Chapter 18: Collecting plant genetic resources and documenting associated indigenous knowledge in the field: a participatory approach

P. Quek
Bioversity International Asia, Pacific and Oceania Regional Office Serdang, Malaysia
E-mail: p.quek(at)cgiar.org
E. Friis-Hansen
Danish Institute for International Studies (DIIS, Politics and Governance Group), Strandgade 56, DK-1401 Copenhagen, Denmark
E-mail: efh(at)diis.dk

This chapter is a synthesis of new knowledge, procedures, best practices and references for collecting plant diversity since the publication of the 1995 volume Collecting Plant Diversity; Technical Guidelines, edited by Luigi Guarino, V. Ramanatha Rao and Robert Reid, and published by CAB International on behalf of the International Plant Genetic Resources Institute (IPGRI) (now Bioversity International), the Food and Agriculture Organization of the United Nations (FAO), the World Conservation Union (IUCN) and the United Nations Environment Programme (UNEP). The original text for Chapter 18: Collecting Plant Genetic Resources and Documenting Associated Indigenous Knowledge in the Field: A Participatory Approach, authored by L. Guarino and E. Friis-Hansen, has been made available online courtesy of CABI. The 2011 update of the Technical Guidelines, edited by L. Guarino, V. Ramanatha Rao and E. Goldberg, has been made available courtesy of Bioversity International.

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Abstract

Over the past 15 years, there has been a paradigm shift in participatory approaches to collecting traditional knowledge associated with plant genetic resources from extracting knowledge for a scientist to use to a focus on how local communities can benefit from involvement with scientists. This reflects an increasing recognition of the fundamental role that farmers continue to play in generating and maintaining the diversity of landraces.

During this period, the plant genetic resource community has shifted emerging recognition of the value of traditional knowledge to general acceptance that a comprehensive approach, such as the methodology of a traditional knowledge journal (TKJ) is needed. This methodology shifts the control of the documentation from the scientist to the community itself. Before collecting ethnobotanical data, scientists play a role in empowering farmers and communities to document their knowledge by themselves. Then, the scientists seek permission to jointly use the knowledge documented. Prior informed consent and material transfer agreements are now an inherent part of ethnobotanical data collecting. The role of ex situ and in situ conservation has taken a new direction with an increased understanding of the links between local culture and the conservation of plants by the community.

Introduction

The 1995 version of this chapter provided an introduction to participatory techniques for collecting the indigenous (traditional) knowledge associated with plant genetic resources. In the mid-1990s the use of social science methods in the plant genetic conservation community was a novelty, and the 1995 chapter provided an overview of the two methodologies widely known at the time – rapid rural appraisal (RRA) and participatory rural appraisal (PRA) – and how these participatory techniques could be used in the “memory banking approach” (Sandoval 1994) to document indigenous knowledge as part of genetic resource conservation. The 1995 chapter discussed more informant-led approaches to collecting indigenous knowledge about plant genetic resources, including the use of local gatekeepers and cognitive mapping of landraces.

Since 1995, participatory approaches have become the mainstream in most aspects of development assistance (for an overview see Friis-Hansen and Kyed 2009). There has been an overall shift from using participation in an instrumental way (to involve the community and extract knowledge in ways defined by external actors) to using participation as part of the community-empowerment process, often in conjunction with more instrumental approaches. Participatory methods for documenting traditional knowledge for plant genetic resources has also shifted direction – from the extraction of knowledge for the use of scientists to a focus on how local communities can benefit from involvement with the scientists. The methodology of a traditional knowledge journal (TKJ) addresses documentation needs at the community level and facilitates its use by scientists. TKJ has been supported by Bioversity International over the last decade; however, this support has mostly been at project conferences. The approach has not yet become an integrated part of the collection of plant genetic resources.

Current status

The process of documenting the traditional knowledge of communities about plant genetic resources can be perceived as exploitation when communities do not benefit from it. The main issues include language, recognition and protection (Quek et al. 2009).

From the community’s perspective, the data collected and the papers produced are in the scientist’s language, so the content is not available to the community. When scientists finish their work, there are usually no funds provided for any translation to benefit the community, and the community loses the possibility of complementing their indigenous knowledge with the scientific knowledge. For the scientists, the knowledge they have captured is in a translated or filtered form and makes reinterpretation difficult, and the original source of the knowledge might no longer be available. In addition, there is no recognition of the farmer as the source of the knowledge.

Before scientists can use the knowledge of communities that have oral traditions, they need to assist the community in documenting this knowledge in their own language for their own use. Then the community’s knowledge may only be used with a citation. This process avoids the one-sided approach where traditional knowledge (TK) is studied without any benefit to the community. The TKJ methodology was developed on the premise that farmers and community members have knowledge that is valid for scientific use and that empowering farmers to do their own documentation addresses the problem of knowledge erosion and enables scientists to have access to the information.

This methodology was first proposed by Quek and Zhang (1997) and has since been developed further and used by several organizations in the Asian region. Figures 18.1 and 18.2 illustrate the methodology, which was also described by Padulosi et al. (2002).

The process starts with the scientist helping the farmer to develop a paper that is authored by the farmer and acknowledges the scientist’s assistance. The scientist then develops his or her interpreted version of the paper or collects the ethnobotanical data and cites the farmer’s paper after obtaining permission to use it. The farmer’s paper can be in any format –from paper for those who can write to audio and video tapes.

Having the farmers’ knowledge documented in their own language enables communities to reuse their traditional knowledge in a manner that is similar to the way scientific communities reuse their knowledge. The farmer is recognized as the author of the paper because the scientist and others will cite it as the source of the information. This allows cultural and social information to become available to be validated by the community for reuse; other farmers can react as well. Knowledge captured in the farmer’s paper is the original source and therefore can be reinterpreted by different scientists if the community allows. This makes reinterpretation of the knowledge possible as science progresses.

Figure 18.1: The farmer’s journal	Figure 18.2: Re-using knowledge

The question one might ask is why we should be concerned about the traditional knowledge of the community when what we are really interested in is data for the conservation of the materials. The answer is that an understanding of the community’s knowledge will provide an understanding of the conservation of plant genetic resources in situ.

At the subsistence level, where most farmers are illiterate, their knowledge is usually passed on by word of mouth. Traditional groups of people have devised different methods of preserving their knowledge by embedding it in folklore, songs and sayings, as well as in their cultural arts and practices. In the process, one can expect the information to change along the way as some information will undoubtedly be omitted or added. Thus, any documentation has to take into account the possibility of such changes over time.
Table 18.1 shows the outcome of the oral tradition of knowledge transmission:

• The knowledge is lost when the knowledge holder passes away.

• The knowledge becomes threatened if there are no recipients for it (e.g., the younger generation is no longer interested).

• The knowledge becomes unwanted (e.g., when it is easier to access commercial drugs than herbs).

• The knowledge becomes just a story when the plants and/or materials used are no longer available (e.g., when they become extinct).

Table 18.1: A Missing Component in Knowledge Transmission

Empowering communities to document their knowledge helps to promote in situ conservation because they then become more interested in maintaining their plant genetic resources. It also validates their knowledge and helps to promote the sharing of knowledge among the community, especially among the youth and children (Naming et al. 2010).

It is extremely important to think about the process prior to community participation. The experiences described here are based on work carried out by the Yunnan Academy of Agricultural Sciences (YAAS) (Dai et al. 2008), the Kyanika Adult Women’s Group (KAWG), the Sarawak Biodiversity Centre (SBC) and the Platform for Agrobiodiversity Research-Climate Change (PAR-CC) project. SBC has 10 years of experience in implementing the TKJ methodology, and they have developed a framework (figure 18.3) that is workable and well received by the ethnic communities (Naming et al. 2010; Tu et al. 2010).

Figure 18.3: Documentation framework for traditional knowledge used by the Sarawak Biodiversity Centre (SBC). Source: Tu et al. (2010)

The documentation process

For the long term, it is good to have communities develop their own vision and mission statements for their reasons for conserving their knowledge. A form for prior informed consent (PIC) will need to be signed by both the community and the scientist. A sample PIC, which was used by PAR-CC, is shown in the box below. It conforms to the code of ethics of the International Society of Ethnobiology (see http://ethnobiology.net/code-of-ethics).

The community should start by making an inventory of plants. It is important to have the list of plants validated by the community in order to clarify names (e.g., a plant can be known by more than one name and, in some cases, a name might be used for more than one plant). To assist in the validation process, members of the community are taught how to make herbarium specimens, which are useful during the documentation process because they provide a framework for the expert to talk on. Experts on various plants are identified by the community, based on the inventory.

Oral documentation can be made on simple tape recorders and video recorders. With the plant specimen in front of the expert, he or she is asked, “What do you want to tell your grandchildren about this plant?” This process allows the community to document their knowledge in a way they are comfortable with. It also facilitates recall and helps ensure the completeness of the knowledge recorded.

The community is encouraged to develop their own ethnobotanical garden so that the children can use the tapes to learn about the useful plants and to maintain knowledge within the community. The process helps to ensure that the knowledge is at least conserved within the community and that it will be available for sharing when the community is ready to share. It also allows the knowledge to evolve over time. In communities where herbalists might claim that their knowledge is a secret, it is still important to emphasize that they should document the knowledge and keep it so that at their death, the knowledge can still be handed over to whoever they have chosen. Otherwise, the cliché “a library is burnt when an elder passes away” becomes a reality.

This gives the community ownership of the knowledge documented; they even have the right to deny the scientists permission to access the knowledge.

Future challenges/needs/gaps

The TKJ methodology may seem to put a hurdle before the scientist collecting ethnobotanical data. The need to assist the community in documenting their traditional knowledge might seem to make their job harder, and the significant increase in cost in terms of both human and financial resources is likely to be the main challenge for widespread use of the TKJ methodology. In the long run, however, once the community has documented their knowledge, then collecting ethnobotanical data becomes similar to conducting a literature review on the plant concerned. Any missing information can be discussed with the knowledge holder, building up the knowledge within the community at the same time.

The process reduces knowledge erosion, and the merging of traditional and scientific knowledge into a common citation system can be realized. This not only provides recognition of the knowledge holder but also empowers the community.

