Systemwide Review of Plant Breeding Methodologies in the CGIAR

Systemwide Review of Plant Breeding Methodologies in theCGIARIPGRI/INIBAP Sub-Panel ReportMontpellier, France, April 17 – 20, 2000Calvin O. QualsetTable of Contents Page1. Background and Nature of the Review 31.1. Introduction and terms of reference 31.2. INIBAP’s Crop Mandates 31.3. Definitions and Concepts 31.4. Methodology for the INIBAP Review 41.5. Acknowledgements 42. Musa as a Global Food Resources 53. Complex Evolution and Major Types of B&P 54. Genetic Improvement Strategies 54.1. Traditional Breeding Programs 54.2. Biotechnology 65. INIBAP 65.1. Objectives 65.2. Operational Aspects 75.3. Relevance to Plant Improvement 76. Responses to ToR Goals 87. Recommendations 108. List of Acronyms 121. Background and Nature of the Review1.1. Introduction and Terms of ReferenceThis review of plant breeding methodologies used for banana and plantain at INIBAP, a networking organization of the International Plant Genetic Resources Institute (IPGRI), is part of a systemwide review of all of the CGIAR Centres having genetic improvement of crop plants in their portfolio. The review was motivated by Recommendation 4 of the System Review relating to integrated gene management (IGM) and addresses primarily the extent to which biotechnology has or will be integrated into Centre plant improvement programs. Further, the Terms of Reference (ToR) state, “The aim was to assess the possibility of freeing up resources, implicitly by reducing the resources involved with conventional practices, so that applications of new techniques could be expanded as appropriate. Specific terms of reference guiding the Subpanel activities are as follows:•Assess effectiveness of methodologies in use for each crop, giving particular consideration to cost-effectiveness, to efficacy in achieving set goals and to optimal integration of different tools, molecular technologies in particular.•Assess the trends and strategies for incorporating new methodologies and the mechanisms in place to guide choices in breeding methodology and in research.Aspects of access and the consequences of chosen methodologies in delivery of goods must also be considered.•Assess opportunities in synergies within each centre between its various crop improvement programmes, between individual centres giving consideration to similarities in crops, genome synteny and breeding themes, and between centres and other institutions. The latter involves assessment of opportunities for outsourcing.1.2 INIBAP’s Crop MandatesINIBAP addresses globally all of the many types of banana and plantain crops in the genus Musa, and to a minor extent, Ensete, as a genetic resource for Musa. Within the CGIAR, Musa research and plant breeding is conducted at the International Institute of Tropical Agriculture (IITA) targeted for sub-Saharan Africa.1.3 Definitions and Concepts (taken from the IITA review of plant breeding technologies)The conceptual view of ‘integrated gene management’ was adopted as being an overriding strategy involving gene conservation, all modes of manipulation of genes for crop improvement, and the strategies for deploying genes in cropping systems. Further, plant breeding is defined in a broad sense as being an applied science that usesinformation and technologies from several disciplines, including genetics, plant physiology, plant pathology, entomology, agronomy, nutrition and end-use technology, and social sciences. Plant breeding involves identifying targeted traits for improvement, discovery of gene resources to address the targeted traits, and a strategy for introducing into crop plants new forms of traits through single- or multi-gene systems. The latter is the main focus of this review.Traditional plant breeding is a term used in reference to hybridization and selection schemes or mutation induction as a means to genetically modify plants. Biotechnology includes, for the purposes of this review, the use of in vitro methods for multiplication or propagation of genotypes via cell, tissue, or organ culture; the use of molecular genetic markers linked to genes of interest for gene transfer and for rapid and efficient selection of desired combinations of traits; and the use of gene transformation, an asexual means to introduce gene constructs into a plant genome, which will be replicated stably during subsequent sexual or asexual propagation.1.4. Methodology for the INIBAP ReviewC.O. Qualset visited the INIBAP headquarters on April 19-20, 2000 in Montpellier after a visit to an INIBAP partner, The International Tropical Crop Improvement Laboratory at the Catholic University at Leuven (KUL), Belgium on April 17-18, 2000. Qualset was a member of the team that reviewed plant breeding at IITA, including banana and plantain, in March 2000. This report follows some aspects of the IITA report; for example, the definitions adopted which are consistent with the ToR for this review. As a point of reference and gage of progress in Musa improvement, Qualset was a member of the External Programme and Management Review (EPMR) team for IPGRI in 1996-97 when a detailed review INIBAP was completed.Materials provided for review:In-depth Center-Commissioned External Review (CCER) of the INIBAP Programme. March 2000;Annual reports;Copies of slides from lecture presentations at KUL and INIBAP;Reprints and reports from KUL;Report: Banana streak virus: a unique virus-Musa interaction? (1998);Report: Biotechnology applications for banana and plantain improvement (1993); Report: PRO Musa: A global programme for Musa improvement (1998);INIBAP and IITA responses to a questionnaire prepared by TAC Secretariat.1.5. AcknowledgementsThe review visitation process was efficiently co-ordinated by Emile Frison, Director, INIBAP and Rony Swennen, Director, International Tropical Crop ImprovementLaboratory, KUL. Great appreciation is expressed to all of the staff for