafosse 

Multimedia productions
Sara Fajardo
Hugh Rutherford
Isabel Corthier 

Web development
Moises Rosario
Andrea Prado 

Design and infographics
José Enrique Torres 

Photo captions and credits 

Sliders:
Sweetpotato vine distribution in Mozambique (CIP/I. Corthier).
Jan Kreuze in the lab. (Credit CIP/J. Torres).
Genetic markers facilitate breeding resilient potatoes with characteristics local people want. (Credit CIP/H. Rutherford).

Sub-menus:

Discovery:
Jan Kreuze in the lab. (Credit CIP/J. Torres).

Innovation:
Ms Tirhas Woldu and her daughters, of Tigray, Ethiopia, enjoy orange-fleshed sweetpotato. (Credit CIP/A.Frezer).

Impact:
A combination of sweetpotato planting material, agronomic training and nutrition education has helped millions of rural families improve their food and nutrition security. (Credit CIP/I. Corthier).

Next-generation breeding:
Research assistant Monica Santayana works on a project to crossbreed potato and its wild relatives (Crop Trust/M. Major).

Stopping sweetpotato pathogens:
Scientist Barack Wanjawa tests the LAMP assay for sweetpotato viruses in Kenya (KALRO/A. Mulwa).

Triple advantage:
By storing sweetpotatoes in dry sand and using them to produce planting material, farmers are able to plant and harvest the nutritious crop earlier (CIP/M. Cherinet).

Potatoes for prosperity:
Farmer Doris Kagendo Gikunda, of Meru county, with the high-yielding CIP potato variety Unica (CIP/V. Atakos).

Sweet resilience:
Thousands of farmers received sweetpotato planting material to replace crops destroyed by Cyclone Idai (CIP/I. Corthier).

Asian appetites:
Nutrition education in Bangladesh (CIP/S.Quinn).

CIP at a glance:
Credit CIP/H. Rutherford

CIP in CGIAR:
Credit CIP/I. Corthier

Communication data 2019:
Credit CIP/S. Quinn

Board of Trustees:
Credit CIP/J.Torres

July 2020 

ABOUT  | CIP ACHIEVEMENTS | CREDITS

ABOUT  | CIP ACHIEVEMENTS | CREDITS

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