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   Genebank  Manual


Genebank manual

Genebank manual   Introduction
 
History of ICRISAT germplasm collection
 
Facilities for germplasm conservation and management
 
Genebank operations
 
Sections
Germplasm Assembly
  Plant Quarantine
  Registering New Germplasm
Seed Processing
  Seed Storage
  Germplasm Distribution
  Germplasm Utilization
  Monitoring
  Germplasm Regeneration
 
Characterization and Preliminary
Evaluation

  Taxonomic Classification
 
Further Reading
 

 

Introduction

Managing and Enhancing the Use of Germplasm - Strategies and Methodologies

Crop diversity is part of the biological diversity and contributes towards achieving food security, poverty alleviation, environmental protection and sustainable development. Crop diversity is being eroded rapidly in important food crops mainly because of replacement of traditional landraces by modern, high yielding cultivars, natural catastrophes (droughts, floods, fire hazards, etc), as well as large scale destruction and modification of natural habitats harboring wild species. Genetic variation in traditional landraces and wild species is essential for crop improvement, eg, to combat pests and diseases and to produce cultivars better adapted to constantly changing environments. The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) responded to this need by establishing a Genetic Resources Unit in 1979. The specific objectives were assembly, conservation, maintenance, characterization, evaluation, documentation and distribution of germplasm of the mandate crops [sorghum (Sorghum bicolor (L.) Moench), pearl millet (Pennisetum glaucum (L.) R. Br.), chickpea (Cicer arietinum L.), pigeonpea (Cajanus cajan (L.) Millsp.) and groundnut (Arachis hypogaea L.) and their wild relatives; and six small millets [finger millet (Eleusine coracana (L.) Gaertn.), foxtail millet (Setaria italica (L.) Beauv), barnyard millet (Echinocloa crusgalli (L.) Beauv.), kodo millet (Paspalum scrobiculatum L.), little millet (Panicum sumatrense Roch. ex Roem. & Schult) and proso millet (Panicum miliaceum L.)] (Fig.1).

ICRISAT genebank is one of the world’s largest repositories for the genetic resources of its mandate crops, with over 119,000 accessions from 144 countries. The germplasm at ICRISAT genebank was assembled through donations from various institutes and by launching germplasm collection missions in areas of origin and diversity of the mandate crops. These were conducted jointly with national agricultural research systems (NARS), universities and international institutes. Since 1991, collections were also stored as base collection in the long-term conservation facilities at -20°C and at present, about 90% of the total collection is in the long-term storage.

History of ICRISAT germplasm collection

ICRISAT acquired about 8,961 sorghum accessions from the Indian Agricultural Program of the Rockefeller Foundation collection in 1974 through the All India Coordinated Sorghum Improvement Project (AICSIP) and another 3,000 accessions of the missing collections from the duplicate sets maintained in the USA (Purdue and Fort Collins) and Puerto Rico (Mayaguez). Initially, ICRISAT also acquired over 2,000 pearl millet germplasm accessions assembled by the Rockefeller Foundation in collaboration with the Indian Council of Agricultural Research (ICAR) in New Delhi, and another 2,000 accessions collected by the Institut Francais de Recherche Scientifique pour le Développement en Coopération (ORSTOM) in Francophone West Africa.

Figure 1. Mandate crops of ICRISAT: Sorghum (A), pearl millet (B), chickpea (C), pigeonpea (D) and groundnut (E) and small millets (F)
- diversity of panicle and seed traits.

The chickpea and pigeonpea germplasm initially acquired by ICRISAT consisted of the material originally collected and assembled by the former Regional Pulse Improvement Project (RPIP), a joint project of the Indian Agricultural Research Institute (IARI); United States Department of Agriculture (USDA); and Karaj Agricultural University in Iran. Sets of this germplasm from different agricultural research institutes in India and Iran, and the USDA were donated to ICRISAT in 1972. ICRISAT also acquired over 1,200 chickpea accessions from the Arid Lands Agricultural Development Program (ALAD), which has its headquarters in Beirut (Lebanon), and was supported by the Ford Foundation (USA), International Development Research Center (IDRC), Canada and of late from International Centre for Agricultural Research in Dry Areas (ICARDA), Syria and USDA, USA. Similarly, much of the groundnut germplasm initially assembled at ICRISAT was received from the collections maintained by the Indian national programs such as the National Research Center for Groundnut (NRCG), Junagadh, India, and the Southern Regional Plant Introduction Station and North Carolina State University, USA.

