Crop Genebank Knowledge Base

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Overview: Testing tissue-culture material of clonal crops for pests

Contributors to this section: CIP, Nairobi, Kenya (Ian Barker); CIP, Lima, Peru (Carols Chuquillanqui, Segundo Fuentes, Ivan Manrique, Giovanna Muller, Wilmer Pérez, Reinhard Simon, David Tay); FERA, UK (Derek Tomlinson, Julian Smith, David Galsworthy, James Woodhall).

In the face of climate change and the urgent need to realise varieties with improved resilience to weather extremes the importance of germplasm collections for breeding is ever apparent. These collections must be made available with assurances of authenticity and freeness from pests1.

1Pest is used as by the definition of FAO to include both pests and disease, and extends to LMO

Crops covered and pest focus
User perspective


Some of the steepest challenges presented by climate change map onto developing countries where already marginal areas of land for production are potentially taken beyond the tipping point of production. Where these countries also map to some of the populations with the highest growth rates, any aspiration to meet the Millennium Development Goals for poverty reduction will require critical change.

A key element in meeting the challenge of climate change will be the cultivation of crops with superior adaptive traits and the cultivation of crops in new areas. The task before the plant breeder is therefore evident. Critical to this aim will be the sharing and movement of well characterised crop germplasms. It is the primary and historic mandate of the CGIAR to be the custodian of many of the most important collections of germplasms, notably of the staple crops of the poor, and to make these available as a global public good.

However, whilst the principle of sharing germplasm as a global public good is recognised, it is incumbent on the CGIAR to ensure that the germplasm are of a specified quality. Trueness to type (authenticity) and viability are the foremost and most evident criteria, but it is also required that germplasms are free of pests prior to movement. Within the literature are numerous records of pests spreading through breeding, and probably via tissue-culture material, with devastating consequences. And thus there is a cruel irony when the good intentions of breeders in sharing material for altruistic ends results in new pest introductions and steeper challenges to climb.

The IBPGR_GPG2 is specifically aligned to ensure seed originating from germplasms is available with assurances of pest-free status, by identifying the best practices that should be entailed to makes such claims. This section specifically looks at tissue-culture material of some of the main clonal crops.

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This section aims to provide a ‘How to guide’ for parties requiring to test tissue-culture plants of clonally propagated crops for pests. In a series of stepwise processes the user is guided through stages of:

  • Pest list identification for tissue culture plants
  • Prioritisation of pest list in the context of the users needs
  • Quality assurance within pest diagnostic laboratory procedures
  • Identification of analytical techniques available for diagnosis and detection
  • Review of analytical techniques in the context of the users requirement and resources available
  • CIP case studies on potato and sweet potato

Information is further supplied on how the testing approach selected can be validated against a quality assured framework.

The premise for the process is based upon the principle of Systematic Review, whereby the end-point (the approach you take) is clearly defined, traceable and repeatable.

Whilst it is not the intention to provide any prioritisation of pests or recommendations on analytical methods, example is made where existing information is available. The example of the International Potato Centre and its approach to accreditation of a plant health passport for its international germplasm collections in Peru for potato and sweet potato is extensively presented.

In this context the section aims to be a living and dynamic resource and provides provision for further population. It helps to identify current gaps in knowledge and best practices and encourages the international community to address these areas.

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Scope: clonal crops covered and pest focus

The section identifies with the 5 main clonal starch crops. Namely, banana, cassava, irish potato, sweet potato and yam. We recognise that many other crops can be propagated by tissue-culture and, if untested, present a pathway for pest spread. Mindful of this, the section is rich in ‘the principle of approach’ and not dogmatic as to what should be applied.

Primarily the resource identifies the need to test for virus and phytoplasms, although some bacterial and fungal pests may equally be of concern. The approach described also allows address for the detection of genetically modified material within tissue culture material.

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The user and framing the question

As a user of the section, you will have in mind a question. In developing the section, we have tried to position ourselves as a user so as to better identify the question and answer the section can assist in delivering.

Foremost this section aims to inform parties interested in sending or receiving tissue-culture material of clonal crops from a source outside the country i.e. international, trans-boundary movement. In this context we recognise an absolute requirement for the identification of all tissue-culture associated pests and application of analytical methods that give rigorous assurance on pest status. In all probability the user will have a zero tolerance for pests. In the context of the CGIAR germplams collections, zero tolerance of pests within the germplasms is a mandatory requirement.

However, the section can also be used to support tissue-culture multiplication for in-country dissemination. In this context the question may be different, in that rather than looking to test for all pests (some that will be over very low probability of presence if not reported in the country or region) a list of a few priority pests may be identified. This allows for country and regional differences to be prioritised over a global pest list.

A further facet of a question is the scale and level of assurance that is required. In testing a small number of tissue-culture plants sophisticated and highly sensitive analytical approaches may be affordable, but if these plant numbers are significant the pragmatics of scale and cost may point towards the use of other methods that are better suited to high throughput. Not invariably, but sometimes, the choice of method identifies with a trade-off on sensitivity to detect, and the user will need to weigh the risks associated with such an outcome.

Reviewing the choice of analytical approach may also identify that the user does not have access to the ‘best’ methods, but can do other methods which have been shown to be less suitable. This again requires the user to attribute what is acceptable risk in the choice of method taken and the required purpose.

