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Learning resources

Pre-breeding for Effective Use of Plant Genetic Resources: E-learning course

This e-learning course was produced by the Global Partnership Initiative for Plant Breeding Capacity Building (GIPB) as part of a comprehensive strategy to develop a critical mass of personnel skilled in the genetic improvement of crops. This course aims at strengthening capacities at the interface between germplasm conservation and its use in plant breeding. The course was jointly sponsored by Bioversity International, Food and Agriculture Organization of the United Nations and the Global Crop Diversity Trust using the GIPB platform.

Pre-breeding refers to all activities designed to identify desirable characteristics and/or genes from unadapted materials that cannot be used directly in breeding populations and to transfer these traits to an intermediate set of materials that breeders can use further in producing new varieties for farmers. It is a necessary first step in the use of diversity arising from wild relatives and other unimproved materials.

Created using the latest digital technology, the interactive, self-paced learning tool covers a range of theoretical and practical topics from the basic concepts and applications of prebreeding to germplasm management to germplasm distribution and regulatory issues.

Every lesson achieves a specific set of learning objectives, using interactive step-by-step instructions and exercises which help reinforce the internalization of the subject matter. The course is complemented by bibliographic references including on-line resources and a glossary of terms. Structured stand-alone Units allow the learner to take the course as a whole or select specific lessons depending on individual needs and circumstances.

The target audience for this e-learning course is primarily germplasm curators and plant breeders and their support and collaborating personnel. University lecturers and students, extension agents, seeds specialists, field technicians and research managers engaged in germplasm management and/or crop improvement will also find this course very useful.

Please access the course here

 

Spatial Analysis of Plant Diversity and Distribution


Also available in
French and Spanish

Authors: Scheldeman, Xavier and van Zonneveld, Maarten. 2010. Bioversity International, Rome, Italy. ISBN 978-92-9043-880-9

This training manual is intended for scientists and students who work with biodiversity data and are interested in developing skills to effectively carry out spatial analysis based on (free) GIS applications with a focus on diversity and ecological analyses.

These analyses offer a better understanding of spatial patterns of plant diversity and distribution, helping to improve conservation efforts. The training manual focuses on plants of interest for improving livelihoods (e.g. crops, trees and crop wild relatives) and/or those which are endangered.

Spatial analyses of interspecific and intraspecific diversity are explained using different types of data:

  • species presence
  • morphological characterization data
  • molecular data

Although this training focuses on plant diversity, many of the types of analyses described can also be applied for other organisms such as animals and fungi.

The manual is based on specific exercises, based on real project data. In order to use the manual, you will also need to download the relevant exercise data (listed below). All links below lead to the Bioversity International website.

Download the training manual:
Training Manual on Spatial Analysis of Plant Diversity and Distribution (12 MB)

Download the exercise data as:
A  single file (473.9 MB)  (which by unzipping creates the different folders used in the manual)

Or separate zip files for the different exercises:

 2.1 Importing observation data (103 KB)
 2.2 Importing climate data (258.2 MB)

 3.1 Basic elements (121.7 MB)
 3.2 Export to Google Earth (1.0 MB)

 4.1 Quality control – Administrative units (13.6 MB)
 4.2 Quality control – Atypical points (3.9 MB)

 5.1 Species diversity (4.0 MB)
 5.2 Diversity - Phenotypic data (8.4 MB)
 5.3 Diversity - Molecular marker data (4.0 MB)
 5.4 Conservation strategies (6.8 MB)

 6.1 Realized niche (12 KB)
 6.2 Potential distribution (9.8 MB)
 6.3 Climate change (29.7 MB)
 6.4 Gap analysis (12.7 MB)

See also additional resources related to this topic:  Mapping the ecogeographic distribution of biodiversity and GIS tools for plant germplasm collectors

 

Importance of crop wild relatives


Allium pskemense B. Fedtsch. in Uzbekistan.

Watch a video at Vimeo about the importance of crop wild relatives.

Crop wild relatives are the unrecognized and often unnoticed backbone of plant breeding programmes.  Toby Hodgkin, Principal Scientist at Bioversity, explains the significance of crop wild relatives and the struggle to conserve them. 
 

