Specialized collections

There remain many ways of achieving the same goal of secure conservation of germplasm, maintaining viability and genetic integrity of the world’s crop diversity. Development of best practices needs to take into account the options available, their consequences, disadvantages and advantages for reaching the desired output. Strategic analysis and planning are the first steps in priority setting among options to develop recommendations on what might be the a group of best practices that are both efficient, effective and practical and can be easily used in many genebanks.

An important issue for analysis and planning is the funding of conservation efforts and the efficient use of scarce resources. The recommendation on a best practice is often a balance between what is best scientifically and what has a good cost-benefit ratio that can easily be applied in many crop genebanks.

In addition to the crop germplasm, many genebanks have assembled specialized collections, DNA and other genetic and genomic materials and the related information used in research to identify genes of value in genebank collections. Some genebanks also hold collections of plant pests and disease organisms, beneficial organisms and other elements of biological diversity used in research for crop improvement and enhancement of ecosystem productivity, resilience and sustainability. Many national genebanks hold collections of minor crops which are important for food security and are under-researched which have been termed neglected and underutilized species.

Currently there are no documented strategies to support the enhanced management of these specialized collections. Since many are under-researched, there is also little available information on practices and procedures to ensure their long term conservation.

The following pages cover the results of activities on collecting information about these collections and developing strategies for the management of:

• Genetic stocks
• Non-plant taxa
• Underutilized species

Neglected and underutilized species

Contact person for Neglected and underutilized species: Michael Hermann, Crops for the Future, Malaysia

Neglected and underutilized species are often considered “minor crops” because they are less important than staple crops and agricultural commodities in terms of global production and market value. However, from the standpoint of the rural poor who depend on many of these species for their food security, nutrition and incomes, they are hardly “minor”. In addition, these so called “minor crops” can also make significant contributions to ecosystem stability and cultural diversity.
There is need to strengthen the capacity of stakeholders to maintain and enhance the biological assets of the rural poor by enhancing and developing a broader range of species adapted to diverse environments. These species can ultimately provide new opportunities for better nutrition and income generation.

Taking into account that resources are limited, it is important to compile, analyse and promote the development of priority–setting approaches at the local, national and international levels for management of these under-researched species. This would greatly aid stakeholders to establish priorities for research, development and conservation actions on neglected and underutilized species. For such a broad spectrum of species, different stakeholders are involved at various points in production, processing, marketing and consumption; therefore, mechanisms for priority setting need to capture the diversity of interests, opportunities and potentialities at different levels.

Research priority setting methods usually have an economic or social focus. Particular weight is given to social participatory methods due to the value attributed to underutilized species by the rural poor. Despite the currently more favorable climate for conducting research on underutilized species, there remains a disproportionate gap between research funding needs and successful resource mobilization (Withers 2005). Nevertheless, if the vision is set on integrated research for development, alliances with different organizations and institutions outside the specific area of biodiversity, agriculture and research should be fostered. This will enable different actors to contribute to the solution of different problems of target groups and in turn will represent more efficient results in terms of the livelihoods of producers, communities and target organizations.

To enhance relevance of NUS research for communities, three basic issues should be considered:

• Strengthen and promote local organizations or groups to be committed with research initiatives. Communities must feel they own the initiative and this will only happen when they are part of the whole process, from the formation of the main idea to the planning and execution of the process itself.
• Develop flexible projects and proposals that can be adjusted progressively according to their evolution. Many times projects are developed with specific objectives, outputs and deliverables over a period of time and this will in some ways restrict changes. A certain level of flexibility will allow communities and organizations to have a say and adjust proposals, ensuring that the results achieved are not only of scientific relevance but over all are relevant for end users.
• Foster interaction with diverse institutions and organizations at local, regional and national levels. Many times when communities are setting priorities for research and development, we will see that the constraints usually go beyond our specific lines of work. There are times when constraints in infrastructure, services, health and other issues can be so strong that they will limit the contribution that can be made by research in agriculture. This is why fostering interactions with other institutions of diverse nature and scope becomes vital. Integrating the agricultural research agenda on NUS with other agendas such as education, health, services and others will not only increase relevance of research, but it will also increase chances of achieving higher impact towards improving the livelihoods of the poor.

Some options for setting priorities for future engagement have been developed through a consultative process with genebanks managing these collections. Key research areas for future work were identified as: genetic characterization of promising new species; on-farm and in situ conservation of underutilized species; characterization of genetic variability to assess habitat change due to human-induced variables; the potential of underutilized species to enhance resilience; invasive species; nutrition research; intellectual property rights; trade related issues; use of biotechnology methods.

