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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
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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.
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.
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.
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.
References and further reading
Bradbury JF. 1986. Guide to Plant Pathogenic Bacteria. CAB International.
CABI. http://www.cabi.org/. 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: http://www.cabi.org/compendia/cpc/ 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: http://delta-intkey.com/ffl/www/_wintro.htm 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: http://www.dpvweb.net/ 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: http://nt.ars-grin.gov/fungaldatabases/ 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: www.ncbi.nlm.nih.gov/ICTVdb/ Date accessed 20 April 2010.
Index Fungorum Partnership. 2004. Index fungorum. [online] Available from URL: http://www.indexfungorum.org/NAMES/NAMES.asp 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.
Luc M, Sikora RA, Bridge J, editors. 2005. Plant Parasitic Nematodes in Subtropical and tropical Agriculture. CAB International,
National History Museum. 2010. The Global Lepidoptera Names Index. [online] Available from URL: http://www.nhm.ac.uk/research-curation/projects/lepindex/ Date accessed 20 April 2010.
ProMed Mail [online]. Available from URL: http://www.promedmail.org/ Date accessed 20 April 2010.
ScaleNet. All about scale insects. http://www.sel.barc.usda.gov/scalenet/query.htm Date accessed 20 April 2010.
Smith IM, Dunez J, Lelliott RA, Phillips DH, Archer SA. 1988. European Handbook of Plant Diseases. Blackwell Scientific Publications,
The American Phytopathological Society. Plant Disease Notes: An International Journal of Applied Plant Pathology. ASPnet [online] Available from URL: http://www.apsnet.org/pd/ 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.
Pest list identification and prioritization
Contributors to this section: CIP, Lima, Peru (Carols Chuquillanqui, Segundo Fuentes, Ivan Manrique, Giovanna Muller, Willmer Pérez, Reinhard Simon, David Tay); CIP, Nairobi, Kenya (Ian Barker); FERA, UK (Derek Tomlinson, Julian Smith, David Galsworthy, James Woodhall).
How to develope a pest list appropriate to vegetatively propagated plants in tissue culture
The word 'pest' here is as defined in the International Plant Protection Convention IPPC). It encompasses all harmful biotic agents ranging from viroids to weeds and Living Modified Organisms (LMOs).
The production of a pest list is essential to support and facilitate the movement of plant germplasm between countries. The production of such lists is in accordance with the International Plant Protection Convention (IPPC) principles of transparency and cooperation and helps importing countries assess the risk involved in the importation of the germplasm. Pest lists are simply lists of pests associated with a particular host or group of hosts. They may be related to any defined geographical are but most are global, regional or national in perspective.
When considering movement of germplasm in tissue culture the pest list can be narrowed down considerably to include only those organisms that present a risk in tissue culture material. These include viruses, viroids, phytoplasmas and latent and nutritionally demanding bacteria.
Pest list initiation
A pest list should be obtained when a decision has been made to import a plant commodity. The type of material to be imported and the perceived risk of contamination by pests associated with that material will govern the detail required in the list. Thus vegetative propagating material (e.g. potato tubers, cassava cuttings, banana setts) will present a high risk of transmitting a wide range of pests, seeds will present a lower risk and tissue culture material will present the lowest risk. The list should include all the pests that could be introduced with the plant material being imported (see the prioritisation of pests in a pest list document).
Although the information required will vary the information usually required includes:
Scientific name of the pest
Common name of the pest
Synonyms
Former names
Presence or absence in the importing country
Presence or absence in the exporting country
Distribution in importing country
Distribution in exporting country
Quarantine listing by relevant national and regional plant protection organisations
Information that may also be useful to include in the pest list includes:
Type of organism e.g. saprophyte/secondary pathogen/vector etc.
Notes on importance/risk of the pest
Plant part attacked
Symptoms
Likelihood of pest being carried on above ground plant parts
Likelihood of pest being carried on bare (soil free) roots
Likelihood of pest being carried with seed
At this stage it is useful to check with National Plant Protection Organisations of importing and exporting countries for existing pest lists for the plant host being imported as well as any synonyms of the host and closely related species if there is a chance of important pests switching hosts in the countries (or in-country areas) under consideration. Life stages of the plant host may also need to be considered.
Information sources
A first priority is to check plant disease records for the local and exporting country. Available scientific reports, annual and other reports from agricultural research stations and plant health authorities should also be consulted when available. Information may also be obtainable from the regional plant protection organisation covering the countries involved in the transfer of the plant material. Contact details for both national and regional plant protection organisations are available on the IPPC website (www. ippc.int). A list of regional plant protection organizations and their member countries is provided in Appendix 1. References to country and regional disease lists are available (Waller, 2002). However, it is then advisable to conduct a literature search even if pest lists are available for the plant host in the importing and exporting countries. The reason for this is that such lists are often infrequently updated and the pest situation can change within a short period of time (e.g. the increase in the number of recognised cassava mosaic geminiviruses in Africa over recent years).