With the documentation system in place, the community will need tools to manage the knowledge it wishes to share. We need to find ways of using information technology to assist the community in creating a database of traditional knowledge.

Access and benefit sharing is a gap that we need to close so that communities feel comfortable with the sharing process. At present only the material transfer agreement (MTA) of the International Treaty on Plant Genetic Resources for Food and Agriculture is available, but a simple model is needed – one that is understandable and implementable by the community.

There is also concern about the loss of traditional knowledge as a result of changing lifestyles, changing priorities, the availability of modern amenities and diminishing dependence on natural resources among indigenous communities (Manurung et al. 2010). An additional concern is rural-urban migration, which poses challenges for communities with closed cultural links to their plants. Moving away from their communities risks the loss of their traditional varieties, especially heirloom varieties, as their culture erodes. Based on the PAR-CC project in Sarawak, where heirloom varieties of rice are maintained by households, based on their culture, there is a need to find ways to allow households to conserve their heirloom seeds longer than they do with traditional methods so that they can move to urban areas for short periods to be with their children and then return to continue their rice-growing culture. It is also possible that genebanks could provide a form of “seed hotel” service so that unclaimed heirloom varieties could be integrated into the national collection, especially for heirloom varieties not shared outside the family.

Issues of knowledge ownership need to be addressed because members of the community might claim individual ownership for knowledge not known to others in the community. This will have an impact on future access and benefit sharing and will need to be resolved to ensure knowledge ownership by the community.

National programmes around plant genetic resources should be stimulated to use the TKJ as an integrated part of their collecting methodology. Experience with attempts to use participatory approaches to collection of local knowledge, such as TKJ, in connection with collection missions, should be evaluated. The TKJ methodology actually prepares the community before the germplasm collection begins and facilitates the use of PRA tools and other assessment methods familiar to scientists.

Conclusions

Within the past decade and a half, the plant genetic resource community has moved from accepting traditional knowledge as a valuable source of information, to embracing the TKJ methodology, which places control over the knowledge is compiled and access to it in the hands of the community rather than the scientist.

The TKJ methodology addresses the need for documentation at the community level and facilitates its use by scientists. It is a step that comes before the scientist’s use of the knowledge and allows the information to be cited. Communities involved in such work will also be involved in conservation at the community level, which will reduce knowledge erosion and facilitate future access to valuable information about plant genetic resources.

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References and further reading

Ceccarelli S, Guimarães EP, Weltizien E, editors. 2009. Plant Breeding and Farmer Participation. Food and Agriculture Organization of the United Nations, Rome.

Dai L, Chengli You, Quek P. 2008. Indigenous Knowledge and Agro-Biodiversity. China Science Press, Beijing.

Friis-Hansen E, Bhuwon S, editors. 2000. Participatory Approaches to the Conservation and Use of Plant Genetic Resources. International Plant Genetic Resource Institute, Rome.

Friis-Hansen E, Kyed MH. 2009. Participation, Decentralization and Human Rights: A Review of Approaches for Strengthening Voice and Accountability in Local Governance. Social Development Department, the World Bank, Washington DC.

Manurung R, Naming M, Tu CL. 2010. Traditional knowledge of genetic resources: its documentation and conservation. In: Mirfat AHS, Salma I, Mohd Rani MY, Mohd Norowi H, Mohd Shukri MA, Erny Sabrina MN, Noor Sarinah MN, Siti Noor Aishikin AH, Nor Asiah I, editors. Second National Conference on Agrobiodiversity Conservation and Sustainable Utilization, Agrobidiversity for Sustainable Economic Development. Malaysian Agricultural Research and Development Institute (MARDI), Malaysia. pp.53.

Naming M, Yu RA, Tu CL. 2010. Traditional knowledge conservation and transmission of agrobiodiversity: sharing of experiences by the Penan community in Mulu Sarawak. In: Mirfat AHS, Salma I, Mohd Rani MY, Mohd Norowi H, Mohd Shukri MA, Erny Sabrina MN, Noor Sarinah MN, Siti Noor Aishikin AH, Nor Asiah I, editors. Second National Conference on Agrobiodiversity Conservation and Sustainable Utilization, Agrobidiversity for Sustainable Economic Development. Malaysian Agricultural Research and Development Institute (MARDI), Malaysia. pp.54.

Padulosi S, Leaman D, Quek P. 2002. Challenges and opportunities in enhancing the conservation and use of medicinal and aromatic plants. Journal of Herbs, Spices and Medicinal Plants 9(4): 243–267. And in: Johnson CB, Franz C, editors. Breeding Research on Aromatic and Medicinal Plants. The Haworth Herbal Press, Abingdon, UK. pp.243-267.

Quek P, Lim ES. 2008. Possible approaches for protection and sharing of traditional knowledge for Malaysia communities. In: Mohd. Shukor Nordin, Salma Idris, Mohd. Said Saad, editors. Agrobiodiversity in Malaysia. Malaysian Agricultural Research and Development Institute (MARDI), Malaysia. pp.141–149.

Quek P, Zhang Z. 1997. Documenting indigenous knowledge: the need for an IK journal. IPGRI-APO Newsletter No.23, August.

Quek P, Manurung R, Naming M, Kimonyi JM, Dai L, Abraham M, Eyzaguirre P, Morimoto Y, Maundu P, Zhang Z. 2009. The traditional knowledge journal (TKJ) methodology empowers communities to document their traditional knowledge. Poster presentation at Knowledge ShareFair for Agricultural Development and Food Security, 20–22 January 2009. Bioversity International, Rome.

Sandoval VN. 1994. Memory banking protocol: a guide for documenting indigenous knowledge associated with traditional crop varieties. In: Prain GD, CP Bagalanon, editors. Local Knowledge, Global Science and Plant Genetic Resources: Towards a Partnership. Proceedings of the International Workshop on Genetic Resources. UPWARD, Los Baños. pp.102–122.

Tu, CL, Naming M, Jovita ER. 2010. Sarawak’s experience – documenting traditional knowledge of useful plants among Sarawak’s indigenous communities. In: Manurung R, Abdullah ZC, Ahmad FB, Kuek C, editors. Biodiversity- Biotechnology: Gateway to Discoveries, Sustainable Utilization and Wealth Creation. Proceedings of the International Symposium, Kuching Sarawak, Malaysia, 19–21 November 2008. Sarawak Biodiversity Centre (SBC), Kuching, Malaysia. pp.112–116.

Internet resources

AGP Knowledge Resources, Plant Production and Protection Division, FAO: www.fao.org/agriculture/crops/core-themes/theme/seeds-pgr/know_res/en

Participation (online courses, discussion, etc.), Informal Working Group on Participatory Approaches & Methods, FAO: www.fao.org/Participation

Literature review of stakeholder participation, Sustainable Development Department, FAO: www.fao.org/sd/PPdirect/PPre0074.htm

Participatory Methodologies, Institute of Development Studies: www.ids.ac.uk/go/research-teams/participation/-power-and-social-change-team/participation-themes/participatory-methodologies

International Society of Ethnobiology: http://ethnobiology.net

International Society of Ethnobiology Code of Ethics: http://ethnobiology.net/code-of-ethics

Other resources

For training in TKJ methodology for scientists and community members, contact

Chief Executive Officer
Sarawak Biodiversity Centre (SBC)
KM20 Jalan Borneo Heights Semengoh
Locked Bag No. 3032
93990 Kuching, Sarawak, Malaysia

Tel: +60 8 2 610610
Fax: +60 2611535
E-mail: tk(at)sbc.org.my

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Chapter 28: Processing of germplasm, associated material and data

M. Mackay
Bioversity International, Rome, Italy via dei Tre Denari 472/A 00057 Maccarese, Rome, Italy
E-mail: m.mackay(at)cgiar.org
A. Alercia
Bioversity International, Rome, Italy via dei Tre Denari 472/A 00057 Maccarese, Rome, Italy
E-mail: a.alercia(at)cgiar.org

This chapter is a synthesis of new knowledge, procedures, best practices and references for collecting plant diversity since the publication of the 1995 volume Collecting Plant Genetic Diversity: Technical Guidelines, edited by Luigi Guarino, V. Ramanatha Rao and Robert Reid, and published by CAB International on behalf of the International Plant Genetic Resources Institute (IPGRI) (now Bioversity International), the Food and Agriculture Organization of the United Nations (FAO), the World Conservation Union (IUCN) and the United Nations Environment Programme (UNEP). The original text for Chapter 28: Processing of Germplasm, Associated Material and Data, authored by J. A. Toll, has been made available online courtesy of CABI. The 2011 update of the Technical Guidelines, edited by L. Guarino, V. Ramanatha Rao and E. Goldberg, has been made available courtesy of Bioversity International.

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Abstract

	A handheld GPS device, which is one of the central technologies in a new CIAT project on site-specific agriculture. (Photo: Neil Palmer/CIAT ).

Together, the material and associated information assembled prior to the completion of a collecting mission represent the most important outcome of the mission. Furthermore, any accessions or reference materials are of little value unless accompanied by the associated information that facilitates their use. There have been few changes to the activities involved with the processing of germplasm, associated material and data acquired during plant collection missions since the original version of these guidelines was published. Changes primarily relate to technological advances and standardization of descriptors, which allow much of the information associated with the mission to be captured electronically, either during or after the actual mission. These include notebook computers, personal digital assistants (PDAs), smartphones, digital cameras and geographic positioning systems (GPS). The data-collection forms used in the past are no longer available but contemporary technology, along with data standards, allow these to be quickly developed and customized for specific genera and situations. Several international initiatives have occurred since 1995; these offer updated information that mainly relates to the data component. This chapter provides guidelines to assist in the processing of germplasm and reference samples along with associated data.