A review and analysis of the research and development activities involving underutilized plant species was carried out by
the CGIAR Centres.

Adoption of the strategies and priority-setting mechanisms proposed in these documents should ensure that research and management of these important but underutilized crop genetic resources meets the real needs of communities, and that selection of subjects for research will serve as models for wider application for other underutilized species of the same type (vegetables, fruits, grains).

References and further reading

Withers L. 2005. Strategic approaches for funding work on underutilized Species. The Global Facilitation Unit for Underutilized Species, Rome, Italy. Available from: http://www.underutilized-species.org/documents/PUBLICATIONS/underutilized_species_funding%20strategy.pdf. Date accessed: 06 December 2010.

Genetic stocks

Contact persons for Genetic stocks:  Dave Ellis, CIP

Contributors to this section: Bioversity International, France (Nicolas Roux, Mathieu Rouard, Elizabeth Arnaud); CGIAR, CAS-IP, Italy (Victoria Henson-Apollonio, Francesca Re Manning); USDA, USA (Dave Ellis); Kansas State University, USA (Bikram Gill); GCP, Mexico/CIRAD, France (Jean Christophe Glaszmann); NIAS, Japan (Makoto Kawase); NIG, Japan (Nori Kurata); IAEA, Austria (Pierre Lagoda); University of Nottingham, UK (Sean May); ICARDA, Syria (Francis Ogbonnaya); IRRI, Philippines (Ruaraidh Sackville Hamilton); ICRISAT, India (Shivali Sharma); NBPGR, India (Shyam Sharma); CIAT, Colombia (Joe Tohme); University of Bologna, Italy (Roberto Tuberosa); AfricaRice, Benin; CIMMYT, Mexico; IITA, Nigeria; SGRP; SINGER.

Through a survey and a workshop organised with partners within and outside the CGIAR, it was possible to develop a position paper  with recommendations for CGIAR genebanks in the handling of genetic stocks collections. Read a summary below.

Summary

Genetic stocks, broadly defined as plants or populations generated and/or selected for genetic studies, represent a unique and growing class of extremely valuable germplasm which, depending on crop, type of genetic stock and user community may represent genetic resources of either transient or long-lasting value. Genetic stocks can be divided into three general groups: cytological stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids), mutants (e.g. induced/insertion mutants, tilling populations) and germplasm sets (e.g. mapping populations, parental lines, reference germplasm). Any genetic stock collection can represent a few lines to tens of thousands of lines and therefore can potentially offer a challenge, as well as a burden, to genebank managers from the standpoint of storage and maintenance. Another challenge with genetic stock collections is the rapidly changing technology used to develop new genetic stocks which may make older collections obsolete. Therefore, the genebank manager is faced with having to predict the long-term value, and hence the need for long-term maintenance, of any given collection. Despite the contrasting options of long-term value for some collections versus short-term value for other collections, there is no question that genetic stock collections should be preserved and that the global system, including CG genebanks, need to play a role in their preservation.

Of upmost importance are programs to document and list existing and future genetic stock collections for all major crops. Such a list would be dynamic, needing continual updating as new stocks are generated. For the major target crops no comprehensive list currently exists, even for wheat, maize and rice. Results from our initial survey indicated that:

• Genetic stocks exist for all focus crops (rice, wheat, barley, maize, chickpea, cassava, banana);
• Collections vary in size and complexity between crops;
• Current funding for collection maintenance and distribution is mostly from project, and less from core, funds;
• Collections are not uniformly catalogued and usually not available on line;
• There is little coordination of collections between sites or crops;
• A majority of collections are distributed for no charge;
• Institutions generally do not have distribution policies in place. 

Genetic stock collections primarily exist in:

• Individual academic laboratories;
• University genetic stock centers with multiple faculty sharing responsibility for maintenance and development of collections;
• Government genetic stock centers;
• As accessions in conventional genebanks.