Key information sources include American Phytopathological Society (APS), CAB abstracts, EPPO as well as more general internet searches (e.g. Google). Recent reviews or books dealing with pests of particular crops are especially useful and can be relatively easily located using internet searches of key words (e.g. viruses, cassava).
Useful starting points are the CABI Crop Protection Compendium and the CABI Forestry Compendium. Searching by host in these compendia can generate a crude list of pests associated with the host, which can then be augmented by searches on the EPPO PQR system. It is useful to include all known synonyms of the pest even if these have not been used for some time.
In some cases, it may be necessary to consider all organisms associated with a particular host and therefore, consideration must be given to whether it is a genuine pest, secondary pathogen or just an incidental record.
Searches on the APS website, CABI compendia and EPPO PQR will have generated a crude pest list. This needs to be divided into the following categories of organism: viruses and viroids, bacteria, phytoplasmas, fungi (including Oomycetes), arthropod pests and nematodes. Some organism groups may be ignored if it is considered that the risks associated with transmission in the material being shipped between countries is minimal (e.g. arthropod pests in tissue culture material). Special attention may need to be given to other groups which can readily be spread in this material (e.g, viruses, viroids, phytoplasmas and some bacteria in tissue culture material).
The ‘crude list’ will need to be augmented by specific searches for each pest group. Key sources for each group are listed below:
Pathogens - general
Pro-Med Plant Disease Reports (http://www.promedmail.org)
Viruses and viroids
ICTVdB (http://www.ncbi.nlm.nih.gov/)
DPV (http://www.dpvweb.net/)
Viroids (http://www.ncbi.nlm.nih.gov/genomes/genlist.cgi?taxid=12884&type=0&name=Viroids)
Bacteria
Bradbury, 1986.
The International Society of Plant Pathology (ISPP) (http://www.isppweb.org/).
Phytoplasmas
Old names as well as names under the revised nomenclature (Firrao et al. 2004) should be searched.
Fungi
Farr et al. (undated).
http://www.indexfungorum.org/
Dictionary of the Fungi, 10th Edition. 2008. Edited by Kirk PM, Cannon PF, Stalpers JA.
Arthropods
CABI Arthropod Name Index (1996)
Hill, 1983 – Tropical Pests
Hill, 1987 – Temperate Pests
Insects
Pest Fruit Flies of the World (http://delta-intkey.com/ffl/www/_wintro.htm)
Lepindex – Global Lepidoptera Names Index (http://www.nhm.ac.uk/research-curation/projects/lepindex/)
Scalenet (http://www.sel.barc.usda.gov/scalenet/query.htm)
Nematodes
Esser RP, 1991.
Luc et al. 2005.
Names of organisms change as more taxonomic information becomes available and so it is important to check the currently approved names of the organisms as well as all synonyms and obsolete names.
One useful general resource is the Catalogue of Life website (http://catalogueoflife.org) and (http://www.species2000.org/) which provides the currently accepted names for a wide range of organisms. Approved fungal names and synonyms are available on the Indexfungorum website (www.indexfungorum.org), whilst approved bacterial and phytoplasma names are available on the ISPP website (http://www.isppweb.org) and in Fiarro et al., (2004) respectively.
Testing
Contributors to this section: CIP, Lima, Peru (Carols Chuquillanqui, Segundo Fuentes, Ivan Manrique, Giovanna Muller, Willmer Pérez, Reinhard Simon, David Tay); CIP, Nairobi, Kenya (Ian Barker); FERA, UK (Derek Tomlinson, Julian Smith, David Galsworthy, Rebecca Weekes)
Ring testing
Proficiency testing
Diagnostic protocols for sweet potato germplasm
Contributors to this section: CIP, Lima, Peru (Carols Chuquillanqui, Segundo Fuentes, Ivan Manrique, Giovanna Muller, Willmer Pérez, Reinhard Simon, David Tay, Liliam Gutarra); CIP, Nairobi, Kenya (Ian Barker); FERA, UK (Derek Tomlinson, Julian Smith, David Galsworthy, James Woodhall).
The following sections provide information on the pests that are within scope of the ISO 17025 accreditation on sweet potato at CIP, Lima, Peru. The information provided includes full biological and control data on the pest, information on distribution and quarantine and detail of the diagnostic approach taken, and serves as a essential reference guide.