ICRISAT soon added germplasm to enlarge the world collections of the five mandate crops by collection or assembly of landraces and wild relatives from areas threatened by genetic erosion. Between 1974 and 2008, ICRISAT launched 216 collection missions in areas of diversity and collected 9,011 sorghum, 10,841 pearl millet, 4,228 chickpea, 3,873 pigeonpea and 2,776 groundnut accessions. Apart from ICRISAT’s own collection efforts and the major donors cited above, several other international and national organizations, individuals and donations from Ethiopian Sorghum Improvement Project (Ethiopia), Gezira Agricultural Research Station (Sudan), NARS and agricultural universities in India were responsible for augmenting the collections.

All incoming germplasm samples are examined by the Indian Plant Quarantine Services with the assistance of the National Bureau of Plant Genetic Resources (NBPGR), India for exotic diseases and pests. The Indian Government has set up a quarantine unit within the ICRISAT, Patancheru campus to ensure prompt and expeditious inspection and clearance of seed shipments and receipts.

Facilities for germplasm conservation and management

All the ICRISAT mandate crops and small millets produce orthodox seeds, which can withstand desiccation to low moisture content. Therefore, seed storage is the principle method of conservation of their genetic resources. Seeds are stored in controlled environments in the genebank to prolong seed viability. This process minimizes the frequency of regeneration, which is expensive and involves the danger of genetic shifts. Wild species of groundnut and chickpea, which do not produce adequate quantity of seeds, are maintained as live plants either in the special facilities created or in a greenhouse; and wild species of pigeonpea, sorghum and pearl millet are maintained in the field genebank at ICRISAT, Patancheru.

The genebank at Patancheru has the following facilities for germplasm conservation and maintenance:

  • A short-term storage at 18–20ºC and 30–40% RH, with a capacity of 680 m3 for temporary holding of seeds while they are dried and prepared for subsequent transfer to medium- and long-term storage.
  • Two medium-term storage rooms with a capacity of 210 m3 each and three rooms with a volume of 125 m3 each, at 4ºC and 20–30% RH to hold active collections
    (Fig. 2).
Figure 2. Inside view of the medium-term store at ICRISAT genebank, Patancheru, India.
  • Four long-term storage rooms at –20ºC each with a volume of 125 m3 to store base collections of germplasm (Fig.3).
  • A seed drying room and two drying cabinets with a combined volume of about 100 m3 at 15ºC and 15% RH.
  • An air-cooled screen house with an area of 402 m2 and a special facility for maintaining and regenerating wild species of groundnut that do not produce and/or produce less seed. The special facility includes installation of 500 (90.0 cm diameter × 83.3 cm high × 5.5 cm thick) Reinforced Cement Concrete (RCC) rings for growing individual accessions, a 240 m3 capacity underground water sump for collecting rainwater from the nearby buildings for irrigation, and a 1.2 meter high chain link fencing around, housing the area for RCC rings (Fig. 4).
  • A field genebank with sufficient area allocated on long-term basis for wild species of sorghum, pearl millet and pigeonpea.
  • A seed laboratory for conducting germination tests, seed technology research and cytological work.
  • Access to sufficient field space in each cropping season on ICRISAT campus at Patancheru for regeneration, field characterization and evaluation of germplasm.

To meet the demand for germplasm of mandate crops from African countries and to facilitate easy access to the germplasm collections, ICRISAT also established medium-term cold stores run at 4ºC and 20–30% RH at Nairobi, Kenya; Bulawayo, Zimbabwe and Niamey, Niger to hold working collections, core and mini core collections and reference sets of composite collections.

Figure 3. Inside view of the long-term store at ICRISAT genebank, Patancheru, India.

Figure 4. Facilities for regeneration and maintainance of groundnut wild relatives at ICRISAT.

At Patancheru, the storage chambers are constructed on a modular principle with prefabricated panels and have mobile shelving, each capable of accommodating about 20,000 seed accessions. The genebank has a standby generator to cope with power failure. Each medium- and long-term storage room has standby refrigeration and dehumidification systems. In addition, audible and visual electronic alarms and fire warning systems help maintain the desired conditions and safeguard the germplasm against fire hazards. All genebank cold rooms and seed drying facility are linked to a computer system and to the security services for safe and secured maintenance of genebank.