The first category includes large holdings of individual genetic stock collections which are the most vulnerable to lose due to changes in funding, research direction and retirement of the principal scientist who developed and distributed the collections to the user and research communities. The second category, genetic stock centers at Universities, are generally at lesser risk, yet are also vulnerable as they are often supported with short-term funds, such as grants, which are continually subject to uncertainties in ongoing funding. Government or nationally run genetic stock centers and accessions in genebanks are the most stable in terms of funding however these too can suffer from retirements or changes in direction of key personal if not linked to a broader national genetic resources system or supported by long-term funds from user groups. Genebanks in the global system, such as CG genebanks, although subject to funding fluctuations, are viewed as the most stable and are deemed as having a role in the short- and long-term preservation of genetic stocks collections.

Issues for genebanks committing to the storage and/or maintenance of genetic stock collections include:

• Predicting the potentially transient nature of use and value of any one particular genetic stock collection;
• Having the resources for the often difficult regeneration of thousands of genetic stock lines;
• Having dedicated staff and technology for specialized quality control of regenerated genetic stock lines;
• Special challenges, including financial, for genetic stock collections of clonal material.

Thus, unlike conventional plant germplasm collections, where genebanks commit to the long-term storage of all unique germplasm, an initial decision to the level of commitment for long- versus short-term maintenance has to be done by the genebank manager/curator prior to acceptance of the genetic stocks collection. A decision tree outlining options for the genebank manager has been developed to aid in this decision. The genebank manager/curator must use the knowledge from the provider, the user community and his/her own personal knowledge of the crop and technology, to make decisions as to the acceptance of genetic stocks on a long- versus short-term basis.

The acceptance of genetic stock collections by the global system for the long-term would be similar to any other germplasm accession where the genebank manager/curator would make the commitment for distribution and maintenance (including long-term storage, regeneration and quality control) of the collection. In contrast, if the user community, provider or genebank manager/curator feels the genetic stock collection may not have sufficient long-term value to warrant the commitment of resources for long-term maintenance, the collection could be rejected or accepted under conditions for short-term storage and distribution. One example of how a genebank might handle a genetic stock collection on a short-term basis could be a mapping population where the donor provides a limited number of seed (100-1000 seed) for each line in the population and the genebank only makes the commitment to store and distribute the seed until the donated supply is exhausted. No commitment for regeneration of the lines would be made at the time of acceptance, yet based on use (requests for germplasm) and resources, this short-term commitment could be revised at a later date if desired for one or more of the lines. As new technologies and new genetic stocks are developed, the genebank manager/curator must have the flexibility based on potential long-term value of the collection, available resources and the demands for routine germplasm to inactivate existing genetic stock collections when they become obsolete (e.g after 10 years).

Procedures for managing and accessing genetic stock collections will require a commitment from both the provider and the genebank to adhere to genebank best practices and to continue to meet the needs of the user community. Policies for the maintenance of collections will need to evolve as the technologies advance and change. Genebank functions and funding will need to be tailored to efficiently meet new demands posed from these collections to ensure the global system can sustainably meet their needs and those of crop communities to continue building food security and sustaining productivity.

References and further reading

SGRP 2011. Report prepared by Nicolas Roux, Mathieu Rouard and Dave Ellis for the Global Public Goods Programme Phase 2 of the System-wide Genetic Resources Programme. Genetic Stocks Management Workshop, Bologna, Italy 28-29 April 2010. System-wide GeneticResources Programme, Rome, Italy. Available here.

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Non-plant taxa for food and agriculture

Contact person for Non-plant taxa for food and agriculture: Fen Beed, IITA, Uganda

Contributors to this section: IITA, Uganda (Fen Beed, Muris Korkaric).

Agriculture and food production are facing numerous challenges. The World Bank estimates that the global demand for food will double within the next 50 years. At the same time arable land is decreasing due to land pressure and loss of fertile soil through unsustainable farming practices, and pests and diseases continue to cause loss of agricultural products. Climate change and increased globalization and cross border trade are likely to add new layers of complexity to these challenges. Consequently, agriculture and food production will have to be intensified. Not only will existing technologies and knowledge have to be improved and implemented, but agriculture will also need innovative approaches to move from short-sighted and unsustainable farming towards a system which can meet future challenges.

Therefore, a greater understanding is needed which views agriculture as a complex system of interactions. To optimize this system, all of it components have to be understood and their importance acknowledged. Crops are at the end point of food production and therefore naturally in focus, but throughout their development uncountable direct and indirect interactions with other organisms occur. Microorganism and insects provide important functions and services for agriculture and they are inextricably connected with ecosystem resilience, crop health, soil fertility, productivity and food quality. Unfortunately, this important role is largely underestimated and their potential to solve problems of modern agriculture has still not been sufficiently exploited.