Introduction

While much of the work involving the processing of germplasm, associated material and data is determined during the planning phase of a collecting mission, actually completing these activities may require significant onsite decision making regarding procedures and processes to ensure that the material and its associated information are both as complete and accurate as possible. Since 1995, little has changed in the processing, drying, cleaning, treatment and phytosanitary inspection, sharing out, packaging and dispatch of collected samples. However, in the case of gathering and handling data, there have been some significant changes, mostly associated with the availability of new technologies and the standardization of descriptors to facilitate data gathering, management and storage during the collecting mission, so that their use in research and plant improvement can be facilitated. There are also more options for safety duplication today. International initiatives, such as the International Treaty on Plant Genetic Resources for Food and Agriculture and the Global Crop Diversity Trust, bring additional responsibilities and resources for collectors. And there are many online resources to assist in the planning and execution of collecting missions. These change constantly, but internet search engines enable the most current resources to be quickly located and assessed.

Current Status

The International Plant Genetic Resources Institute (IPGRI) changed its operating name to Bioversity International in 2006. All reference to IPGRI in the original text should now read as ‘Bioversity’.

Since 1995, there have been ongoing technological developments that provide opportunities to electronically capture most, if not all, of the data previously written onto data-collection forms. At that time, most information from collecting missions was captured as hardcopy/written text on standard forms, and photographic records were based on film technology. Today, digital photography has mostly replaced film-based photographs and also provides options for storing and sharing data more widely than what was possible with film-based photographs and slides. Additionally, new technologies can now make the capture, processing, storage and distribution of data much more accurate and efficient.

There are three technological advances relevant to this chapter:

• Portable computers, personal digital assistants (PDAs), smartphones and global positioning systems (GPS) all allow the accurate capture of pertinent data in the field.

• Digital photography makes the capturing, labelling and duplication of images much easier than what was possible in 1995. Image files, together with associated metadata, can be downloaded to computers as required.

• Environmental data associated with collection sites can be electronically harvested using geographic information system (GIS) technology.

The portable computer, now mostly represented by notebook/laptop and netbook designs, allows data to be captured in situ on electronic text-based forms (facsimiles of hardcopy forms) entered directly into a database. This allows ‘data standards’ to be enforced by enabling the operator to select input based only on the accepted standards for the specific data being recorded. For example, the options for ‘biological status’ in the FAO/IPGRI List of Multi-crop Passport Descriptors (MCPD) (FAO/IPGRI 2001) can be fixed in the database as the only permitted values for this data field. More recently, other options have become available for electronically capturing collecting-mission data onsite. These include the PDAs, GPS and smartphones. They employ a number of common operating systems, most of which have GPS and database applications to facilitate the ease of capturing information, processing and storing it, and ensuring quality.

A GPS device can determine the georeference of the collecting site simply and accurately (Kaplan and Hegarty 2006)). The use of a standard geographical datum, such as WGS84, is recommended and should be part of the georeference annotation. Many modern smartphones also have GPS functionality, providing an alternative option for capturing georeferences.

Digital photography, together with associated computer software for annotating, editing and enhancing digital images, allows significant additional information to be captured and reviewed in situ before accepting it for inclusion with the other information associated with each germplasm and/or reference sample.

While time is precious during actual collecting activities, it can be a simple process to capture additional data outside collecting hours. One example would be to harvest environmental information about each collecting site from continuous surface layers of such data stored on a personal computer. These data could include climatic data, such as that available from WorldClim (Hijmans et al. 2005) or other sources (De Pauw 2002). This type of information can be generated in advance by creating continuous surface digital maps for the region where the collecting mission is to take place, for environmental parameters from point data using the ‘thin-plate smoothing spline’ method (Hutchinson and Corbett 1995), as implemented in ANUSPLIN software (Hutchinson 2000). Then the value of each parameter can be extracted from the digital maps for each collecting site and associated with the germplasm sample. Adding value to germplasm in this way requires the use of GIS technology, such as Diva GIS (Hijmans et al. 2001).

The data can be dispatched as hardcopy (computer-generated, typed or handwritten) or on electronic media, or they can be transmitted electronically. A hard copy of the data should accompany sample shipments.

Although many organizations develop their own collecting forms according to their specific needs, this has led to difficulties in data exchange. To address this challenge, Bioversity International, in collaboration with crop experts, promotes the standardization of descriptors, and many crop descriptor lists include a crop-specific collecting form. A useful source of Bioversity descriptors and derived standards is available on the Bioversity website (www.bioversityinternational.org/?id=3737).

Germplasm should be duplicated in at least two other collections. While some base collections are still able to provide a duplication service, it is also recommended that duplication in ‘significant international collections’ (including the CGIAR international collections) be ensured. There is also the option to have material securely backed up in the Svalbard Global Seed Vault (www.croptrust.org/main/arcticseedvault.php?itemid=211).

The IPGRI software mentioned in the earlier version of this chapter, in the section on processing reference samples, no longer exists. Relevant information and descriptors for creating electronic tools for data collection are available from various sources, including Bioversity’s website (www.bioversityinternational.org). Additional information and resources are available from a number of other sites, including the Kew Royal Botanic Gardens (www.kew.org) and the Australian National Botanic Gardens (www.anbg.gov.au). A data-collecting template for direct use or for developing a customized tool for data input will soon be available from Bioversity International.

Future challenges/needs/gaps

Data standards are crucial to the long-term utility of all information gathered during collecting missions. Without accepted standards, information about collecting sites is less easily shared, putting correct identification of germplasm accessions at risk. It is imperative that the MCPD List of passport descriptors (FAO/IPGRI 2001) be used in all collecting activities to facilitate the effective access to and use of collection-site data.

Interoperability and/or linkages between information systems should be a goal behind documenting collection-site data. Interoperability allows systems to work together (inter-operate), thereby sharing data, while links allow users to identify a source of information in one system and then move to the second system using tagged URLs in the first system. These and similar technologies allow many systems to contribute to a greater store of information.

Conclusions

While there have been no significant changes in handling seed and reference samples during the collecting mission, a number of advances in the form of new technologies and standardized descriptors are now widely used for information capture, quality enhancement, processing, storing, distribution and ensuring that the collected germplasm can be more easily utilized in research and breeding programmes.

Updates primarily involve the capturing of data electronically in standardized format, the use of electronic storage and distribution technologies, and the associated shift from using paper forms for data collection and distribution.

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References and further reading

De Pauw E. 2002. An Agro-Ecological Exploration of the Arabian Peninsula. ICARDA, Aleppo, Syria.

FAO. 1993. International code of conduct for plant germplasm collecting and transfer. Appendix E of Report of the Conference of FAO Twenty-seventh Session, Rome, 6–24 November 1993. FAO, Rome.

FAO/IPGRI. 2001. Multi-Crop Passport Descriptors. FAO and IPGRI, Rome.

Hijmans RJ, Guarino L, Cruz M, Rojas E. 2001. Computer tools for spatial analysis of plant genetic resources data: 1. DIVA-GIS. Plant Genetic Resources Newsletter 127:15–19. Available online (accessed 20 January 2012): www.diva-gis.org/docs/pgr127_15-19.pdf.

Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25:1965–1978. Available online (accessed 20 January 2012): www.worldclim.org/worldclim_IJC.pdf.

Hutchinson M. 2000. ANUSPLIN Version 4.1. User Guide. Centre for Resource and Environmental Studies, Australian National University, Canberra, Australia.

Hutchinson M, Corbett J. 1995. Spatial interpolation of climatic data using thin plate smoothing splines. In: FAO, editor. Co-ordination and Harmonisation of Databases and Software for Agroclimatic Applications: Proceedings of an Expert Consultation Held in FAO Rome, Italy, from 29 November to 3 December 1993. FAO, Rome.

Kaplan ED, Hegarty CJ. 2006. Understanding GPS: Principles and Applications. Artech House, London.

Internet resources

Australian National Botanic Gardens: www.anbg.gov.au

Bioversity International: www.bioversityinternational.org

Bioversity International Collecting Missions Database: http://singer.cgiar.org/index.jsp?page=coll-sample-data

Bioversity International Descriptor Lists and Derived Standards: www.bioversityinternational.org/?id=3737

DIVA-GIS: www.diva-gis.org

FAO/IPGRI Multi-Crop Passport Descriptors (MCPD): www.bioversityinternational.org/nc/publications/publication/issue/faoipgri_multi_crop_passport_descriptors.html

Global Crop Diversity Trust: www.croptrust.com

International Treaty on Plant Genetic Resources for Food and Agriculture: www.planttreaty.org

Royal Botanic Gardens, Kew: www.kew.org

Svalbard Global Seed Vault: www.croptrust.org/main/arcticseedvault.php?itemid=211

WorldClim: www.worldclim.org

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Chapter 3. An introduction to plant germplasm exploration and collecting: planning, methods and procedures, follow-up

J. M. M. Engels
Bioversity International, Maccarese, Rome, Italy
E-mail: j.engels(at)cgiar.org

This chapter is a synthesis of new knowledge, procedures, best practices and references for collecting plant diversity since the publication of the 1995 volume Collecting Plant Diversity: Technical Guidelines, edited by Luigi Guarino, V. Ramanatha Rao and Robert Reid, and published by CAB International on behalf of the International Plant Genetic Resources Institute (IPGRI) (now Bioversity International), the Food and Agriculture Organization of the United Nations (FAO), the World Conservation Union (IUCN) and the United Nations Environment Programme (UNEP). The original text for Chapter 3: An Introduction to Plant Germplasm Exploration and Collecting: Planning, Methods and Procedures, Follow-up, authored by J. M. M. Engels, R. K. Arora and L. Guarino, has been made available online courtesy of CABI. The 2011 update of the Technical Guidelines, edited by L. Guarino, V. Ramanatha Rao and E. Goldberg, has been made available courtesy of Bioversity International.

Dedication: This chapter is dedicated to the late Dr R. K. Arora, co-author of the original chapter, who passed away after a brief illness in March 2010.

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Abstract

	Collecting in Kephalonia,Greece. (Photo: S. Petitt; Source: www.cam.ac.uk)
	All collecting information is carefully recorded. (Photo: A.Vezina/Bioversity International)

The significant developments that have occurred in information technologies and molecular genetics and genomics have had a direct and beneficial impact on germplasm exploration and collecting. The powerful information-management tools that are now available to collectors allow them to combine many different data sets and to extract much more practically useful and relevant information for the planning of collecting missions as well as the collecting itself. Furthermore, the political and legal situations regarding the status of and ownership of plant genetic resources have changed drastically over the past 15 years. The implementation of the Convention on Biological Diversity (in 1993), the International Treaty on Plant Genetic Resources for Food and Agriculture (in 2006) and the establishment of the Nagoya Protocol (in 2011) have had and continue to have a significant impact on matters related to the access and benefit sharing of plant genetic resources. Ethical considerations and awareness have also evolved and have become more important for individual scientists when collecting germplasm in foreign countries.