 

The International Treaty on Plant Genetic Resources for Food and Agriculture

Available in English, Français, Español

Learning module on the International Treaty on Plant Genetic Resources for Food and Agriculture
(External link to Bioversity's website)

The aim of this learning module is to develop knowledge and skills to implement the International Treaty on Plant Genetic Resources for Food and Agriculture and to use The Treaty’s standard material transfer agreement (SMTA). 

The module, availabel in English, French and Spanish, contains practical exercises to reinforce an understanding of the impact and working of International Treaty law in the types of situations that professionals in plant genetic resources can expect to face. It also includes background lecture notes, PowerPoint presentations, references to relevant laws and policies with links to the documents and a bibliography for further reading.

While designed for a 2-day workshop, the materials can also be used separately to support classroom teaching.

This module updates and replaces the session on the International Treaty in the 2005 training module on Law and Policy of Relevance to the Management of Plant Genetic Resources

The learning module is also available on CD. If you wish a copy for personal use or for use in education or training workshops, please contact Ewa Hermanowicz (This email address is being protected from spambots. You need JavaScript enabled to view it.).

You can find some videos and a slideshow about the ITPGRFA here.

Management strategies references

Publications on Management strategies

Genetic identity

Booklet of CGIAR Centre Policy Instruments, Guidelines and Statements on Genetic Resources, Biotechnology and Intellectual Property Rights. Statements on Genetic Resources, Biotechnology and Intellectual Property Rights, Version II - Rome, July 2003, 51 pp. Click here to open this publication (0.7 MB)

Guiding principles for CGIAR Centres' policies to address the possibility of unintentional presence of transgenes in ex situ collections. Click here to open this publication

Hernandez-Suarez CM, Montesinos-Lopez O, Crossa J, McLaren G. 2008. Probability models for detecting transgenic plants.. Seed research Science 18: 77–89.

Hirano R, Jatoi SA, Kawase M, Kikuchi A, Watanabe N. 2009. Consequences of ex situ Conservation on the Genetic Integrity of Germplasm Held at Different Gene Banks: A Case Study of Bread Wheat Collected in Pakistan. Crop Sci 49:2160-2166.

Safe Transfer of Germplasm (STOG)

For specific references on pests and diseases please check the STOG pages.

Ahmed KM, Ravinder Reddy Ch.1993. A Pictorial guide to the identification of seed borne fungi of sorghum, pearl millet, finger millet, chickpea, pigeonpea and groundnut. Information Bulletin No. 34. Patancheru, A.P. 502 324 India: International Crops Research Institute for the semi-Arid Tropics. 200 pp.

Chakrabarty SK, Anitha K, Girish AG, Sarath Babu B, Prasada Rao RDVJ, Varaprasad KS, Khetarpal RK, Thakur RP. 2005. Germplasm exchange and quarantine of ICRISAT mandate crops. Information Bulletin No. 69. Rajendranagar 500 030, Andhra Pradesh, India: National Bureau of Plant Genetic Resources; and Patancheru 502 324, Andhra Pradesh, India: International Crops Research Institute for the Semi Arid Tropics. 80pp.

CABI, Crop Protection Compendium, 2007  CD-ROM Edition, www.cabicompendium.org/cpc

Compendium of barley diseases, 1997, Second Edition, Edited by D.E. Mathre. APS Press. St Paul, MN. USA. ISBN 0-89054-180-9.

Compendium of Corn Diseases. 1999. Third Edition. Editor, Donald White. APS Press, St. Paul, MN. USA. ISBN 0-89054-234-1.

Compendium of Wheat Diseases and Pests. 2010. Edited by William W. Bockus, Robert L. Bowden, Robert M. Hunger, Wendell L.
Morrill, Timothy D. Murray, and Richard W. Smiley. APS Press, St. Paul, MN. USA. ISBN 978-89054-385-6.

Mew TW, Misra JK. 1994. A manual of Rice Seed Health Testing. IRRI, Manila, The Philippines, 114,pp.