“Non-plant taxa” in the context of this report are bacteria, fungi, oomycetes, viruses, insects and nematodes. These can be found in almost every compartment of the world and their diversity far exceeds those of plants. In one single gram of soil over a billion bacteria can be found, but fewer than 5% have been described or named. For fungi it is estimated that there are about 1.5 million species and only 5% are described. In comparison, almost all of the estimated 420,000 existing seed plants are known and described. From this still largely untapped pool of genetic resources modern agriculture uses only a fraction. Therefore the potential to use non-plant taxa genetic resources to improve agriculture and provide new solutions is enormous.

In their relevance to food and agriculture, organisms of the non-plant taxa can be divided into beneficials – those that support crop and forage production – and those that hinder food production, pathogenic and spoilage organisms. The beneficials perform many functions and services for food and agriculture. A few examples:

• Microbes can enhance the nutrient supply to plants. Examples are nitrogen fixing Rhizobia or arbuscular mycorrhizal fungi that are associated with the provision of phosphorus to the plant roots.
• The maintenance of a high diversity of plant species requires a correspondingly high level of diversity in the soil microbial community.
• Microorganisms can confer enhanced disease resistance to plants by inducing systemic resistance.
• Entomopathogenic nematodes and fungi are used in integrated pest management to control insect pests.
• Biopesticides not only increase yields, but also decrease the use of fungicides and pesticides, reducing their health risks to farmers and consumers.
• The value of insects as pollinators has been estimated at US$208 billion, which equals about 10% of the total global value of agricultural food production. Insects have further importance as biocontrol agents and as soil ecosystem engineers and regulators.
• Pests and disease causing organisms are needed for resistance breeding.

Currently there are no common strategies, policies or best practices for the management of these genetic resources but international standards are documented and followed in many cases. A recent survey collected information on the current inventories held across the CGIAR and its partners and compared management procedures with international repositories.

Useful web linkages for collection management

Collection guidelines
OECD: Best practices guidelines for BRCs - The most recent best practices for quality management, biosecurity, building capacity, preservation of biological resources and data management. http://www.oecd.org/dataoecd/7/13/38777417.pdf

The UKNCC Biological Resource: Properties, Maintenance and Management. Provides all the information required to run a biological resource collection. Details techniques used for preservation and characterization of strains and lists the uses and properties of over 5000 micro-organisms. http://www.ukncc.co.uk

Guidelines for Collection Quality Management Standards and Catalogue production - CABRI (Common Access to Biological Resources and Information) guidelines. http://www.cabri.org

World federation for culture collections (WFCC) Guidelines for the establishment and operation of collections of cultures of microorganisms - 2nd Edition, June 1999 Revised by the WFCC Executive Board. http://www.cabri.org/guidelines/micro-organisms/M100Ap1.html

ISO 9000. ISO 9000 is a family of standards for quality management systems, maintained by the International Organization for Standardization and is administered by accreditation and certification bodies. http://www.iso.org/iso/iso_catalogue.htm

MINE (Microbial Information Network for Europe). The MINE project developed standards (e.g. Minimal Data Sets) for information related to microorganisms. (Gams, W. et al. 1988. Structuring strain data for storage and retrieval of information on fungi and yeasts in MINE, the Microbial Information Network Europe. Journal of General Microbiology 134, 1667-1689)

Collecting and preserving Insects and Mites - Produced by the Agricultural Research Service of the United States Department of Agriculture. Can be accessed online http://www.ars.usda.gov/SP2UserFiles/ad_hoc/12754100CollectingandPreservingInsectsandMites/collpres.pdf 

Collecting and Preserving. Nematodes - A Manual for Nematology by. SAFRINET, the Southern African (SADC) LOOP of BioNET-INTERNATIONAL. Compiled by the National Collection of Nematodes Biosystematic Division; ARC – Plant Protection Research Institute Pretoria, South Africa. http://www.spc.int/pps/SAFRINET/nem-scr.pdf

Barcoding
CBOL (Consortium for the Barcode of Life). CBOL is an international initiative devoted to developing DNA barcoding as a global standard for the identification of biological species. http://www.barcoding.si.edu/

QBOL (Quarantine Barcoding of Life). QBOL is a project financed by the 7th Framework Program of the European Union that makes collections harboring plant-pathogenic quarantine organisms available. Informative genes from selected species on the EU Directive and EPPO lists are DNA barcoded from vouchered specimens. In the next 3 year the sequences, together with taxonomic
features, will be included in an internet-based database system. http://www.qbol.org/UK/