Introduction

Since the first edition of these Technical Guidelines in 1995, there have been significant changes in policy, science and technology that have had a direct impact on exploration and collecting plant genetic resources.

Current Status

Molecular tools

The technological developments that have taken place in molecular biology and genetics over the past 10 to 15 years (particularly the enormous decrease in the price of genotyping) have revolutionized our understanding of the way genetic diversity is spread across populations, species and genepools. This, combined with the new power of information management (including bioinformatics), provides a much better basis for the plant collector to understand the taxonomy of a crop genepool, the sampling strategy to be followed, the sites to visit for collecting and how to optimize the conservation of genetic diversity in collections. There are strategies on how the content of crop collections can be improved (Van Treuren et al. 2009). For example, an optimization strategy that builds on the concept of core collection has been proposed. It relies on hierarchically structuring the crop genepool and assigning a relative importance to each of its different components. The resulting optimized distribution of the number of accessions is compared with the actual distribution, which allows under- and over-representation within a collection to be identified. This proposed optimization strategy is applicable to individual genebanks, as well as consortia of cooperating genebanks, which makes it relevant for ongoing activities aimed at sharing responsibilities among institutions, such as A European Genebank Integrated System (AEGIS) (http://aegis.cgiar.org).

Because of the increased importance of the exchange of DNA samples for research, it is important to include this in the overall collecting strategy. This means that good-quality, properly sampled plant material will become increasingly important, as will knowledge of the considerable differences among species as to which organs or plant parts are the most suitable for DNA extraction. For a very recent and complete publication on collecting for DNA banking, see Gemeinholzer et al. (2010). This paper gives guidelines for all the tasks required for pre-DNA isolation of samples, from both plants and animals. It includes information about sampling strategies, methodological considerations for collecting different types of plant tissues, strategies for tissue preservation and DNA isolation in the field, relevant logistics and safety considerations in the field, labelling of samples and recording essential information, transportation practices from the field to the laboratory and necessary equipment. Further details can be found in Chapter 40 of these Technical Guidelines (on collecting DNA for conservation), and Prendini et al. (2002) provide an earlier overview of this particular field.

In 2004, Bioversity conducted an international survey on the application of DNA technology in their genebanks, and of the 243 respondents, 51 (20.9%) indicated that they store DNA. Almost all of the institutes that store DNA extract it themselves, using standard manual extraction protocols, and one-third of these use commercial kits for DNA extraction. De Vicente and Andersson (2006) list a number of the reasons institutes, including genebanks and other organizations that collect plant genetic resources for food and agriculture (PGRFA), store DNA, as well as which techniques they use to serve their clients.

Information technologies and tools

The increased availability and ease of use of GIS technologies and GPS receivers over the past decade mean that sophisticated spatial analysis can be used routinely to support collecting efforts. Guarino et al. (2002) provide a comprehensive overview of how spatial analysis of the geo-referenced data generated by the process of conservation and use of genetic resources, using GIS, can feed back to enhance and facilitate the process and, indeed, to add value to germplasm collections. GIS allows the extent and distribution of diversity to be analysed and, thus, in the context of this collecting manual, allows the following activities to be undertaken more efficiently:

• ecogeographic surveying: the process of collating information on the taxonomy, genetic diversity, geographic distribution, ecological adaptation and ethnobotany of a plant group, as well as on the geography, ecology, climate and human setting of the study area. Such surveys can allow the identification of areas that are likely to contain genetic resources with specific traits or taxa of interest, areas that are highly diverse, areas that would complement other areas in conservation efforts, areas that contain material that is currently missing or underrepresented in collections, and areas where the genetic resources in question are threatened with genetic erosion. (See also Chapter 14, of this update, on ecogeographic surveys.)

• fieldwork: including field aids and the timing of collecting missions

• the design, management and monitoring of in situ reserves (Monitoring activity, in particular, is of potential relevance in the context of these Guidelines.)

GIS tools allow one to carry out complex analyses combining different (spatially referenced) data sources and to generate maps. This facilitates the uptake of outcomes by responsible authorities and encourages the development and implementation of conservation policies. Tools such as FloraMap (see http://gcmd.nasa.gov/records/CIAT_FloraMap.html) and DIVA-GIS (www.diva-gis.org) can be used to determine potential distributions, assuming that climatic variables are the principal drivers of the geographic spread of plant species. Examples of the successful application of these tools include the location of wild and rare potato species in Peru (Hijmans and Spooner 2001) and optimizing a collecting mission for a rare wild Capsicum species (C. flexuosum) in Paraguay (Jarvis et al. 2005). Spatial analysis using GIS can also be used to identify regions of particularly high species richness and diversity.

The general accessibility and use of the internet has also revolutionised the sharing of data on biodiversity, geography and the environment. Scheldeman and van Zonneveld (2010) have produced a comprehensive training manual cum technical guide on the spatial analysis of data on plant diversity and distribution. See also Chapter 15/16 and Chapter 19 of this update.

Gap analysis is a systematic approach that allows collectors to target areas that contain traits and taxa that are underrepresented in existing ex situ collections. This method has been developed for crop wild relatives (see http://gisweb.ciat.cgiar.org/GapAnalysis/?p=139). The tool is a joint product of Bioversity International, the International Rice Research Institute (IRRI) and the International Centre for Tropical Agriculture (CIAT). More recently, Maxted et al. (2008) used the gap analysis methodology to identify actual areas for the in situ conservation of crop wild relatives.

Legal and policy changes

In the policy area, the developments that have taken place with regard to access and benefit sharing—particularly those resulting from the International Treaty on Plant Genetic Resources for Food and Agriculture (hereinafter "the Treaty") and a number of protocols and agreements related to the Convention on Biological Diversity—have also had a direct influence on the procedures required to obtain access to genetic resources for collecting and/or exchange. The most recent relevant instrument is the so-called Nagoya Protocol on access and benefit sharing that was agreed upon during the COP 10 meeting in Nagoya, Japan, and has been signed by 92 countries, to date.

Prior informed consent (PIC) needs to be obtained from the relevant authorities in a given country before a collecting mission can be conducted, and access (i.e., permission to transfer the germplasm outside the country) is granted on the basis of mutually agreed terms (MAT), which may include measures that cover sharing with the providing country any benefits that might arise from the commercialization and utilization of the germplasm.

For crops and species that are included on the Annex I list of the Treaty, there is a standard material transfer agreement (SMTA) that needs to be concluded before any germplasm can be legally sent and/or received. (For more details on this, see Chapter 2 of these Technical Guidelines, on legal issues.) For non-Annex I crops, a material transfer agreement, established by the national authorities, needs to be included. However, in some instances (as in Europe) it has been agreed to also distribute germplasm that is non-Annex I material from genebanks with an SMTA that includes a specific footnote on its non-Annex I status.

Because of the political changes that have taken place over the past 10 years or so (and which are expected to continue) with respect to access to genetic resources and benefit sharing, organizations like the centres of the Consultative Group on International Agricultural Research (CGIAR) and individual countries have changed or are in the process of adjusting their collecting procedures to the new requirements. For instance, some countries like the following have established national legislation on access and benefit sharing of PGRFA (the years mentioned in brackets relate to the year of publication of the relevant regulation or law; in the case of the Nordic countries these dates are the same as they refer to a regional Ministerial Declaration on Access and Rights to Genetic Resources adopted in 2003): the Philippines (2005) and a number of European countries, including Bulgaria (2002), Denmark (2003), Finland (2003), France (2006), Hungary (2004), Iceland (2003), Italy (2007), Malta (2004), the Netherlands (2002), Norway (2003), Portugal (2002), Russia (2001), Spain (2007), Sweden (2004) and Switzerland (1999).

The legal situation and status of plant genetic resources has drastically changed and widened over the past 15 years. In many countries, the rights and status of local communities have been recognized, and many individuals have become aware of the importance of their own contributions to genetic diversity. With this in mind, it is important for collectors to inform themselves about the ethical considerations related to genetic resources, which might also have an impact on local and indigenous people. Recently, ethical considerations regarding the collecting, research and use of agricultural biodiversity have been reviewed, and recommendations on ethical issues have been made (Engels et al. 2010). Whereas easy access to genetic resources for breeding purposes is important, there are international agreements and legal frameworks that have been developed to ensure adequate recognition of the contributions of local communities and traditional farmers in creating and nurturing these resources. Consequently, Engels et al. (2010) have applied the code of ethics of the International Society of Ethnobotany to plant genetic resources to create awareness among scientists and policymakers who are concerned with agro-biodiversity research and its potential impact on local communities. Collectors are encouraged to seriously consider the ethical principles presented in the paper and to integrate these principles into their personal ethical framework.

The analysed code of ethics recognizes the inalienability of indigenous peoples, traditional societies and local communities: i.e., the right not to have their traditional territories and the natural resources within them, including related practices, cultures and the associated traditional knowledge, affected by the introduction of new but foreign ideas, inventions, knowledge and other findings. Indigenous communities should have the right to decide whether or not to accept such an introduction. The idea of the inalienability of rights has existed for authors of creative works in the "moral rights" aspect of copyright law, as embodied in the concept of the "integrity" of a created work. And a similar principle is included in Article 20 of the UN Declaration on the Rights of Indigenous Peoples, which states that indigenous peoples have the right to maintain and develop their political, economic and social systems or institutions. An example illustrating this principle is the introduction of new crop varieties with "improved" characteristics, such as short-stemmed teff (Eragrostis tef) in Ethiopia. Such varieties were developed without considering the importance of teff straw as a major source of livestock feed during the dry season.