Mew TW, Gonzales P. 2002. A handbook of Rice Seedborne Fungi. Los Baños (Philippines): IRRI, and Enfield N.H.(USA) Science Publishers Inc. 83 pp.

Policies

The Cartagena Protocol on Biosafety

The Agreement on Trade Related Aspects of Intellectual Property Rights (TRIPS)

IUCN explanatory guide to the Treaty (http://data.iucn.org/dbtw-wpd/edocs/EPLP-057.pdf) (2 MB)

Risk management

Alconero R, Weeden NF, Gonsalves D, Fox DT. 1985. Loss of genetic diversity in pea germplasm by the elimination of individuals infected by pea seedborne mosaic virus. Annals of Applied Biology 106: 357-364.

Benson EE. 2008. Cryopreservation of phytodiversity: A critical appraisal of theory & practice. Critical Reviews in Plant Sciences, 27: 3, 141-219.

Calles T, Dulloo ME, Engels JMM, Van den Houwe I. 2009. Best Practices for Germplasm Management: A New Approach for Achieving Genebank Standards. Bioversity International, Rome, Italy. 52 pp.

CIAT Risk Management Team. 2004. Risk Management at the CIAT genebank operations.

CIP Risk Management Team. 2004.  Genetic Resources Risk Management in CIP.

Clark RL, Shands HL, Bretting PK, Eberhardt SA. 1997. Managing large diverse germplasm collections. Crop Science 37: 1-6.

Clement SL, Griswold TL, Rust RW, Hellier BC, Stout DM. 2006. Bee associates of flowering Astragalus and Onobrychis genebank accessions at a Snake River site in Eastern Washington. Journal of the Kansas Entomological Society 79 (3): 254-260

Ellis D, Gardner C. 2006. Maintaining Genetic Integrity in Germplasm Collections. Paper presented at the APEC Workshop on Effective Genebank Management, June 28, 2006, Suwon, Korea. (Can be obtained from Dave Ellis [ This email address is being protected from spambots. You need JavaScript enabled to view it." ' + path + '\'' + prefix + ':' + addy8792 + '\'>'+addy_text8792+'<\/a>'; //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ])

Fitzsimon J. 2006. Enterprise Risk Management. Good Practice Note No. 10. CGIAR Internal Auditing Unit. (Can be obtained from John Fitzsimon [ This email address is being protected from spambots. You need JavaScript enabled to view it." ' + path + '\'' + prefix + ':' + addy95551 + '\'>'+addy_text95551+'<\/a>'; //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ])

Fitzsimon J. 2007. Conservation and Use of Genetic Resources: Risk Management. Paper presented at the GPG2/GCP Quality Management and Performance Management System Design Workshop, October 2007, Lunteren, Netherlands. (Can be obtained from John Fitzsimon [ This email address is being protected from spambots. You need JavaScript enabled to view it." ' + path + '\'' + prefix + ':' + addy58137 + '\'>'+addy_text58137+'<\/a>'; //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ])

GRC Risk Management Team. 2007. Risk Matrix at the IRRI Genetic Resources Center.

ICARDA Risk Management Team. 2005. Risk Analysis of Genetic Resources in ICARDA.

ICRISAT Risk Management Team. 2007. Risk Management at ICRISAT.

IITA Risk Management Committee. 2008. Risk Assessment Report at IITA. (0.1 MB)

INIBAP Risk Management Team. 2008. Risk Assessment Report at INIBAP Musa Genebank.

Panis B, Thinh NT. 2001. Cryopreservation of Musa germplasm. In: Escalant, Sharrock S, editors. JVINIBAP Technical Guideline 5. International Network for the Improvement of Banana and Plantain. Montpellier, France.

Rao NK, Hanson J, Dulloo ME, Ghosh K, Nowell D, Larinde M. 2006. Manual of genebanks. Handbooks for Genebanks No. 8. Bioversity International, Rome, Italy.

Reed BM, Engelmann F, Dulloo ME, Engels JMM. 2004. Technical guidelines for the management of field and in vitro germplasm collections. IPGRI Handbooks for Genebanks No. 7. International Plant Genetic Resources Institute, Rome, Italy.