Databases, federations and information networks
WFCC – (World Federation of Culture Collections). The WFCC is a Multidisciplinary Commission of the International Union of Biological Sciences (IUBS) and a Federation within the International Union of Microbiological Societies (IUMS). The WFCC is concerned with the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and set up an information network between the collections and their users, to organize workshops and conferences, publications and newsletters and work to ensure the long term perpetuation of important collections. http://www.wfcc.info

WDCM – (World Data Centre for Microorganisms). The WDCM is a comprehensive worldwide directory of culture collections and holdings, and links to databases on microorganisms, biodiversity, molecular biology and genome projects. www.wdcm.nig.ac.jp 

ECCO – (European Culture Collection Organisation). The aim of the organisation is to promote collaboration and exchange of ideas and information about all aspects of culture collection activity. http://www.eccosite.org

UKNCC – (United Kingdom National Culture Collection). The UKNCC co-ordinates the activities, marketing and research of the UK national service collections, with links to strain databases and affiliated collections. www.ukncc.co.uk/

MIRCEN – (UNESCO Microbial Resource Centers). Global network in environmental, applied microbiological and biotechnological research. http://www.biotech.kth.se/iobb/mircen/activities.htm

GBRCN – (Global Biological Resource Centre Network). The aim of the GBRCN is to publicize the benefit of micro-organisms. Provides publicity accreditation quality and authenticity and alleviates bioterrorism suspicion. http://www.gbrcn.org/

EMbaRC - (European Consortium of Microbial Resources Centres). EMbaRC aims at harmonizing the systems for conserving and identifying bacteria and microscopic fungi in the different European countries and also at developing DNA banks and reinforcing biosafety. The goal is also to preserve and valorize microbiological biodiversity. http://www.embarc.eu/

Straininfo.net - The StrainInfo.net Bioportal currently integrates data from 55 Biological Resource Centres (BRCs) into an integrated strain database. A single portal interface, with direct pointers to the relevant information at the collections' websites, and provides both historical traces and geographic distribution of the strains they keep in culture. In addition, this information is automatically linked to related sequences in the public domain and refers to all known scientific publications that deal with the organism. www.straininfo.net.

Access and benefit sharing
CBD – (Convention on Biological Diversity). Website of the Convention on Biological Diversity. www.biodiv.org

MOSAICC - (Micro-Organisms Sustainable use and Access regulation International Code of Conduct). MOSAICC is a voluntary Code of Conduct, a tool to support the implementation of the Convention on Biological Diversity at the microbial level, in accordance with other relevant rules of international and national laws. http://bccm.belspo.be/projects/mosaicc/

Bonn Guidelines: The "Bonn Guidelines on Access to Genetic Resources and Fair and Equitable Sharing of the Benefits Arising out of their Utilization" are voluntary guidelines to assist governments in the structuring of national and regional legislation and mechanisms to ensure fair access to genetic resources, and sharing of benefits from these resources. http://www.cbd.int/abs/bonn.shtml

References and further reading

Barba M, Van den Bergh I, Belisario A, Beed F. 2010. The need for culture collections to support plant pathogen diagnostic networks. Research in Microbiology. Institut Pasteur. Microbial research commons: From strain isolation to practical use. 161; (6) p 472 - 479.

FAO. 2009. Background Study Paper No. 48 for the Secretariat of the Comission on genetic resources for food and agriculture: The Impact of Climate Change on Countries’ Interdependence on Genetic Resources for Food and Agriculture. Chapter 5 authored by Fen Beed: The Impact of Climate Change on Interdependence for Microbial Genetic Resources for Agriculture. pp 37 - 47.  Available here.   

Feed B. 2009.  Impact of Climate Change on the Interdependency between Countries in the Use and Exchange of Microorganisms – presentation given at the Global Microbial Commons Workshop, 25-26th March, Brussels, 2009. Available: http://biogov.cpdr.ucl.ac.be/Biov_FAO_Workshops/Beed%20Fen.pdf.

Korkaric M, Beed F. 2010. Why manage non crop biodiversity? IITA R4D Edition 4 - March 2010, p 15-18. Available here (2.3 MB).

Miller SE, Beed FD, Harmon CL. 2009. Plant Disease Diagnostic Capabilities and Networks. Annual Review of Phytopathology 47: 15-38.