Any research programme aimed at traditional farmers must first assess the needs and requirements of these farmers and include the intended users of the new variety in decisions on the specific breeding objectives for any given crop. Participatory plant-breeding approaches, which are included in a number of development projects, address this principle squarely and are increasingly seen to result in better-adapted and more sustainable varieties (see also Chapter 18 of these Technical Guidelines, on: a participatory approach to collecting plant genetic resources and documenting associated indigenous knowledge in the field). Consequently, in the context of initiatives on participatory breeding and crop improvement that include the collecting of genetic diversity from local farming communities, it would make good sense to involve the local farmers in such collecting activities in a participatory manner.

The principle of equity is another key consideration in the Convention on Biological Diversity and is an important component of the benefit-sharing arrangements that are expected to be established between the researcher or collector and the local people when obtaining and subsequently using agro-biodiversity or local knowledge. It is also one of the principles in the Code of Ethics of the International Society of Ethnobotany (http://ethnobiology.net/code-of-ethics) and is included in the UN Declaration on the Rights of Indigenous Peoples (http://www.un.org/esa/socdev/unpfii/documents/DRIPS_en.pdf): the recognition that indigenous peoples must be fairly and adequately compensated for their contributions to research activities and outcomes involving their knowledge. The FAO Code of Conduct for Germplasm Collecting and Transfer (www.fao.org/nr/cgrfa/cgrfa-global/cgrfa-codes/en) also includes the equitable sharing of benefits arising from the use of collected germplasm.

Future challenges/needs/gaps

• Worldwide, the lack of sufficient and well-qualified human capacity has been reported and experienced in areas that are of critical importance to the collecting of genetic resources, e.g., taxonomy, genetics and ecology (FAO 2010). This is a serious challenge for global conservation efforts, and the organizations connected with conservation at different levels must take action to correct the situation.

• Whereas for a (few) major crops it has been reported that a large part of their genetic diversity is present in ex situ collections, many other crops, particularly the so-called "neglected and underutilized" species, and the crop wild relatives are significantly underrepresented at the species level—and even more so at the level of genetic diversity within species (FAO 2010).

• We now have a better understanding of the extent and nature of gaps in ex situ collections than we did when the first version of these Technical Guidelines was written; however, the picture is still far from complete. The use of molecular data to improve our understanding on the extent, nature and distribution of genetic diversity, more detailed field surveys and better geo-referencing of accessions will be very helpful to more accurately identify gaps and redundancy within and among collections as well as in a given genepool as a whole (FAO 2010).

• As the linkages between in situ and ex situ conservation have not been well defined, at least from a legal perspective, and, for many crop genepools, clear conservation strategies are missing to guide genebanks and their curators, it is not always clear whether it is better to collect from farmers’ fields or natural habitats and store the germplasm ex situ or to keep it in situ/on-farm.

• The potential role of DNA samples and the storage of sequence information for conservation purposes is not fully recognized or established, and this (among other reasons) seems to hamper genebanks in moving forward faster with this technology in the management and distribution of genetic resources.

Conclusions

As a number of the changes and technological developments mentioned above are addressed in more detail in other chapters of these Technical Guidelines, the reader is advised to read the chapters or sections in which these developments and technologies/tools/methods are more fully described. Due to the ever-increasing amount of information the scientific community is producing on many of the species we are interested in collecting, studying and/or using in improvement programmes, there is a danger of information overload, and consequently, it is important to be very clear about the objective of a given exploration or collecting effort and to use the available information to the benefit of that effort.

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References and further reading

De Vicente MC and Anderson MS (eds). 2006. DNA banks-providing novel options for genebanks? Topical Reviews in Agricultural Biodiversity. International Plant Genetic Resources Institute, Rome, Italy. Click here to download this publication. (0.7 MB)

Engels JMM, Dempewolf H, Henson-Apollonio V. 2010. Ethical considerations in agro-biodiversity research, collecting, and use. Journal of Agriculture and Environmental Ethics 24:107–126. DOI 0.1007/s10806-010-9251-9.

FAO. 2010. The Second Report on the State of the World's Plant Genetic Resources for Food and Agriculture. Food and Agriculture Organization of the United Nations, Rome. Available online (accessed 28 October 2011): www.fao.org/agriculture/crops/core-themes/theme/seeds-pgr/sow/sow2/en.

Gemeinholzer B, Rey I, Weising K, Grundmann M, Muellner AN, Zetzsche H, Droege G, Seberg O, Petersen G, Rawson DM, Weigt LA. 2010. Organizing specimen and tissue preservation in the field for subsequent molecular analyses. In: Eymann J, Degreef J, Häuser C, Monje JC, Samyn Y, Vanden Spiegel D, editors. ABC-Taxa, Volume 8. Manual on Field Recording Techniques and Protocols for All Taxa Biodiversity Inventories, Chapter 7. pp.129–157.

Guarino L, Jarvis A, Hijmans RJ, Maxted N. 2002. Geographic information systems (GIS) and the conservation and use of plant genetic resources. In: Engels JMM, Ramanatha Rao V, Brown AHD, Jackson MT, editors. Managing Plant Genetic Diversity. CAB International, Wallingford, UK. pp. 387–404. Available online (accessed 16 February 2012): http://gisweb.ciat.cgiar.org/sig/download/biological_mapping/guarino.pdf.

Hijmans RJ, Spooner DM. 2001. Geographic distribution of wild potato species. American Journal of Botany 88(11):2101–2112. Available online (accessed 18 February 2012): www.amjbot.org/content/88/11/2101.full.pdf.

Hunter D, Heywood VH, editors. 2011. Crop Wild Relatives: A Manual of In Situ Conservation. Issues in Agricultural Biodiversity. Earthscan, London.

Jarvis A, Williams K, Williams D, Guarino L, Caballero PJ, Mottram G. 2005. Use of GIS in optimizing a collecting mission for a rare wild pepper (Capsicum flexuosum Sentn.) in Paraguay. Genetic Resources and Crop Evolution 52(6):671–682. Available online (accessed 18 February 2012): http://ddr.nal.usda.gov/handle/10113/18374.

Kameswara Rao N, Bramel PJ, editors. 2000. Manual of Genebank Operations and Procedures. Technical Manual No. 6. International Crops Research Institute for the Semi-Arid Tropics, Andhra Pradesh, India. Available online (accessed 18 February 2012): http://pdf.usaid.gov/pdf_docs/PNACJ826.pdf.

Maxted N, Dulloo ME, Ford-Lloyd BV, Iriondo J, Jarvis A. 2008. Gap analysis: A tool for complementary genetic conservation assessment. Diversity and Distribution 14(6):1018–1030.

Maxted N, Kell SP. 2009. Establishment of a Global Network for the In Situ Conservation of Crop Wild Relatives: Status and Needs. FAO Commission on Genetic Resources for Food and Agriculture, Food and Agriculture Organization of the United Nations, Rome. (mimeograph)

Prendini L, Hanner R, DeSalle R. 2002. Obtaining, storing and archiving specimens for molecular genetic research. In: DeSalle R, Giribet G, Wheeler W, editors. Techniques in Molecular Systematics and Evolution. Series: Methods and Tools in Biosciences and Medicine. Birkhauser, Basel. pp. 176–248.

Scheldeman X, van Zonneveld M. 2010. Training Manual on Spatial Analysis of Plant Diversity and Distribution. Bioversity International, Rome. Available online (accessed 6 October 2011): www.bioversityinternational.org/training/training_materials/gis_manual/gis_download.html.

Van Treuren R, Engels JMM, Hoekstra R, Van Hintum ThJL. 2009. Optimization of the composition of crop collections for ex situ conservation. Plant Genetic Resources 7:185–193.

Internet resources

A European Genebank Integrated System (AEGIS): http://aegis.cgiar.org

Diva-GIS: www.diva-gis.org

FAO Code of Conduct for Germplasm Collecting and Transfer: www.fao.org/nr/cgrfa/cgrfa-global/cgrfa-codes/en

FloraMap: http://gcmd.nasa.gov/records/CIAT_FloraMap.html

Gap Analysis: http://gisweb.ciat.cgiar.org/GapAnalysis/?p=139

International Society of Ethnobotany (ISE): http://ethnobiology.net

International Treaty for Plant Genetic Resources for Food and Agriculture: www.planttreaty.org

Nagoya Protocol on Access and Benefit Sharing: www.cbd.int/abs

Standard Material Transfer Agreement: www.planttreaty.org/content/what-smta

United Nations Declaration of the Rights of Indigenous Peoples (UNDRIP): www.un.org/esa/socdev/unpfii/documents/DRIPS_en.pdf

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Chapter 41: Gap analysis: A tool for genetic conservation

N. Maxted
School of Biosciences University of Birmingham, Edgbaston Birmingham, UK
E-mail: n.maxted(at)bham.ac.uk
N. P. Castañeda Álvarez
International Center for Tropical Agriculture (CIAT)—Bioversity International Cali, Colombia and School of Biosciences University of Birmingham, Edgbaston Birmingham, UK
E-mail: n.p.castaneda(at)cgiar.org
H. A. Vincent
School of Biosciences University of Birmingham, Edgbaston Birmingham, UK
E-mail: holly.vincent(at)gmail.com
J. Magos Brehm
School of Biosciences University of Birmingham, Edgbaston Birmingham, UK
E-mail: joanabrehm(at)gmail.com

This chapter is a synthesis of new knowledge, procedures, best practices and references for collecting plant diversity since the publication of the 1995 volume Collecting Plant Diversity: Technical Guidelines, edited by Luigi Guarino, V. Ramanatha Rao and Robert Reid, and published by CAB International on behalf of the International Plant Genetic Resources Institute (IPGRI) (now Bioversity International), the Food and Agriculture Organization of the United Nations (FAO), the World Conservation Union (IUCN) and the United Nations Environment Programme (UNEP). The 2011 update of the Technical Guidelines, edited by L. Guarino, V. Ramanatha Rao and E. Goldberg, has been made available courtesy of Bioversity International.

Please send any comments on this chapter using the Comments feature at the bottom of this page. If you wish to contribute new content or references on the subject please do so here.