USDA Forage and Turf Grass Crop Germplasm Committee. 1997. Crop vulnerability statement for forage and turf. (Can be obtained from Blair L. Waldron [ This email address is being protected from spambots. You need JavaScript enabled to view it." ' + path + '\'' + prefix + ':' + addy98738 + '\'>'+addy_text98738+'<\/a>'; //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ])

USDA Maize Crop Germplasm Committee. 2000. Maize report and vulnerability statement. http://www.ars-grin.gov/npgs/cgc_reports/maize00.htm

USDA Potato Germplasm Committee. 2004. Genetic vulnerability in potato. (Can be obtained from John Bamberg [ This email address is being protected from spambots. You need JavaScript enabled to view it." ' + path + '\'' + prefix + ':' + addy19676 + '\'>'+addy_text19676+'<\/a>'; //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ])

USDA Rice Germplasm Committee. 2004. Crop vulnerability statement for rice.
http://www.ars-grin.gov/npgs/cgc_reports/CropVulnerabilityRiceRevised.pdf

USDA Sorghum and Millet Crop Germplasm Committee. 2004. Sorghum and millet vulnerability statement. (Can be obtained from Gary C. Peterson [ This email address is being protected from spambots. You need JavaScript enabled to view it." ' + path + '\'' + prefix + ':' + addy91281 + '\'>'+addy_text91281+'<\/a>'; //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ])

USDA Sweetpotato Crop Germplasm Committee. 2001. Sweetpotato germplasm acquisition, maintenance and evaluation priorities 2001-2006. (Can be obtained from G. Craig Yencho [ This email address is being protected from spambots. You need JavaScript enabled to view it." ' + path + '\'' + prefix + ':' + addy39698 + '\'>'+addy_text39698+'<\/a>'; //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ])

USDA Vigna Crop Germplasm Committee. 2004. Vigna germplasm: Current status and future needs.
http://www.ars-grin.gov/npgs/cgc_reports/vignarpt2004.pdf

USDA Wheat Crop Germplasm Committee. 1996. Wheat vulnerability report.
http://www.ars-grin.gov/npgs/cgc_reports/1996_wheatcgc_report.pdf

Decision support tool

Altoveros NC, RV. Rao. 1998. Analysis of information on seed germplasm regeneration practices. In Regeneration of Seed Crops and their Wild Relatives: Proceedings of a Consultation Meeting, 4-7 December 1995, ICRISAT, Hyderabad, India, ed. J. M. M. Engels, and R. R. Rao. Rome: IPGRI.

Burstin J, Lefort M, Mitteau M, Sontot A, Guiard J. 1997. Towards the assessment of the costs of genebank management: conservation, regeneration, and characterization. Plant Varieties and Seeds 10: 163-172.

Calles T, Dulloo ME, Engelsn JMM, van den Houwe I. 2007. Best practices for germplasm management: A new approach for achieving genebank standards. Bioversity International.

Chakrabarty SK, Anitha K, Girish AG, Sarath Babu B, Rao PRDVJ; Varaprasad KS, Khetarpal RK, Thakur RP. 2005. Germplasm exchange and quaantine of ICRISAT mandate crops. Information Bulleting No. 69. Plant Quarentine Laboratory, ICRISAT, Patancheru.

Day-Rubenstein K, Heisey P, Shoemaker R, Sullivan J, Frisvold G. 2005. Crop genetic resources: An economic appraisal. A report from the economic research service. Economic Information Bulletin Number 2. United Stated Department of Agriculture.

De Boer L. 1992. Economies of scale and input substitution in public libraries. Journal of Urban Economics 32 (2): 257-268.

ECPGR. 2008. A strategic framework for the implementation of a European genebank integrated system (AEGIS). Discussion Paper.European Cooperative Programme for Plant Genetic Resources (ECPGR) .

Engels JMM, Rao RR. 1998. Regeneration of Seed Crops and their Wild Relatives. Rome: IPGRI.