In all the above scenarios, the section aims to give support in the users decision-making, not in making the decision, but n framing it and any uncertainty that resides about the choice and testing pathway taken.

Some limitations of the section and the need to share opinions

This resource, in its use, requires a level of expert knowledge in deciphering the risk associated with priority pests and the choices of analytical methods. It also accepted that for all the crops and pests that are likely to be identified the level of knowledge and uncertainty associated with potential harm (consequences of introduction) and efficacy of the analytical approach is uneven. Some pests are well described with a strong body of appropriate information and experience, whereas others are relatively undescribed and require decisions to be made without a wealth of experience to draw on. Likewise some pests, though well described, provide particularly challenging targets for diagnostics. Examples like Banana Streak Virus where there is integration of the virus into plant genomes is an evident example. Likewise the need to detect satellites of Cassava Mosaic Disease presents a subjective challenge.

To recognise these limitations is not weakness, but to identify future strengths and if the section can form a background for greater debate on the risks associated with pests then it will have served a substantial purpose. We encourage you to work collectively, to share ideas and to develop the best systems as meets your needs.

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References and further reading

Bradbury JF. 1986. Guide to Plant Pathogenic Bacteria. CAB International.

CABI. Date accessed 20 April 2010.

CABI Arthropod Name Index on CD-Rom. 1996. Gives information on synonyms and links to old Review of Applied Entomology volumes (including pre-1973).

CABI CPC. CABI Crop Protection Compendium. [online] Available from URL: Date accessed 20 April 2010.

Carroll LE, White IM, Freidberg A, Norrbom AL, Dallwitz MJ, Thompson FC. 2004. Pest Fruit Flies of the World: Larvae. [online] Available from URL: Date accessed 20 April 2010.

DPV Web. Descriptions of plant viruses. EPPO PQR, 2005. EPPO Plant Quarantine Information Retrieval System, Version 4.6, 2007 1 Rue le Notre, 75016, Paris, France [online] Available from URL: Date accessed 20 April 2010.

Esser RP. 1991. A computer ready check list of the genera and species of phytoparasitic nematodes including a list of mnemonically coded subject categories. Florida Dept. of Agriculture and Consumer services, 185 pp.

Evans K, Trudgill DL, Webster JM, editors. 1993. Plant parasitic nematodes in temperate agriculture. CAB International, Wallingford, 648 pp.

Farr DF, Rossman AY, Palm ME, McCray EB. undated. Fungal Databases, Systematic Botany & Mycology Laboratory, ARS, USDA. [online] AVailable from URL: Date accessed 24 July 2007.

Firrao G, Andersen M, Bertaccini A, Boudon E, Bove JM, Daire X, Davis RE, Fletcher J, Garnier M, Gibb KS, Gundersen-Rindal DE, Harrison N, Hiruki C, Kirkpatrick BC, Jones P, Kuske CR, Lee IM, Liefting L, Marcone C, Namba S, Schneider B, Sears BB, Seemuller E, Smart CD, Streten C, Wang K. 2004. 'Candidatus Phytoplasma', a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. International Journal of Systematic and Evolutionary Microbiology 54, 1243-1255.

Hill DS. 1983. Agricultural Insect Pests of the Tropics and their control, 2nd Edition. Cambridge University Press, London, 746 pp.

Hill DS. 1987. Agricultural Insect Pests of Temperate Regions and their control. Cambridge University Press, London, 660 pp.

ICTVdb. The Universal Virus Database of the International Committee on Taxonomy of Viruses. Colombia University. [online] Available from URL: Date accessed 20 April 2010.

Index Fungorum Partnership. 2004. Index fungorum. [online] Available from URL: Date accessed 20 April 2010.

Jeffries CJ. 1998. Potato: FAO/IPGRI Technical guidelines for the safe movement of potato germplasm. International Plant Genetic Resources Institute. Rome, Italy. Available here (1.9 MB)

Jeppson LR, Keiffer HH, Baker EW. 1975. Mites Injurious to Economic Plants, University of California Press, Berkley, 614 pp.

Kirk PM, Cannon PF, Stalpers JA, editors. 2008. Dictionary of the Fungi, 10th Edition. CABI, UK.

Luc M, Sikora RA, Bridge J, editors. 2005. Plant Parasitic Nematodes in Subtropical and tropical Agriculture. CAB International, Wallingford, 871 pp.

National History Museum. 2010. The Global Lepidoptera Names Index. [online] Available from URL: Date accessed 20 April 2010.

ProMed Mail [online]. Available from URL: Date accessed 20 April 2010.

ScaleNet. All about scale insects. Date accessed 20 April 2010.

Smith IM, Dunez J, Lelliott RA, Phillips DH, Archer SA. 1988. European Handbook of Plant Diseases. Blackwell Scientific Publications, Oxford.

The American Phytopathological Society. Plant Disease Notes: An International Journal of Applied Plant Pathology. ASPnet [online] Available from URL: Date accessed 20 April 2010.

Waller JM. 2002. Regional and country lists of plant diseases pp 287-308. In: Waller JM, Lenne JM,  Waller SJ, editors. Plant Pathologist’s Pocketbook. CAB International 2002, 516 pp.

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