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References for this chapter

Internet resources for this chapter

Abstract

Gap analysis is a well-established conservation technique used by ecological conservationists to identify areas in which selected elements of biodiversity are represented. Through comparison with existing in situ protected-area networks, it identifies habitats or ecosystems that need additional protection. However, the methodology has recently been adapted for application in the context of broader agro-biodiversity conservation, to encompass both in situ and ex situ strategies for conserving genetic diversity. The extended methodology involves the following steps: (a) circumscription of target taxon and target area, (b) assessment of natural diversity through a review of intrinsic taxonomic, genetic and ecogeographic diversity combined with threat assessment, (c) assessment of current complementary between in situ and ex situ conservation strategies, (d) reformulation of the conservation strategy through analysis of the differences between the pattern of natural, intrinsic diversity and the elements of that diversity already effectively represented by existing in situ and ex situ conservation actions. The methodology is reviewed and illustrated using various temperate and tropical examples of crop wild relatives and landraces.

Introduction

When the original text for chapter 14 of these Technical Guidelines, on ecogeographic surveys, was being prepared, knowledge of the early application of ecological gap analysis was limited and still in the early stages of development (Burley, 1988; Margules et al., 1988; Margules, 1989; Pressey and Nicholls, 1989; Pressey et al., 1993). However, an extensive literature on “gap analysis” (i.e., how to identify areas in which selected elements of biodiversity are underrepresented) has subsequently arisen, including Margules and Pressey (2000) Balmford (2003), Brooks et al. (2004), Lipow et al. (2004), Dietz and Czech (2005), and Riemann and Ezcurra (2005). Although within the wider conservation community, the literature on gap analysis was originally and is still primarily applied to indigenous forests (particularly on small islands rich in endemic species), the technique has recently been extended to agro-biodiversity conservation, encompassing conservation strategies for both in situ and ex situ genetic diversity. Maxted et al. (2008a) showed how the existing methodology might be adapted for more general conservation use and proposed a specific methodology. Subsequently, gap analysis has rapidly established itself as the methodology for conservation planning (FAO, 2009; Maxted and Kell, 2009; Parra-Quijano et al., 2012a; Ramírez-Villegas et al., 2010). As stressed in the update of chapter 14 on ecogeographic surveys, the current application of gap analysis techniques is not replacing ecogeography; it has, in effect, subsumed ecogeography as an element within the broader, more schematic gap analysis protocol. As such, ecogeographic surveys will continue to be routinely undertaken, but increasingly within the broader context of gap analysis. Therefore, chapter 14 can be seen as a sister chapter to this chapter, which specifically addresses gap analysis and should be read in conjunction with that chapter. Both ecogeographic surveys and gap analysis form essential components in planning for plant genetic-resource conservation.

The basic premise of gap analysis is that the target taxon’s ecogeographic and genetic distribution and diversity are compared with the elements that are currently actively conserved.¹ The “gap” is therefore the component of the target taxon’s ecogeographic and genetic distribution and diversity that is not currently actively conserved and which becomes the conservation priority. As such, the protocol for genetic gap analysis involves four steps: (a) circumscription of taxa, (b) identifying the breadth of ecogeographic and genetic distribution and diversity for the target taxa, (c) matching current in situ and ex situ conservation actions with the breadth of ecogeographic and genetic distribution and diversity to identify the conservation “gaps” and (d) formulating a revised in situ and ex situ conservation strategy (Maxted et al., 2008a).

¹ “Active conservation” is where the target taxon population is specifically managed to maintain its diversity, as opposed to “passive conservation” where the site is managed and it is hoped that the target taxon population benefits from the general site-based management.

Current status

Circumscription of target taxon and target area

The first step in the gap analysis protocol is to establish the taxonomic (e.g., genus, section or species) and geographic (e.g., global, regional, country or provincial) breadth of the analysis. The approach that has largely been applied thus far is for individual analyses to focus on distinct crop genepools, see Maxted et al. (2005), Maxted et al. (2008b) and the CIAT-IRRI-Bioversity International GapAnalysis project (http://gisweb.ciat.cgiar.org/gapanalysis). However, in terms of establishing in situ and ex situ conservation priorities, it might be of greater practical value and more cost efficient to establish multi-genepool conservation targets irrespective of individual genepool results, so collection or establishing genetic reserves is led by overall targets for plant genetic resources. This multi-genepool approach was taken by Maxted et al. (2012) for the temperate legume genera Cicer, Lathyrus, Lens, Medicago, Pisum and Vicia species (see figure 41.1) and by Whitehouse (2011) for the in situ conservation of temperate cereal genera Avena, Aegilops, Hordeum, Secale and Triticum (see figure 41.2). Interestingly, both the legume and cereal analysis showed the area at the northern end of the Bekaa Valley in Lebanon and Syria to be a target for in situ and ex situ conservation action for both wild legumes and cereals. Both analyses showed some coincidence between undertaking the analysis for each genepool separately and the combined legume or cereal analyses, but for the legumes, the chickpea and the oat genepools, the individual analyses were quite distinct from the combined analyses.

Figure 41.1: Complementarity analysis for Cicer, Lathyrus, Lens, Medicago, Pisum and Vicia species. Source: Maxted et al. (2012).

Figure 41.2: Complementary analysis Avena, Aegilops, Hordeum, Secale and Triticum species. Source: Whitehouse (2011).

Further, the International Center for Tropical Agriculture (CIAT) in collaboration with the International Rice Research Institute (IRRI) and Bioversity International undertook a gap analysis to identify the gaps in the ex situ collections of the crop wild relatives (CWR) of 13 crop genepools² (figure 41.3) (see http://gisweb.ciat.cgiar.org/gapanalysis), using all the species in the genus as the basis of the analysis. The conclusion was that if overall conservation of plant genetic resources is the aim, combining genepools for analysis may be an effective technique for identifying the highest priority sites but individual genepool priorities might be missed where the included taxa deviate from the combined norm, so a combination of using the individual and combined genepool approach is recommended.

² Pigeon pea (Cajanus), chickpea (Cicer), finger millet (Eleusine), barley (Hordeum), lentil (Lens), pearl millet (Pennisetum), bean (Phaseolus), sorghum (Sorghum), wheat (Triticum and Aegilops), faba bean (Vicia), cowpea (Vigna) and maize (Zea).

Figure 41.3: Priorities for in situ and ex situ conservation of the crop wild relatives of 13 genepools: (A) Taxa-level priorities (B) Genus-level priorities

Source: http://gisweb.ciat.cgiar.org/gapanalysis.

In the case of the CIAT study, a large number of taxa and areas were identified as priorities for conservation. As seen in figure 41.3, the number of taxa requiring further conservation is concentrated in a wide proportion of the African continent and northern Australia. When these priorities are summarized at the genus level, places where four different genera are potentially found is Madagascar, followed by central Africa, northern Australia and western Mexico. What all these priority regions have in common is the absence of large protected areas that could serve for the in situ conservation of the plant genetic resources of the crops aforementioned.

Subsequently, it has been proposed that gap analysis should not be based on the whole genus alone, but should also consider the analysis of the priority species as well, the reason being that in larger genera, the bulk of the species that are unlikely to be of immediate potential use might mask the ecogeographic distribution of those species of highest potential value. This can be illustrated by the case of cowpea relatives in sub-Saharan Africa. Moray and Maxted (2012) compared the results of analysing the whole genus of 124 Vigna taxa with the 14 Vigna taxa present in the primary (gp1) and secondary genepools (gp2), those most closely related to cowpea, and, perhaps not surprisingly, found the results were distinct (see figures 41.4 and 41.5). The conclusion was that if you are trying to establish the priority areas for ex situ or in situ conservation, then, as funds are likely to be limiting, the gap analysis should consider the priority taxa alone as well as the whole genus, allowing an informed decision to be made as to where to focus conservation. As noted in chapter 14, a Harlan and de Wet Global Priority Checklist of CWR Taxa (Vincent et al., 2012) is now available for 173 crop genepools, based on a published genepool and taxon group concept (see www.cwrdiversity.org). This will guide those wishing to establish which CWR should be included in gap analysis based on their priority as trait donors for breeding.

Figure 41.4: Complementary analysis for all 124 African Vigna taxa. Note: The darker green squares represent the highest priority regions for conservation, while the orange and red squares identify areas of lower priority. Source: Moray and Maxted (2012).

Figure 41.5: Complementary analysis for 14 priority African Vigna taxa (primary and secondary CWR taxa). Source: (Moray and Maxted (2012).

A third option would be to give different weights to different species in the analysis, based on their relative rarity. See Arponen et al. (2005) and Venevsky and Venevskaya (2005) for further discussion of weighted endemism. This approach has yet to be widely applied in the context of genetic resources but is available in the WorldMap software (see internet resources, below). It is also advisable not to ignore the wider potential genepool, which might contain further non-genepool and taxon group-concept priority taxa with useful traits, especially if tertiary genepool taxa have previously been used in breeding.

Assessment of natural diversity

The level of diversity occurring within the target taxon must be defined at the taxonomic, genetic or ecogeographic levels (i.e., how many taxa occur in the circumscribed taxon and what is their ecogeographic pattern of distribution).

Assessment of taxonomic diversity

Assessing taxonomic diversity involves listing the taxa encompassed by the taxonomic circumspection, whether for the entire genus or for genera (as in the case of Triticum aestivum, which has priority species in three genera: Aegilops, Amblyopyrum and Triticum). This is likely to involve identifying the accepted classification for the target taxon by consulting specialist publications and taxon experts, or searching online sources of information. As noted above, the analysis will usually be based on the highest priority taxa in genepool GP1B or GP2 or, if the genepool concept is unavailable, the equivalent taxon group TG1-3. Genepool and taxon group concepts with the included accepted taxa and synonyms are listed in the Harlan and de Wet Global Priority Checklist of CWR Taxa (Vincent et al., 2012) (see www.cwrdiversity.org).

Assessment of genetic diversity

Having established the list of taxa to be included in the gap analysis, the next step would be to collate existing data or generate new data on the inherent genetic diversity within those taxa. However, this might not be realistic because the knowledge about inherent patterns of genetic diversity is often limited and it could be too resource intensive to collate de novo. Consequently, genetically based approaches to conservation assessment, either in terms of “richness” (the total number of genotypes or alleles present regardless of frequency) or “evenness” (the evenness of the frequencies of different alleles or genotypes), can therefore only be applied to the most highly prioritized taxa. However, proxy or surrogate measures of genetic diversity may be applied, and it can be argued that ecogeography can act as an adequate proxy when there is a lack of specific data on genetic diversity. It should be remembered, however, that using any proxy will not be as accurate as using primary data.