their clarity of presentations and responses to inquiries.2. Musa as a Global Food ResourceBananas and plantains (B&P) are tropical crops grown in Latin America, Asia, and Africa. Together bananas and plantains rank number 4 among the staple food crops in world production. Annually, this amounts to about 55 million tonnes of banana and 30 million tonnes of plantain. There are two main production systems of B&P: (i) dessert bananas, being produced in large plantations for export to foreign markets and (ii) numerous end-use types grown by small-holdings farmers in Africa, Asia, and Latin America. B&P are mostly consumed as fruits, but people of India and Ethiopia eat stem hearts. Beer bananas are fermented to produce beer in Africa. There are many more uses of B&P, such as starchy or sweet flour produced from dried fruit. Discarded plant parts are often consumed by livestock.3. Complex Evolution and Major Types of B&PMusa is a genus in the monocotyledonous family, Musaceae. The basic chromosome numbers of species in the section Eumusa, the most important section for economic plants, are 10, 11, and 14. Musa is a rhizomatous functional perennial, being regenerated from lateral branches or suckers. Domesticated B&P arose from wild diploid species, Musa acuminata (AA genomes) and M. balbisiana (BB genomes). No diploid types arose during the early domestication process, but have been improved by plant breeding as the first step in producing improved varieties (clones). Polyploidization produced AAA and AAAA (dessert) types for example, and hybridization along with polyploidization produced AAB (plantain) and ABB (cooking and beer) types. The cultivated forms are mostly seed sterile triploids, thus forming a class of crop plants that must be reproduced by clonal propagation and extraordinary tricks must be applied to produce improved sterile types by plant breeding.4. Genetic Improvement StrategiesFrom a plant breeding point of view, B&P improvement must be viewed as quasi-independent breeding programs for each of many different crop forms and multiple end-uses. Thus B&P breeding is complex because of the many types and adaptation zones, even for the same type, and complex genetics due to polyploidy. On this is superimposed perennial growth habit and host plant resistance needed for a plethora of pests and diseases.4.1 Traditional Breeding Programs have been successful in producing new diploids and hybrid tetraploids, particularly in Honduras. Several breeding strategies have beenemployed, including recurrent selection from 2n x 2n crosses, production of 2n x 3n hybrids and selection of 4n types, and 4n x 2n to produce 3n types. Progress in hybridization and selection approaches has been slow with a certain amount of intractability for transferring traits from wild species to acceptable forms. Some hybridizations are especially difficult and embryo rescue techniques have been developed to overcome cross-incompatibility.The most successful breeding program has been in Honduras, where a 30-year intensive hybridization and selection program has produced varieties having disease resistance derived from diploid species (FHIA hybrids from Honduras). There are very few breeding programs currently active relative to the global importance the B&P crops. An almost complete list of organizations that have active genetic improvement programs include IITA (Nigeria), EMBRAPA (Brazil), FHIA (Honduras), CRBP (Cameroon), Banana Board, (Jamaica ) and CIRAD (Guadeloupe, France). There are no significant breeding programs in Asia. The global financial investments in traditional B&P breeding is far below other major crops and most of the investment is in traditional breeding programs all of which are generally believed to be greatly underinvested.4.2 Biotechnology is an important component of B&P improvement, but present applications useful to farmers are tissue culture for disease-free stocks and propagation of planting stocks. Gene transformation technology is well developed both with particle bombardment and Agrobacterium. Genomic mapping (RFLP and SSR) is advanced for the A genome, but not for the B genome. Marker-assisted selection is planned in several breeding programs, but no cases are in practice up to now. Transgenic plants, carrying antimicrobial protein genes, have been produced and readied for field testing since 1996, but yet no field tests have been done. There are many appropriate targeted traits for transformation, including genes for resistance to black Sigatoka, nematodes, Fusarium, banana streak virus, banana bunchy top virus (for which no natural resistance has been found), insects, improved fruit quality, vaccines against human diseases, and environmental stresses.5. INIBAPINIBAP is a networking organization within the International Plant Genetic Resources Institute. Its headquarters is in Montpellier, France with regional offices in Africa (Cameroon and Uganda), the Philippines and Costa Rica. The annual operating budget for INIBAP is about $4 million. Most of which is used for collaboration grants.5.1. ObjectivesAs an organization that facilitates research and development, its objectives are fourfold: I.To strengthen national Musa research programsII.To promote regional collaboration on Musa researchIII.To organize and coordinate a global research effortIV.To collect and distribute information on banana and plantain5.2. Operational AspectsINIBAP functions through four projects in the project system of IPGRI: Germplasm Management, Genetic Improvement, Information and Communication, and Regional Activities.INIBAP receives funds from CGIAR donors and special grants. These funds are outsourced to collaborators for specific projects. INIBAP has no research labs under its direction, but does maintain and distribute Musa genetic resources through its International Transit Center at KUL. It manages networks, such as PRO Musa, which have brought