A field-deployable diagnostic tool to fast track quality assured seed potato in Kenya

Symptoms of potato brown rot with bacteria oozing from potato eyes

Bacterial wilt, caused by Ralstonia solanacearum species complex (RSSC), is a serious threat to potato production in Sub-Saharan Africa. Ralstonia is one of the most significant limitations to clean seed production, an essential component of high yields. It has resulted in 30-100% potato yield losses putting a huge dent in the food security and livelihoods of many smallholder farmers.

In many countries, seed potato certification standards have zero tolerance for bacterial wilt pathogen and can lead to the rejection of an entire potato field for seed. This therefore puts certified seed potato production that barely meets 2% of total area planted with potato in Kenya at a high risk. There are a few seed merchants that produce certified seed potato and increasing quantities of certified seed is a major priority to improve yields and meet the increasing food demands. International Potato Center (CIP) in collaboration with the Kenya Plant Health Inspectorate Service (KEPHIS) validated the cost-effective field deployable loop-mediated isothermal amplification (LAMP ) assay for the detection of Ralstonia from stem, leaf, tuber and soil. This will speed up the seed inspection and certification process.

To this end, through the support from GIZ-BMZ funded project on “Improved Diagnostics and genetic/molecular diversity of Ralstonia from Kenya and Uganda” CIP and KEPHIS conducted a two-day training aimed at capacity building of East African countries’ seed regulatory and phytosanitary authorities as well as private diagnostic clinic personnel on the use of “field deployable LAMP assay to detect Ralstonia from stem, tuber and soil sample. The training, held at the KEPHIS Plant Quarantine and Bio-safety station at Muguga, Kenya, brought together 40 participants from Ethiopia, Kenya, Malawi, Rwanda, Tanzania and Uganda, who went through theoretical and practical sessions.

Isaac Macharia, General Manager for Phytosanitary Services at KEPHIS, highlighted the need for sensitive, reliable and affordable diagnostic tools in Ralstonia detection from stem, tuber and soil samples.  “Since it is field deployable, it will speed up our decision-making for the imports at the port of entry. This would also reduce customer complaints on contamination during transportation of samples to the laboratory,” he said.

The trainees got hands-on training on how to detect Ralstonia from stem, tuber and soil where they participated in extraction, preparation and testing samples using the LAMP assay. They were also taken through the assay validation process where they were shown sigmoid curves that show positive tests for Ralstonia. Trainees were impressed with the technology as it requires fewer reagents, simple laboratory skills and expertise and helps in making informed and fast decisions on whether to accept or reject potato seed in the field. George Ngundo, senior inspector and diagnostician at KEPHIS Muguga appreciated the use of the technique as it is specific and suggested adoption and use during inspections, surveillance and at border points. He further added that, other protocols for diagnosis of various diseases using LAMP assay should be developed.

The current seed potato certification process in Kenya involves traditional laboratory tests such as ELISA (Enzyme-Linked Immunosorbent assay) and PCR (Polymerase chain reaction) in the diagnosis of the bacterial wilt pathogen. Field deployable LAMP assay has proved to be efficient and effective as it is sensitive, rapid, accurate as compared to ELISA and PCR tests and does not require sending samples to the lab for analysis. The introduction of the field-deployable LAMP assay has a significant advantage over the standard ELISA and PCR tests in its suitability for on-site diagnosis be it farmers field or point of entry. It also takes a short time to get the results (0.3 to 1 hour) while other methods can take 2 to 120 hours. Furthermore, the fact that it requires less expertise and its cost effectiveness means that medium and large-scale producers can easily integrate LAMP assay into self-assessment of their seed quality.

Kalpana Sharma, Plant Pathologist from CIP, is confident that faster decision-making arising from less than an hour of using the field-deployable LAMP assay versus the current 14-day practice by KEPHIS, would not only help famers to go for seed or ware potato market but also encourage small and medium-scale producers to become certified seed producers with greater certainty, thus promoting seed sector investment and growth.

Indeed, it will improve the efficiency of seed potato certification processes and seed quality control mechanism thereby increasing the availability of certified seed,” said CIP’s Kalpana Sharma. “Increased accessibility of certified seed to farmers, both large-scale and smallholder, of an assured quality, will positively affect the farming households by reducing their bacterial wilt related losses. In addition, farmers will further benefit from reduced cost for certified seed” she said.

Read more journal articles on LAMP assay

Kubota R. et al. 2008. Detection of Ralstonia solanacearum by loop-mediated isothermal amplification. Phytopathology 98:1045-1051.

Lenarcic R. et al. 2014. Loop-mediated isothermal amplification of specific endoglucanase gene sequence for detection of the bacterial wilt pathogen Ralstonia solanacearum. PLoS One 9:e96027.

Okiro L.A. et al. 2019. Comparative evaluation of LAMP, qPCR, conventional PCR, and ELISA to detect Ralstonia solanacearum in Kenyan potato fields. Plant Disease 103:959-965.



Kenya, seed potato