Project Outline


Seed degeneration of roots, tubers and bananas

PDF Version of Outline

SECTION C. Description of research project

C1 Title of project: (15 words)

Developing tools for describing, quantifying and managing diseases causing degeneration of planting material in RTB

C2 Summary of project: (100 words)

This project aims to develop practical solutions to the problem of degeneration of planting material. The outputs of the research will be a (suite of) simple model(s) that will predict degeneration (and eventually pathogen virulence) under scenarios applicable to RTB farmers and producers of clean planting material. These models will be simplified into decision support systems (DSS) that are appropriate for different end-users. This research also aims to identify the viral pathogens that cause degeneration in RTBs as these are often the most elusive amongst the pathogens causing degeneration and the extent of their contribution to degeneration remains unknown. In the particular case of viruses we will take advantage of the currently ongoing effort to map the pan-African sweetpotato virome using next-gen sequencing technology to include all other RTBs in the survey and thus map the viruses present in RTBs throughout Africa with selective sampling in Asia and Latin America for better understanding of the approach. A planning workshop is anticipated during the initial months that will have as it aim the development of a more detailed project plan including a logical framework.

C3 What is the rationale for the project considering criteria for eligibility? (150 words)

Degeneration of planting material is a (the?) primary problem of vegetatively propagated crops, including the RTBs. In sexually propagated crops, many pathogens are filtered out in the process of seed production. Furthermore, for the RTBs, there are no simple solutions, such as chemical control, for managing the diseases causing degeneration. There have been efforts to promote systems (regulated or non-regulated) by which planting material can be cleaned and multiplied for distribution to farmers but for many reasons these do not provide a solution for the majority of farmers in developing countries. Preliminary studies show that on-farm or local disease management strategies may be relatively effective, but the biological processes underlying degenerative diseases (as well as clear identification of pathogens involved) are poorly understood. New knowledge generated in this project should lead to readily applicable disease management solutions that can be implemented in the context of both on-farm and commercial production of planting material.

C4 What is the specific purpose of the activity? (100 words)

The purpose is to develop tools that will allow more accurate estimation of the damage caused by degenerative diseases and the effectiveness and feasibility of solutions (for priority setting). Additionally, this activity will produce knowledge needed to develop effective tools (guidelines or DSS) for farmers and commercial seed producers for reducing losses through reversing or reducing the rate of degeneration. These activities will greatly enhance productivity of RTBs in developing countries since degenerative diseases are among the most economically important production constraints.

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C5 What are the tools, methods, and data to be used for the activity? (300 words)

Modeling will be done in the laboratory of Dr. K. Garrett at Kansas St. Univ (KSU); building on existing models developed in the area of virus epidemiology. A post-doctoral scientist with appropriate modeling/GIS skills will be hired for the project. We anticipate that the initial models will be ready by the end of 2012, but these will be refined throughout the project. After the first stage of model development, a series of field studies will be planned for year 2 to i) validate models and ii) produce data to re-parameterize models. On-station and on-farm trials will be implemented in the third year to further refine models and begin validation/adaptation of simple DSS for on-farm and commercial seed production. These trials will involve the identification and quantification of degenerative pathogens in sequential generations of vegetatively propagated RTBs, as well as parameters describing specific processes in the disease cycles of the pathogens, or the effects of factors such as weather and control interventions. In addition, epidemiological studies of specific pathosystems will be carried out in order to support model parameterization.

Initially, we will make use of surveys performed in an ongoing project to determine the sweetpotato virome in Africa. This work will be extended through the project proposed here to include cassava, potato, yams and bananas in Africa as well as in selective sites in Asia and Latin America. The method used (siRNA sequencing and assembly) enables the detection of all viruses or viroids present in the plants (both known and novel ones), thus giving an overview of the presence of degenerative viral diseases in different regions. In subsequent years, surveys will be expanded in greater depth in Latin America and Asia and also include technologies to detect other types of degenerative diseases. Degenerative pathogens will be catalogued and when necessary identified with these techniques in areas where on-station and on-farm trials will be done for model validation (as described above), thus ensuring that model parameters are pathogen specific.

A team of researchers at different centers will coordinate project activities. The team will work closely with KSU in developing the modeling work, and will partner with NARS in target regions. NARS partners will provide knowledge and coordinate on-station and on-farm experimentation.

We anticipate a yearly workshop to present and assess data generated and refine plans for the following year. The final workshop will focus on publication of data and a proposal for scaling out. We will make use of tools to facilitate collaboration and joint authorship such as Skype, Google Docs and/or Dropbox.

C6 What is the impact pathway anticipated for the activity and potential impact? (200 words)

Numerous analyses have identified seed degeneration as one of the major constraints to efficient production of vegetatively propagated crops. This degeneration is caused primarily by plant pathogens and among these, viruses are generally considered to be the most important. Reduction of incidence of these pathogens leads to greater productivity, even without additional inputs. Preliminary research has demonstrated a high potential for on-farm (ware or seed

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producer) management of these diseases, although with a high degree of variation, as little is known of the epidemiology of degenerative diseases. Research done in this project will lead to practical training procedures and simple decision support systems that both farmers and commercial seed producers can use to slow down, halt and in certain cases reverse degeneration of planting material. Since these disease management interventions require minimal inputs by farmers, increased yields translate directly into greater profit and/or food security. The research planned in this project will provide information on the organisms responsible for degeneration of planting material in RTB as well as simple models for predicting the health status of planting material based on biophysical conditions and resulting from disease management interventions. These models will then be used to establish DSS to help farmers and seed producers know when it is practical to implement disease management practices, what type of intervention may be most effective and what level of control can be expected. The tools will also help researchers and policy makers plan training interventions and predict the relative potential benefits of different interventions (e.g, the potential role of host resistance in managing degeneration).

C7 Research plan:

Sub-activity, phase or step

Start date

End date

Planning workshop to review state of the art and define detailed project plan
2012
2012
Determine viruses infecting RTBs in field grown crops using universal next- generation sequencing technique
2012

2014

Catalogue viruses and other pathogens infecting RTBs in field grown crops using classical diagnostic and universal next-generation sequencing techniques

2013

2014
Develop theoretical framework for predicting health status of planting material under different biophysical scenarios and different interventions.
2012
mid 2013

Review existing knowledge on viruses infecting RTBs in order to provide initial parameter values for models

2012

2012

Test framework above in on-station and on–farm trials; measure parameters for model refinement.
2013
End 2014
Develop simple decision support systems for improved production of planting material (reduced or reversed degeneration)
2013
End 2014
Hold yearly workshops to assess progress, process data and plan subsequent activities; specific training may be attached to workshops
2012
2014
Publish new knowledge generated through review described above and project activities
 2012
2014

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C13 What is the communications strategy for the activity? (150 words)

For now partners communicate via Email and use Dropbox. We will soon develop a plan for a Web page – perhaps a temporary one until the meeting then a more permanent one – this should probably be coordinated with the CRP so that there are not many different styles or websites.