As an example of the use of data on genetic diversity in conservation planning, van Zonneveld et al. (2012) used microsatellite markers to understand the spatial genetic diversity of Annona cherimola throughout the Andean region in Peru, Ecuador and Bolivia, finding places with the highest genetic diversity (southern Ecuador and northern Peru), places that are a priority for in situ conservation (southern Ecuador and northern Peru) and existing gaps in ex situ collections (southern Ecuador). In a classic study, Ferguson et al. (1998) investigated the relationship between ecogeography and genetic diversity in the wild lentil genepool. The distribution and genetic diversity of Lens culinaris subsp. orientalis show that the subspecies is geographically distributed from western Turkey to Tajikistan, but if the genetic diversity is partitioned into 10 clusters, then the bulk of the genetic diversity is focused almost entirely in the western part of the fertile crescent; thus, in this case, ecogeographic data would not be an adequate proxy for genetic diversity as it would indicate ex situ sampling or the establishment of an in situ genetic reserve across the geographic distribution rather than concentrating both in the western Fertile Crescent, as indicated in figure 41.6. Whether genetic diversity is studied or, as commonly occurs, ecogeography is used as a proxy for genetic diversity, an additional assessment will need to be made of the genetic diversity that exists in natural taxa or populations in order to determine if it is well represented by the samples held in genebanks or by populations represented in protected areas or genetic reserves.

Figure 41.6: Distribution of Lens culinaris subsp. orientalis divided into 10 clusters of genetic diversity. Source: Ferguson et al. (1998).

Assessment of ecogeographic diversity

As there is a lack of knowledge of natural patterns of genetic diversity for the vast majority of crop wild relatives, it is often necessary to employ some form of proxy measure such as ecogeographic diversity (merely because of the prohibitive cost of undertaking genetic diversity studies de novo), even if we know that it might not be an adequate proxy of genetic diversity. Assessing ecogeographic diversity involves the collation of secondary information on the ecology and geography of the species under study (see chapter 14; Guarino et al., 2006; Maxted and Guarino, 2003). The collation and analysis of ecogeographic data is discussed in detail in the original version of chapter 14, along with its update, and so will not be reiterated here.

Recently, Parra-Quijano et al. (2012b) extended the concept of ecogeographic analysis by creating and testing an ecogeographic land characterization map for Spain. The map characterized the habitat preferences of plant species and their adaptations to the environment. Subsequently, this map was used for identifying ecogeographic gaps by comparing those categories represented in ex situ facilities with the categories occurring within the potential niche of the species (Parra-Quijano et al., 2011a). During the collection stage, Parra-Quijano et al. (2011a) identified two populations of Lupinus angustifolius, each occurring in different ecogeographic categories and displaying different phenotypes that may be understood as the adaptation response to these ecological characteristics. Using a similar approach, Ramírez-Villegas et al. (2010) performed a principal component analysis with 19 bioclimatic variables. They took the first two components and divided each into 20 different classes to compare the potential coverage of each species with the germplasm coverage and then assigned numerical scores according to the level of ecological representativeness in germplasm facilities.

Ecogeographic data is useful for determining the habitat requirements of a particular group of plant species and for understanding sympatric distributions of taxa within a genepool. This latter is illustrated in figure 41.7, where a selection of the wild relatives of cultivated tomato (section Lycopersicoides) is grouped according to their bioclimatic requirements. Solanum galapagense (orange polygon) and S. cheesmaniae (aquamarine polygon) are species occurring specifically in the Galapagos Islands (Ecuador). Their niche characteristics diverge from most of the other species in the section, as reflected in the graph. In the case of S. chilense (yellow polygon), part of its habitat requirement coincides with most of the section but a large part also gravitates towards PC1, suggesting a probable adaptation to ecological conditions that is not seen in the rest of the species.

To obtain the most comprehensive view of a taxon’s ecogeographic diversity, data should be collated from herbaria and genebanks (see chapter 14 for a detailed discussion). Herbarium data can be collected from online sources such as GBIF (http://data.gbif.org), personal visits to herbaria, inventories and literature reviews. While germplasm passport data can be obtained from sources such as GENESYS (www.genesys-pgr.org), which brings together information from the germplasm banks in trust with the members of the Consortium of International Agricultural Research Centers (http://singer.cgiar.org), the European ex situ collections (EURISCO, http://eurisco.ecpgr.org) and the plant germplasm system of the United States (www.ars-grin.gov/npgs/searchgrin.html).

Ecogeography is also useful for “predictive characterization”, proposing inferences based on ecological adaptations and the potential identification of desirable traits for adaptation to abiotic and biotic conditions of interest for breeders (such as resistance to insect pests). A specific application of predictive characterization is focused identification of germplasm strategy (FIGS) (see www.figstraitmine.org). This approach combines the information available on climate and ecogeography, species distribution and the distribution of a particular trait of interest (such as resistance to pests or diseases) in order to create environmental profiles of the habitats in which a given population (genotype) might have evolved. FIGS has been used to successfully identify seven new alleles for resistance to powdery mildew (genePm3) from an initial number of 16,089 wheat accessions (see Bhullar et al., 2009). The use of the FIGS methodology can thus aid breeders in identifying the in situ populations or ex situ accessions of crop landraces or wild relatives most likely to contain the traits of interest (MacKay and Street, 2004).

Figure 41.7: Kernel-density plot of the first two dimensions of an assessment based on variables derived from temperature and precipitation, for the section Lycopersicoides, genus Solanum

Threat assessment

This is an important facet of gap analysis, because it facilitates the relative assessment of conservation priorities: those taxa most threatened will have a higher conservation priority than those less threatened.

Threat assessment is now routinely carried out through the application of the IUCN Red List Categories Version 3.1 (IUCN, 2001). Using associated data from herbaria or genebank accessions as a basis for the assessment, the most likely criteria to be used are criterion B (geographic range in the form of either extent of occurrence or area of occupancy) and D (very small or restricted population). Each year more taxa are included in global, regional and national Red Data lists, but until recently only a relatively small number of plant taxa (and particularly CWR taxa) had been assessed.

Recently, a project funded by the European Community specifically undertook an IUCN Red List assessment for priority European CWR diversity (Bilz et al., 2011; Kell et al., 2012). The CWR species were selected on the basis of being native to Europe, the economic importance of their related crop, their relative relationship to the crop (i.e., ease of trait transfer to the crop) and their inclusion on Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture (“the Treaty”). The final list of CWR species to be assessed comprised 591 species in 25 crop genepools/groups, 188 of which were endemic to Europe. However, 20 were subsequently assessed as “Not Applicable”, either due to their marginal occurrence in Europe or because they were introduced to Europe after 1500 AD. The status of the remaining 571 species was assessed at two regional levels: geographical Europe (572 species) and the 27 EU member states. At the European level, 313 (55%) were assessed as “Least Concern”, 166 (29%) as “Data Deficient”, 26 (5%) as “Near Threatened”, 22 (4%) as “Vulnerable”, 25 (4%) as “Endangered” and 19 (3%) as “Critically Endangered”. The priority in Europe would therefore be to focus attention on the 66 “Critically Endangered”, “Endangered” and “Vulnerable” species. This, it is hoped, will prove a useful resource for Europe, but the lack of population data is likely to remain a limitation in wider IUCN Red List assessments in other regions.

In the absence of sufficiently detailed population data to undertake an IUCN Red List assessment, a relatively large ecogeographic dataset can be used to make a more tentative threat assessment. Maxted et al. (2005) proposed and applied a technique referred to as taxon vulnerability assessment in situations where there was insufficient data to permit a formal IUCN Red Listing. Vulnerability to a loss of genetic diversity (and even extinction) can be assessed by compounding seven criteria as follows:

1. Rarity is estimated from the total number of herbarium specimens and genebank accessions of each taxon in the ecogeographic database. It is assumed that in most cases this will provide a true indicator of actual occurrence, unless there is evidence to the contrary or the taxon is cultivated or very rare, both of which cases can lead to relative over-sampling by collectors.

2. Distributional range is calculated by taking a given radius around each collecting locality and then merging the resulting circles, providing an approximation of the overall species range using the methodology described by Hijmans and Spooner (2001).

3. Representation in ex situ collections compared to herbarium collections can provide a relative estimate of whether a species’ genepool is sufficiently sampled ex situ.

4. The relative geographic coverage of ex situ collections is compared to the geographic breadth, based on ex situ conserved accessions and herbarium samples.

5. Intra-species coverage of ex situ collections can be used comparatively for species that have multiple infra-specific categories to estimate if each infra-specific taxon is adequately represented in ex situ collections.

6. The usage potential of a species is particularly relevant for the conservation of plant genetic resources, where there will be a particular incentive for conserving those species with the highest use potential. It might also be the case that species with high use potential are more likely to be threatened due to excessive utilization.

7. An assessment of taxon extinction can be estimated by applying Solow’s equation (Solow, 1993) as proposed by Burgman et al. (1995), which uses a combination of collection timing, frequency and specimen numbers.

Each of these seven criteria is assessed for each species, and a numerical score is recorded. These are then summed to establish relative taxon vulnerability.

Assessment of current conservation strategies

The diversity occurring naturally in situ can be compared to the diversity currently conserved in order to assess the efficiency of both in situ and ex situ conservation techniques and so identify the weaknesses (gaps).

Assessment of in situ conservation

Within the context of plant conservation, the definition of in situ conservation provided by the Convention on Biological Diversity (CBD) (1992) includes two distinct conservation techniques: protected area (genetic reserve) conservation for wild species and on-farm conservation in the case of traditional crop varieties, widely known as landraces. Genetic reserve conservation maintains wild species in their natural surroundings, usually within an existing protected area where the site has been selected and is managed and monitored to maintain the genetic diversity of the target taxa.