Genebank operations

Assembly of germplasm from other plant introduction centers and through collection in areas of known genetic diversity, is the first step in ex situ conservation of crop diversity. Collecting germplasm and its conservation are expensive. Therefore, collections are undertaken only after a critical assessment of the need and assembly is made only of unique landrace germplasm, which is not already represented in the collection. The Convention on Biological Diversity (CBD), which came into force on 29 December 1993 and the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) of 29 June 2004 provides the framework for acquisition and utilization of germplasm. Consistent with Article 15 of the CBD, which recognizes the sovereign rights of nations over their biodiversity, collection and acquisition of germplasm are undertaken with prior informed consent, using Material Transfer Agreement (MTA) on mutually agreed terms. Plant quarantine becomes an integral part of germplasm assembly since importation of exotic germplasm is subject to quarantine regulations of host country.

Following receipt at the genebank, the seed samples are registered and added to the collection if they meet the minimum standards for germination, seed quantity and accompanying passport information. The operational sequence to integrate an accession into the genebank involves cleaning, moisture determination, drying, viability testing and packing. The management of seed collections requires that germplasm accessions be maintained with a high proportion of viable seeds. This involves storage under optimal conditions, periodic monitoring of seeds for viability and quantity, and regenerating them when the situation warrants. Germplasm regeneration is done in postrainy season to get quality seeds. Adequate number of plants are grown and sampled equally to minimize genetic drifts. During regeneration, the genetic integrity of cross-pollinating crops such as sorghum, pearl millet and pigeonpea is maintained by pollination control. In line with the policy of the Consultative Group on International Agricultural Research (CGIAR) on plant genetic resources, ICRISAT has been distributing germplasm free to all bona fide users. However, ICRISAT germplasm collections have been later placed under the auspices of the Food and Agricultural Organization of the United Nations (FAO) following an agreement signed on 26 October 1994 with the FAO. Germplasm samples are distributed under the Standard Material Transfer Agreement (SMTA) in accordance with the International Treaty (ITPGRFA) that prevents the recipients from claiming intellectual property rights (see Annexure 1.1).

 

Characterization and evaluation of the assembled germplasm is essential to facilitate its utilization. This is done using a set of internationally accepted descriptors for stable botanical characters and a few environmentally influenced agronomic and quality traits. The morphological and agronomic characters are scored in field plots during the rainy and postrainy seasons. Characterization and evaluation data facilitate preliminary selection of germplasm by users, while information on country of origin, province and location of collection, and pedigree, among other passport data, permits the selection of germplasm on geographic basis and identification of gaps in the collection.

Work with genetic resources involves management of large volumes of information. Documentation is essential in good genebank management to allow efficient and effective use of germplasm. There are four categories of information associated with each accession related to passport, characterization and evaluation, inventory and distribution details. These data are maintained on computers using relational database management systems (Genebank Information Management System-GIMS), which facilitate sharing as well as easy retrieval of information on origin, morphological and agronomic traits based on predetermined criteria. The information on germplasm is also freely available to users. ICRISAT also ensures access to the passport and characterization data by participating in the CGIAR’s System-Wide Information Network for Genetic Resources (SINGER). The data is accessible through http://SINGER.grinfo.net.

Further Reading

Bramel-Cox PJ and Christinck A. 1998. Participatory methods to enhance the quality of germplasm collections. Pages 1-8 in Participatory Plant Improvement: proceedings of the Workshop on Farmer Participatory Methods in Research and Development for the Semi-Arid Tropics, 27–28 October 1998, ICRISAT, India. Chennai, India: MS Swaminathan Research Foundation.

Brown AHD. 1989. The case for core collection. Pages 136-155 in The use of plant genetic resources. (Brown AHD, Frankel OH, Marshal DR and Williams, eds.). Cambridge: Cambridge University Press.

Chakrabarty SK, Anitha K, Girish AG, Sarath Babu B, Prasada Rao RDVJ, Varaprasad KS, Khetarpal RK and 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. 80 pp. ISBN 92-9066-481-9.

Clayton WD and Renvoize SA. 1982. Pages 672-690 in Flora of Tropical East Africa, Gramineae (Part 3). (Polhill RM, ed.). Rotterdam: AA Balkema.

Ellis RH, Hong TD and Roberts EH. 1985. Handbook of seed technology for genebanks. Volume I. Principles and methodology. Handbook for genebanks. No. 2. Rome, Italy: International Board for Plant Genetic Resources. 210 pp.

Engels JMM and Ramanatha Rao V. 1998. Regeneration of seed crops and their wild relatives. Proceedings of a consultation meeting, 4–7 December 1995, ICRISAT, Hyderabad, India. Rome, Italy: International Plant Genetic Resources Institute.