about increased collaboration among B&P workers globally. The International Musa Testing Program (IMTP) is coordinated by INIBAP with some 50 countries involved in evaluation of new varieties from all breeding programs. INFO MUSA is a research reporter and newsmagazine published by INIBAP. It has comprehensive coverage of current topics and is widely held as the premier publication used by B&P researchers. Also a website is maintained and comprehensive bibliographic services are offered.Recent reviews (EPMR, 1997; CCER, 2000) have examined all of the INIBAP programs and management, hence the present review reports on the plant breeding activities facilitated and supported by INIBAP.5.3. Relevance to Plant ImprovementINIBAP is largely focussed on improvement of B&P by genetic means and the movement of improved, healthy plant materials to farmers in developing countries. Three programs have particular importance to this review and will be briefly mentioned here. KUL and the International Transit CenterA long-standing relationship of INIBAP with the Catholic University of Leuven in Belgium on B&P research has been extremely productive. The International Tropical Crop Research Laboratory, under leadership of Rony Swennen, has developed transformation techniques using biolistics and pioneered the use of cell suspension cultures as targets for transformation. Tissue culture techniques are routinely used and form the basis for the B&P gene bank called the ITC. The ITC produces pathogen-free plantlets for distribution. About 1,200 accessions are included in the gene bank and these are distributed to users around the world. KUL operates ITC for INIBAP. The ITC is an essential and critical component of global B&P improvement, especially for transgenic plants when it will be possible to distribute them.More than 900 transgenic B&P plants have been produced and are maintained by KUL. One group of transgenic plants has been available for field testing since 1996. Theseplants have AMP, antimicrobial proteins, genes that are believed to confer resistance to diseases. Field-testing is essential to confirm this. Collaboration with IITA has been established; however, the Nigerian government does not have a policy in place to permit field-testing of transgenic plants and no plants have been introduced to IITA. This is a general problem for application of genetic modification research with B&P. International Musa Testing ProgramIMTP is a collaborative testing program for new varieties. Special evaluations are designed for evaluation for black Sigatoka and Fusarium reaction. This program started with six sites in Phase I and expanded to 37 in Phase II. The testing program is financed by a grant, but NARS generally provided the testing sites and personnel to support the field-testing. The program is judged as highly successful and has moved into Phase III. This high level of collaboration can provide a platform for future evaluations of transgenic plants. Up to now no transgenic varieties have been included, because, as noted above, field testing transgenic B&P is not yet an accepted practice.PROMUSAINIBAP serves as the secretariat for the PRO Musa network. Officially known as the Global Programme for Musa Improvement, this network is facilitating international workshops, brokering research collaborations, and giving general guidance to B&P research. The following statement appears in a PRO Musa newsletter:The major thrust of PRO Musa is to develop a wide range of improved banana varieties from which growers worldwide can select those most suited to their needs. The programme brings together conventional breeding based on hybridization techniques with genetic engineering and biotechnological breeding approaches.This network appears to have momentum to achieve international sharing of germplasm and information. The “Declaration of Guadeloupe” of 1997 established five working groups, of which one on genetic improvement has great promise for advancing molecular-based breeding. For example, a Banana Genomics Consortium has participation from eight advanced laboratories.6. Responses to TOR GoalsEffectiveness of methodologies in use for each crop, giving particular consideration to cost-effectiveness, to efficacy in achieving set goals and to optimal integration of different tools, molecular technologies in particular.With respect to INIBAP’s role in plant breeding technologies, it supports traditional and new technologies for B&P improvement. It participates in the identification of appropriate targets for improvement and emphasises the need for complementary approaches to Musa breeding. Its close relationship to CIRAD (France) and KUL (Belgium) in developing advanced technologies is a strong point for INIBAP, but also its posting of staff in developing countries with emerging research programs has enhanced the focus on both global and local production problems with B&P.Traditional breeding programs are essential to incorporate the products of transgenic research into varieties, at the same time, molecular marker-assisted selection can be a great asset to hybridization/selection breeding programs.This reviewer believes that adoption of marker-assisted selection in traditional breeding programs can make a great advance in cost reduction, but also would allow the expansion of breeding programs for little added cost. The caveats, of course, are that desirable genes can be discovered (no doubt at rather high cost) and that closely linked markers can be found.Trends and strategies for incorporating new methodologies and the mechanisms in place to guide choices in breeding methodology and in research. Aspects of access and the consequences of chosen methodologies in delivery of goods must also be considered. INIBAP strongly supports the use of new technologies in B&P improvement. It provides leadership in fund-raising the collaborative research. It values the