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Underneath Kenya’s potato fields, a silent killer is at work. Microscopic worms – potato cyst nematodes (PCN)— are ravaging one of East Africa’s key food crops.

Harvest time is a disappointment for potato farmers. They pull wilting potato plants with stunted and often rotting tubers unaware of the culprit: nematodes. 

An invisible war underground

Across Kenya, potato farmers face crop losses—sometimes up to 80%— as a result of nematode infestation. How serious is the problem of potato cyst nematodes in Africa?

“Off the scale”, warns Dr. Daniel Coyne, nematologist and soil health scientist at the International Institute of Tropical Agriculture (IITA). “We are dealing with millions of dollars in lost potato harvests in Kenya due to nematodes.”

Potato (Solanum tuberosum L.) is a crucial crop in Africa, serving as a staple and a major source of income for millions of smallholder farmers and stakeholders, according to the United Nations Food and Agriculture Organisation (FAO).

Africa has low potato yields averaging 14.69 tons/ha compared to the global average of 21.42 tons/ha annually. This is a result of a combination of factors; poor seed quality, climate change, high pest and disease prevalence especially of  the Soft Rot Pectobacteriaceae (SRP) and Potato Cyst Nematode (PCN).

Nematodes are microscopic worms which attack potato roots, stunting their growth and slashing farmers’ yields.  But not for long.

Scientists have developed two new nematode-resistant potato varieties to combat the problematic pest. It is a breakthrough that could save and protect Kenya’s staple. 

After ten years of research, the IITA and partners under a  Standards and Trade Development Facility (STDF) –  a World Trade Organization –  linked project, have released new potato varieties.

The Malakia and Glen varieties can resist PCN. They are high-yielding, and match the traits of the favourite Shangi variety which accounts for 85% of the potatoes eaten in Kenya.

A stealth survivor. PCN was first discovered in Kenya just 10 years ago but has been a potato plague for centuries. Unlike other nematodes, which attack a wide range of crops, PCN has a narrow appetite—potatoes. It can also infect tomatoes and other solanaceous plants.

“It’s a silent killer,” Dr. Coyne says. “PCN basically just sucks the life out of the plant and that’s what they do without any visible symptoms to the farmer. The crop will get chlorosis – loss of the green colouration of the leaves – have reduced growth, reduced yield and smaller tubers.”

Its cysts can lie dormant for decades, waiting for the right chemical signal—a potato root’s exudate—to prey on potatoes.

Science to the rescue

A solution to PCN came from an unexpected source: Scotland. Six years ago, researchers at IITA, Icipe and partners, including the James Hutton Institute, began testing potato lines bred for PCN resistance in the UK. Out of eight candidates, two stood were selected —not just for their resilience, but for traits prized by Kenyan farmers: fast cooking, good flavour, and low dormancy, meaning they sprout quickly for replanting. 

Ironically, what made these potatoes unsuitable for British winters made them ideal for Kenya’s tropical weather conditions for cropping all year-round.

The new varieties need to meet or surpass the traits of  Shangi – the dominant potato variety in Kenya.

“Shangi, by the way, is susceptible to PCN, of course, which is why we’re looking for something to either replace it or go alongside, ” he said.

The scale of PCN densities in Kenya is staggering. Dr. Coyne explains that scientists at James Hutton Institute who helped with the characterization and identification of the new varieties thought that they got the densities wrong because they were so high. The  densities are high probably because of the cropping conditions in Kenya which enable potato growing back to back, which could spread the nematodes.

“We are dealing with massive, huge densities of this pest in just about all fields across Kenya,” he said.

While not a silver bullet for a silent killer, Dr. Coyne adds that the new varieties are a major step towards controlling PNC. With better soil testing, farmer training, and more investment in nematology research, half the battle is won.

Economic impact

PCN and SRP cost East Africa over $600 million in lost production, according to the FAO.

An economic impact assessment by the FAO focusing on productivity, food security and nutrition, trade, and environment highlighted that PCN has been reported in South Africa, Kenya, Uganda, Rwanda, Egypt, Libya, Algeria, Tunisia, and Morocco while SRP is present in South Africa, Zimbabwe and Kenya. 

Kenya has a high PCN incidence at 71.8 percent, with an estimated yield loss of 5.03 tons/ha, while SRP results in a loss of 0.85 tons/ha. Combining the potential incidence and yield loss per unit area, the FAO study estimates annual production losses of 2.4 million tons and 360,000 tons for PCN and SRP, respectively. This translates to total potential production and productivity losses for SRP and PCN of $636 million which underscores the severity of the pest in the region.

In July 2025 the Kenya Plant Health Inspectorate Service (KEPHIS) approved the release of PCN resistant varieties which have been named Malaika and Glen – in Kenya. Scientists are confident the new varieties will tackle PCN and boost potato productivity in Kenya. 

Seeds for Malaika and Glen are currently being multiplied through commercial growers and propagators using stem cuttings. They will be in the farmers hands by September 2025 for planting.

The power of Partnerships

Dr. Coyne notes that the development of the new potato varieties has  been a collaborative effort, thanks to multiple partners. The project to develop, test and evaluate the new varieties was funded by Innovate UK and IPBO.

NemAfrica – a joint icipe/IITA nematology and Soil Health unit – has coordinated and implemented the project in partnership with CIP. The James Hutton Institute provided PCN support, diagnostics, access to funding and backstopping potato work and the James Hutton Ltd has supported the breeding and delivery of new varieties.

Potato farmer Bwana Kamutu planted the first crop of potatoes for first evaluations on his farm and these will be distributed to farmers through the Farmers Hub system in Nyandarua county in central Kenya.

The Syngenta Foundation Seeds2B program hosted the varietal multisite evaluation and then varietal registration in Kenya. Stokman Rozen is stocking and multiplying the clean Tissue Culture  planting material in Kenya and KISIMA will multiply the seed ahead of official release. FIPS Africa through its Keringet propagation unit is also multiplying quality stems by cutting seedlings for distribution through the youth groups. 

Universities have also been key partners in the development of the new varieties with the Jomo Kenyatta University of Agriculture and Technology (JKUAT) assessing new lines for nutrient and physical quality.

Potatoes prosperous future secure for now

The stakes could not be higher for Kenyan farmers. As the PCN continues to spread under their fields, the new potato varieties will boost productivity, hugely, Dr. Coyne affirms.

“The new varieties will probably double the yield. We are all starting from a very low base with a huge yield gap. But with these varieties we can increase yields, probably double them at the moment, and if not, increase them substantially with good quality inputs.”

But for now the future of Kenya’s potatoes is palatable.

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