Food and Agriculture Organization of the United Nations/International Plant Genetic Resources Institute. 1994. Genebank Standards. 13 pp.

Frankel OH. 1984. Genetic perspective of germplasm conservation. Pages 161-170 in Genetic manipulations: Impact on man and society. (Arber WK, Llimensee K, Peacock WJ, Starlinger P, eds.). Cambridge: Cambridge University Press.

Grenier C, Bramel PJ and Hamon P. 2001a. Core collection of sorghum:1. Stratification based on eco-geographical data. Crop Science 41:234-240.

Grenier C, Hamon P and Bramel-Cox PJ. 2001b. Core collection of sorghum: II. Comparison of three random sampling strategies. Crop Sci. 41:241-246.

Guarino L, Ramanatha Rao V and Reid R. (eds.). 1995. Collecting plant genetic diversity. Technical Guidelines, Wallingford, UK: CAB International. 747 pp.

Hamilton NRS and Chorlton KH. 1997. Regeneration of accessions in seed collections: a decision guide. (J Engels, ed.). Handbook for Genebanks No. 5, Rome, Italy: International Plant Genetic Resources Institute.

Hanson J. 1985. Procedures for handling seeds in genebanks. Practical Manual for Genebanks: No. 1. Rome, Italy: International Board for Plant Genetic Resources. 115 pp.

Harlan JR and de Wet JMJ. 1972. A simplified classification of cultivated sorghum. Crop Science 12:172-176.

International Bureau for Plant Genetic Resources (IBPGR) and International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). 1992a. Descriptors for groundnut. International Board for Plant Genetic Resources, Rome, Italy and International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India. 123 pp.

International Bureau for Plant Genetic Resources (IBPGR) and International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). 1993a. Descriptors for sorghum [Sorghum bicolor (L.) Moench]. International Board for Plant Genetic Resources, Rome, Italy and International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India. 38 pp.

International Bureau for Plant Genetic Resources (IBPGR) and International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). 1993b. Descriptors for pearl millet [Pennisetum glaucum (L.) R. Br.]. International Board for Plant Genetic Resources, Rome, Italy and International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India. 43 pp.

International Bureau for Plant Genetic Resources (IBPGR) and International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). 1993c. Descriptors for pigeonpea [Cajanus cajan (L.) Millsp.]. International Board for Plant Genetic Resources, Rome, Italy and International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India. 31pp.

International Bureau for Plant Genetic Resources (IBPGR), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and International Center for Agricultural Research in the Dry Areas (ICARDA). 1993. Descriptors for chickpea (Cicer arietinum L.). International Board for Plant Genetic Resources, Rome, Italy; International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India and International Center for Agricultural Research in the Dry Areas, Aleppo, Syria. 31 pp.

Johns MA, Skroch PW, Nienhuis J, Hinrichson P, Bascur G and Munoz-Schick C. 1997. Gene pool classification of common bean landraces from Chile based on RAPD and morphological data. Crop Sci. 37:605-613.

Kameshwara Rao N and Paula J Bramel. (eds.). 2000. Manual of Genebank Operations and Procedures. Technical Manual no. 6. Patancheru 502 324, Andhra Pradesh, India: International Crops Research Institute for the Semi-Arid Tropics.

Lazarides M, Hacker JB and Andrew MH. 1991. Taxonomy, cytology and ecology of Indigenous Australian sorghums (Sorghum bicolor Moench: Andropogoneae: Poaceae). Australian Systematic Botany 4:591-635.

Liu K and Muse SV. 2005. Power marker: Integrated analysis environment for genetic marker data. Bioinformatics 21:2128-2129.

Mehra KL, Arora RK and Wadhi SR. (eds.). 1981. Plant Exploration and Collection (South Asian Training Course Lectures). NBPGR Science Monograph No. 3. New Delhi, India: National Bureau of Plant Genetic Resources. 132 pp.

Pande S, Kishore GK, Upadhyaya HD and Narayan Rao J. 2006. Identification of sources of multiple disease resistance in mini-core collection of chickpea. Plant Disease 90:1214-1218.

Perrier X, Flori A and Bonnot F. 2003. Data analysis methods. Pages 43-76 in Genetic diversity of cultivated tropical plants (Hamon P, Seguin M, Perrier X and Glaszmann JC, eds.). Montpellier: Enfield, Science Publishers.

Prasada Rao KE and Ramanatha Rao V. 1995. The use of characterization data in developing a core collection of sorghum. Pages 109-116 in Core collection of plant genetic resources (Hodgikin T, Brown AHD, van Hintum Th JL and Morales BAV, eds.). Chichester, UK: A Wiley-Sayee Publication.

