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NextGen Phytosanitation: Rapid Elimination of Viruses from RTB Plants for Crop Improvement and Seed Systems

Project Ongoing

Lengthy phytosanitary cleaning and screening procedures, used to prevent the spread of diseases through the distribution of plant material, are obstacles to the rapid dissemination and use of improved cultivars and genetic gain in clonal crops such as sweetpotato, yam, and cassava. Owing to the need for iterative phytosanitary therapy and indexing cycles until ‘clean’, these procedures significantly delay the testing and release of improved varieties, often resulting in a failure to meet critical planting windows. Methodologies for rapid cleaning and streamlined disease detection are therefore critical to certify that material is virus free.

To develop tools and technologies to generate phytosanitary clean sweetpotato, yam, and cassava germplasm and breeding lines to facilitate rapid dissemination globally of genetic gains from crop improvement programs and agricultural development, especially in sub-Saharan Africa 

Research on meristeming, improved growth media, use of known antivirals, and validation of small RNA sequencing and assembly (sRSA) for virus indexing will be performed at CIP-Lima and IITA-Ibadan for sweetpotato and yam & cassava respectively. Helsinki University will improve the bio-informatics analysis tools and screen potential inhibitors able to control Sweetpotato Virus Disease (SPVD).University of Wisconsin will screen libraries of potential antiviral compounds as new plant therapeutic agents and develop the quickchip for field based diagnostics. Training will be performed in several other African countries.

David Ellis

Avenida la Molina 1895, La Molina, Lima, Peru,

Tel: +51 1 349 6017

Fax: +51 317 5326

Key Project Information

The proposed 3-year research project involves a two-pronged approach to significantly decrease the time needed for detection and phytosanitary cleaning of clonal plant material. First, antiviral therapy and improved tissue culture (TC) methodology will be optimized during the initial in-vitro bulk-up phase of improved lines and germplasm. Second, improved detection methods will be developed using a) small RNA sequence and assembly (sRSA) for lab-based phytosanitary certification and b) a de-gas driven isothermal nucleic acid detection platform (‘QuickChip’) for field and greenhouse testing of propagation materials.


The antiviral therapy will eliminate viruses in plant tissues and/or suppress viral titers during the initial TC phase so that conventional therapy, including meristem isolation, is greatly facilitated. This 4–12-month period provides an opportunity to begin therapy earlier. Improving meristem growth by adjusting TC conditions can significantly shorten this time interval. Both technologies for the second approach, detection of viruses, have been proven for proof of concept and shown great promise in lab-scale experiments with plant viruses (Kreuze et al. 2009; Kashif et al. 2012; Mbanzibwa et al. 2014; Pirovano et al. 2015, Liljander et al. 2015).  The objective is to develop these technologies into operational tools for pathogen detection. The complementary development of the VirusDetect software and the database to house virus sequence information from sRSA will build the resilience of viruses needing detection.


The results will be validated, standardized protocols based on antiviral treatments, improved TC recovery of disease-free plants, sRSA and the QuickChip, fully developed for sweetpotato, yam, and cassava. The results will also be disseminated through partnerships with other larger existing networks for these crops and also through targeted training and capacity building with key NARs partners.


Project Leader: David Ellis 

Project Members: Jan Kreuze (CIP), Lava Kumar (IITA), Gueye Badara (IITA), Jari Valkonenen (Helsinki University), Douglas Weibel (University of Wisconsin – Madison)

Start date October 01, 2016
End date December 31, 2019
Lead organization CIP
Collaborating organizations IITA, University of Wisconsin – Madison, University of Helsinki
Region Global
Countries Peru, Nigeria, capacity building in other African countries
Type of project Development / Dissemination and Research
Financing Sources Bill & Melinda Gates Foundation
Funding Amount (USD) $2,385,906
Members Jan Kreuze


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