• Genetic reserve/protected area assessment: This involves a review of existing protected areas and the species within them that are being actively managed for conservation. As few centralized databases detail which species are being actively conserved in the world’s protected areas, obtaining detailed knowledge of the protected areas in the target area is likely to involve contacting the managers of these areas to ascertain if particular species are present and being actively managed and monitored. It is increasingly possible to use geographic information system (GIS) techniques to compare the protected area spatial layers from the World Database of Protected Areas (http://protectedplanet.net) with species distributional data to predict which priority species are found in which protected areas. But, having matched these datasets, there would still be a need to contact the managers of specific protected areas in order to confirm that the species predicted to be present are indeed present.

• On-farm conservation assessment: Similarly, the on-farm conservation of landraces requires reviewing existing on-farm conservation projects and the crop species included. The review of on-farm conservation is likely to be simpler than the review of protected areas due to the more limited number of on-farm conservation projects and the relative ease of discovering which crop species are included.

In terms of assessing in situ conservation, it must be admitted that there are so few locations where there is currently any effective in situ conservation of agrobiodiversity, the sites where natural target-taxon diversity is located are almost always likely to be those sites where in situ conservation is recommended.

Assessment of ex situ conservation

To assess the gross completeness of material conserved ex situ, a comparison should be made between the unique samples recorded from herbaria versus those from genebanks, although these sources of information can become outdated (Bettencourt et al., 1989). Other sources of material that is currently being conserved can be obtained from botanic gardens, as well as from national and international catalogues, databases and web sites. Herbarium data can be collected from online sources (such as GBIF, http://data.gbif.org), personal visits to herbaria, inventories and literature reviews. Germplasm passport data can also be obtained from sources like GENESYS (www.genesys-pgr.org), which brings together information from the germplasm banks in trust with the members of the Consortium of International Agricultural Research Centers (http://singer.cgiar.org), the European ex situ collections (http://eurisco.ecpgr.org) and the plant germplasm system of the United States of America (www.ars-grin.gov/npgs/searchgrin.html). Other initiatives, such as that of the European Native Seed Conservation Network are now in the process of providing additional wild-species genebank accessions associated with botanic gardens through the European Native Seed Conservation Network Database (ENSCOBASE) (http://enscobase.maich.gr). Depending on the extent and scope of the study, local sources could also be considered for obtaining data. As an illustration, figure 41.8 shows the sampling deficiencies for the crop wild relatives of tomato. The bold line in the graph represents the average representativeness of the dataset used, and the dashed line is the total representativeness. Taxa located below the bold line have fewer samples in ex situ holdings compared with the number of samples in herbaria (ex situ sampling deficient). In this case, the “gap” under-collected species are S. habrochaites, S. corneliomulleri, S. juglandifolium and S. cheesmaniae.

Figure 41.8: Number of genebank samples of the wild relatives of tomato (Solanum lycopersicum) versus total samples (total is calculated by adding germplasm and herbarium samples)

When using ecogeographic distribution as a proxy for data on genetic diversity, the ideal ex situ collection would contain samples from geographically diverse sites spread throughout the entire range of distribution of the crop or species. Such a proxy can be calculated using herbarium and genebank collection data, and the circular area statistic (CA) (Hijmans et al., 2001). CA is calculated by assigning a circle of set radius around each collection, and the total area of those circles for all collections is calculated (counting overlapping regions only once). For collections that are geographically highly concentrated, the CA is relatively low compared to a set of collections that are geographically distributed over a wide region (due to greater overlap in clumped collections). This statistic can be used to compare germplasm collections with all collections (germplasm and herbarium collection data) in order to identify how geographically representative the germplasm collection is. Germplasm collections whose geographic distribution is representative should have a CA statistic similar to that of the entire collection. Conversely, germplasm collections where the geographic distribution is poorly represented would have a low CA compared to the entire collection, due to concentrated ex situ collecting in regions representing only a subset of the wider distribution of the species.

Ramírez-Villegas et al. (2010) used a quantitative approach to determine the requirements for ex situ conservation of the genus Phaseolus, assessing three concepts per taxon level: sampling representativeness, geographical and environmental coverage. Sampling representativeness consists of a comparison between the total number of populations sampled and those sampled as genebank accessions. This is referred to as the sampling representativeness score (SRS). Ramírez-Villegas et al. estimated geographical coverage by comparing the potential distribution of the taxon with the circular statistic (CA) within a 50km radius of the germplasm samples, this value is stored as the geographic representativeness score (GRS). The environmental coverage representativeness (or environmental representativeness score, ERS) is estimated by overlapping the whole geographic extent of the taxon with the two principal components of 19 bioclimatic variables and the corresponding germplasm accessions. The final priority score (FPS) is calculated by averaging SRS, GRS and ERS. The lower the value of FPS, the higher the priority for conserving the taxon. Additionally, Ramírez-Villegas et al. (2010) validated the priority for the conservation list produced after applying this methodology by comparing it with the scores given by a recognized expert on Phaseolus (Dr Daniel Debouck), obtaining a high correspondence with his priorities for conservation (reported as rho=0.788).

Reformulation of conservation strategy

An assessment of the effectiveness of current conservation coverage in relation to natural in situ diversity identifies the element of diversity that is under-conserved, i.e. the “gaps” in the existing conservation strategy, and helps refocus the strategy to conserve the maximum diversity and to fill these gaps. The revised priorities are likely to require complementary in situ and ex situ conservation actions to ensure the comprehensive conservation of the target taxon’s genepool.

In situ conservation priorities

Genetic reserve/protected area

The location and establishment of genetic reserves should be based on the gap analysis outlining the most appropriate location for the genetic reserve. Genetic reserves will commonly be established within existing protected areas because (a) these sites already have an associated long-term conservation ethos and are less prone to hasty management changes associated with private land or roadsides where conservation value and sustainability is not a consideration, (b) it is relatively easy to amend the existing site management to facilitate genetic conservation of CWR species and (c) it means that creating new conservation sites can be avoided, thereby also avoiding the possibly prohibitive cost of acquiring land that had not previously been managed for conservation (Maxted et al., 2008c). Therefore, the simplest way forward in economic and political terms is to locate genetic reserves in existing protected areas, such as national parks or heritage sites. This is likely to provide some benefit to local people and so is also likely to gain their support when participatory approaches are employed.

On-farm conservation priorities

Traditional crop or landrace richness can be used to indicate priority sites for in situ conservation for the on-farm conservation of landraces. Areas that have a high concentration of landraces (either of multiple or individual crops) are desired for on-farm conservation projects.

Ex situ conservation priorities

Species and areas within a species range that have been under-sampled in ex situ collections are highlighted as priorities for future collection and subsequent ex situ conservation.

Future challenges/needs/gaps

In the medium term, the understanding of patterns of genetic diversity and their relation to elements of the landscape will allow us to recognize in more detail where the areas of allele richness and uniqueness are, and if there is a correlation with the local environment, thus confirming the validity of using subrogates of diversity such as ecogeographic methods. These analyses could be performed in genepools or genebank collections that have been largely characterized at the molecular level. Increasing interest in (and need for) conserving key plant species should be prioritized using a gap analysis approach, so that the allocation of resources will target the most important species (whether for food, forage, breeding, cultural matters or any other ecosystem service). And finally, there are different types of refined and structured methodologies for gap analysis in the conservation area. Those methodologies based on computer scripts should use open-source coding and should be user friendly, thereby encouraging their use and avoiding the limitations that licensed software might impose to users with restricted budgets.

Two key global initiatives are currently underway and both have at their heart the gap analysis of agrobiodiversity. The Global Crop Diversity Trust has launched the project on Adapting Agriculture to Climate Change (Guarino and Lobell, 2011), which, in part, aims to systematically sample priority CWR taxa and ensure that the germplasm is stored ex situ in the country of origin, the Millennium Seed Bank and the Svalbard Global Seed Vault. Alongside this, during the 13th regular session of the Commission on Genetic Resources for Food and Agriculture, held in 2011, the FAO was requested to elaborate on the means and opportunities for establishing a global network for in situ conservation and on-farm management of plant genetic resources for food and agriculture in coordination with the Treaty, the Global Strategy for Plant Conservation of the CBD and other relevant stakeholders. Both initiatives use as their starting point the Harlan and de Wet Global Priority Checklist of CWR Taxa and ecogeographic datasets for the included taxa to which the basic gap analysis methodology described above is applied. With so much attention currently being paid to the application of the gap analysis methodology, it should come as no surprise if the methodology itself evolves rapidly, so those wishing to undertake gap analysis should keep abreast of these methodological developments.

Conclusion

Although gap analysis is a fairly recent tool for the conservation of plant genetic resources, it is proving to be an effective instrument in the planning of complementary conservation strategies that encompass both in situ and ex situ applications. It has also shown how the study of the passport collection data of herbarium and germplasm accessions, coupled with ecogeographic analyses, can quantify the completeness of current in situ and ex situ conservation actions and identify gaps in conservation diversity at both the taxon and geographic level, which, in turn, helps in the prioritization of future conservation actions.

This basic methodology has been successfully applied to assist the development of national conservation strategies for CWR diversity in the UK (Maxted et al., 2007) and Israel (Barazani et al., 2008), and, at a monographic scale, the African genus Vigna (Maxted et al., 2005), the FAO CWR project (Maxted and Kell, 2009) and the CIAT-IRRI-Bioversity International GapAnalysis project, showing that the methodology is sufficiently robust to yield useful results that can bolster conservation efficiency. If the conservation community is to meet the challenge of the CBD Strategic Plan “Target 13” by 2020, the status of the genetic diversity of crop and livestock agricultural ecosystems and of wild relatives will have to be improved (CBD, 2010) and tools such as the gap analysis methodology described above are likely to prove essential.

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Internet resources

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The Plant List, working list of all known plant species: www.theplantlist.org

Tropicos®, herbarium resources, Missouri Botanical Gardens, USA: www.tropicos.org

UNEP WCMC World Database of Protected Areas: www.protectedplanet.net

US Genetic Resources Information Network (GRIN): www.ars-grin.gov/npgs/acc/acc_queries.html

World Database of Protected Areas: http://protectedplanet.net

Worldclim Global Climate Layers, 1km resolution grids of climate and derived bioclimate datasets: www.worldclim.org

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