Upadhyaya HD, Bramel PJ and Sube Singh. 2001a. Development of a chickpea core subset using geographic distribution and quantitative traits. Crop Science 41:206-210.

Upadhyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL, Reddy VG and Singh S. 2009b. Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci. 49:1769-1780.

van der Maesen LJG. 1987. Origin, history and taxonomy of chickpea. Pages 11-34 in The Chickpea (Saxena MC and Singh KB, eds.). Wallingford, UK: CAB International.

Reddy LJ, Upadhyaya HD, Gowda CLL and Sube Singh. 2005. Development of core collection in pigeonpea [Cajanus cajan (L.) Millsp.] using geographic and qualitative morphological descriptors. Genetic Resources and Crop evolution 52:1049-1056.

Upadhyaya HD, Bhattacharjee R, Hoisington DA, Chandra S, Varshney RK, Reddy KN and Saxena KB. 2006a. Molecular characterization of pigeonpea [Cajanus cajan (L.) Millspaugh] composite collection. Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil.

Upadhyaya HD, Bramel PJ, Ortiz R and Sube Singh. 2002. Developing a mini core of peanut for utilization of genetic resources. Crop Science 42:2150-2156.

Upadhyaya HD, Dwivedi SL, Gowda CLL and Sube Singh. 2007a. Identification of diverse germplasm lines for agronomic traits in a chickpea (Cicer arietinum L.) core collection for use in crop improvement. Field Crops Res. 100:320-326.

Upadhyaya HD, Gowda CLL, Buhariwalla HK and Crouch JH. 2006b. Efficient use of crop germplasm resources: identifying useful germplasm for crop improvement through core and mini-core collections and molecular marker approaches. Plant Genetic Resources 4(1):25-35.

Upadhyaya HD, Gowda CLL, Pundir RPS, Reddy VG and Sube Singh. 2006c. Development of core subset of finger millet germplasm using geographical origin and data on 14 quantitative traits. Genet Res. and Crop Evolution 53:679-685.

Upadhyaya HD, Gowda CLL, Reddy KN and Sube Singh. 2009a. Augmenting the pearl millet [Pennisetum glaucum (L.) R. Br.)] core collection for enhancing germplasm utilization in crop improvement. Crop Science 49:573-580.

Upadhyaya HD and Ortiz R. 2001b. A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor. Appl. Genet. 102:1292-1298.

Upadhyaya HD, Ortiz R, Bramel PJ and Singh S. 2001c. Development of a groundnut core collection from Asia region. Pages 43-44 in Proceedings of the Diamond Jubilee Symposium (Abstracts). Hundred years of Post-Mendelian Genetics and Plant Breeding - Retrospect and Prospects, 6-9 November 2001. (Kharakwal MC, Mehra RB, eds.). New Delhi, India: Indian Society of Genetics and Plant Breeding.

Upadhyaya HD, Ortiz R, Bramel PJ and Singh S. 2003. Development of a groundnut core collection using taxonomical, geographical and morphological descriptors. Genet. Resour. Crop Evol. 50:139-148.

Upadhyaya HD, Pundir RPS, Gowda CLL, Reddy KN and Sube Singh. 2005. Geographical pattern of diversity for qualitative and quantitative traits in the pigeonpea germplasm collection. Plant Genetic Resources: Characterization and Utilization 3:332-352.

Upadhyaya HD, Pundir RPS, Gowda CLL, Reddy VG and Sube Singh. 2008. Establishing a core collection of foxtail millet to enhance the utilization of germplasm of an underutilized crop. Plant Genetic Resources: Characterization and utilization 7(2):177-184.

Upadhyaya HD, Reddy LJ, Gowda CLL, Reddy KN and Sube Singh. 2006d. Development of mini core subset for enhanced and diversified utilization of pigeonpea germplasm resources. Crop Science 46:2127-2132.

Upadhyaya HD, Reddy KN, Gowda CLL and Silim SN. 2007b. Patterns of diversity in pigeonpea [Cajanus cajan (L.) Millsp.] germplasm collected from different elevations in Kenya. Genet. Resour. and Crop Evol. 54:1787-1795.

van der Maesen LJG. 1990. Pigeonpea: origin, history, evolution and taxonomy. Pages 15-46 in The Pigeonpea (Nene YL, Hall SD and Sheila VK, eds.). Wallingford, UK: CAB International.

Ward J. 1963. Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 38:236-244.

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