Epperson J, Pachico DH, Guevara C. 1997. A costs analysis of maintaining cassava plant genetic resources. Crop Science 37: 1641 - 1649 (1991).

FAO. 2002. International Treaty on Plant Genetic Resources for Food and Agriculture: A global treaty for food security and sustainable agriculture. Food and Agriculture Organization of the United Nations: Rome.

Finch L, Christianson JB. 1981. Rural hospitals costs: an analysis with policy implications. Public Health Reports 96: 423-433.

Fowler C, Hodgkin T. 2004. Plant genetic resources for food and agriculture: Assessing global availability. Vol.2004. 29 ed.

Hardaker JB, Huirne RBM, Anderson JR. 1997. Coping with risk in agriculture. Wallingford: CAB International.

Johnson N, Pachico D, Voysest O. 2003. The distribution of benefits from public international banks: the case of beans in Latin America. Agricultural Economics 29 (2003) 277 - 286. 

Koo B, Pardey PG, Wright BD. 2003. The economic costs of conserving genetic resources at the CGIAR centres. Agricultural Economics 29: 287-297.

Koo Bonwoo, Pardey PG, Wright BD, Bramel P, Debouck D, van Dusen ME, Jackson MT, Rao NK, Skovmand B, Taba S, Valkoun J. 2004. Saving seeds: The economics of conserving crop genetic resources ex-situ in the future harvest centres of the CGIAR. Oxfordshire: CABI Publishing.

Koo B, Wright BD. 2008. The optimal timing of evaluation genebank accessions and the effects of biotechnology. American Journal of Agricultural Economics 82 (4): 797-811.

Li D, Prtichard H. 2009. The science and economics of ex-situ plant conservation. Special issue: Plant science research in botanic gardens.

Liu LG. 2002. The cost functions and scale economies in academic research libraries. Library Trends 2002: 406-420.

Mafla G, Roa JC, Aranzales E, Debouck DG. Handbook of procedures for in-vitro germplasm conservation of the genus Maniot. Genetic Resources - CIAT: Cali.

Pardey PG, Koo B, van Dusen ME, Skovmand B, Taba S. 2001. Costing the Conservation of Genetic Resources: CIMMYT's Ex Situ Maize and Wheat Collection. Crop Science 41: 1286-1299.

Rao NK, Hanson J, Dulloo ME, Ghosh K, Nowell D, Larinde M. 2006. Manual of seed handling in genebanks. Handbook for Genebanks No. 8, Maccarese, Italy: Bioversity International.

Salcedo J, Debouck DG, Torres AM, Guevara C. 2006. Flow Chart of Operations for Bean and Tropical Forage Germplasm. Genetic Resources - CIAT: Cali.

Smale M, Drucker AG. 2007. Agricultural Development and the Diversity of Crop and Livestock Genetic Resources: A Review of the Economics Literature. In Biodiversity Economics, ed. A. Kontoleon, U. Pascual, and T. Swanson. Cambridge: Cambridge University Press.

Smale M, Koo B. 2003. Genetic Resources Policies: What is a Gene Bank Worth? IFPRI: Washington, D.C.: IFPRI, IPGRI, and the Systemwide Genetic Resources Program.

Taba S, van Ginkel M, Hoisington D, Poland D. 2004. Wellhausen-Anderson Plant Genetic Resources Center: Operations Manual, 2004. El Batan, Mexico: CIMMYT Click here to open this manual. (0.5 MB)

Upadhayaya H, Gowda CLL, Sastry DVSSR. 2008. Plant genetic resources management: collection, characterization, conservation and utilization. SAT eJournal (ejournal.icrisat.org) An Open Source Journal published by ICRISAT: December 2006, Volume 6.

Virchow D. 2003. Current expenditures on crop genetic resources activities. In Efficient conservation of crop genetic diversity, ed. D. Virchow. Berlin: Springer-Verlag.

Virchow D. 1999. Spending on conservation of plant genetic resources for food and agriculture: How much and How efficient? ZEF Discussion Papers on Development Policy. Bonn: Center for Development Research.


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