complementary roles of advanced research institutes and developing country research.Access to genetic resources, whether it be to landraces by breeders or to transgenic plants by farmers, is a matter of great concern for all crops. This is especially true for B&P because gene transformation can serve as a means for conserving landraces while protecting the crop from disease and pest losses and improving its dietary qualities. This needs considerable attention, because denied access to any form of superior germplasm in developing countries is denying opportunity for improving the health, nutrition and economy of rural and urban families in developing countries. The IMTP program is successful and can serve ass a model for evaluating transgenic plants on a wide scale. The ITC is a critical facility for distributing healthy genetic materials to researchers. INIBAP’s support of these two activities is highly commended.Promoting access of improved varieties to farmers is an integral component of a breeding program. Distribution and diffusion of new varieties must be intensified in most CGIAR-based programs, not only for B&P, but for crops as well. Two examples were presented during the review where very promising results were emerging with new B&P varieties.In the Kagera region of northern Tanzania the farmers have been affected by the influx of nearly 600,000 refugees. These farmers obtain 25 to 60% of their caloric intake from bananas. Disease resistant varieties are being distributed along with training provided to the farmers in propagation techniques. The second example is a tripartite collaboration between KUL, Leon University, and Oxfam, an NGO, which has resulted in the distribution of 8,000 plants to farmers of Nicaragua. For more info see.ni/~vitro/Opportunities in synergies within and between centres among its various crop improvement programmes, between individual centres giving consideration to similarities in crops, genome synteny and breeding themes, and between centres and other institutions. The latter involves assessment of opportunities for outsourcing.INIBAP is basically a single-commodity program and its synergies with other commodities in CGIAR Centers is minimal. The exception, of course, is IITA where active research on B&P has been in progress for many years, and has already delivered improved varieties for diffusion into local economies in several countries. Greater collaboration between IITA and INIBAP is in order, but the value of INIBAP’s non-competitive, but supporting, role in research should not be underestimated, i.e., INIBAP does not compete for research funds for its own staff and is a broker for fund development on a broad scale.The uniqueness of B&P as crop plants requires specialized multidisciplinary research centers that are dedicated to all aspects of B&P agronomy, pest control, and biology. At the same time, centers in some countries cannot reasonably be expected to have primary leadership role in B&P biotechnology because of practical logistical aspects of unreliable power sources, lack of local maintenance of instruments, and difficult importation of chemicals and genetic tools. Thus, a preferred model for B&P research recommended here is exactly as promoted by PRO Musa, whereby shared responsibility among advanced research institutes and NARS centers concerned with producing and evaluating new varieties is the best practical arrangement for advancing Musa plant breeding research and variety development.INIBAP has been very successful in outsourcing funds to collaborators, providing a good model for other commodity improvement programs.7. RecommendationsThe following comment was made by the review team that examined plant-breeding methodologies at IITA. This reviewer was part of that team, which reviewed all IITA crop assignments, including banana and plantain breeding. It is relevant to the present review, remembering that IITA is a major Center working largely on second-tier crops, from the CGIAR perspective, that are generally not the subject of private sector genetic improvement.“The review team wishes to stress that although we fully agree that new technologies in plant breeding should be expanded this should not be at the cost of ‘traditional’ plant breeding. Methodologies considered at this moment ‘new’ are ‘old’ tomorrow and should become an intrinsic part of all the methodologies available to the plant breeder to be used if needed. All in all, we can conclude that breeding methodologies both old and new, are being used whenever necessary and possible and have lead to commendable successes. No doubt this will also be the case in the future.”The following recommendations are offered as useful for enhancing the global productivity and value of bananas and plantains in general and for INIBAP as issues it should address, support, and facilitate in its leadership role in banana and plantain research and development:R.1. Musa plant breeding programs are scattered, fragmented, of limited scope, have few plant breeders, and insufficient financial resources to meet global needs of expanding populations. It is recommended that efforts be made for greatly expanding genetic improvement programs for all of banana and plantain types.R.2. Integrated gene management is highly relevant to Musa improvement. Innovative means to couple molecular-based technologies with traditional hybridization and selection methods are recommended.R.3. Bananas and plantains were recognized by the CGIAR as critical world food crops only recently. ‘Catch-up’ or accelerated breeding and variety diffusion programs for Musa is essential. It is highly recommended that funding for traditional breeding not be reduced or diverted to molecular-based technologies, rather, increased total investment in Musa research and development will enable production and diffusion of new, most probably, pest resistant, varieties. To meet this recommendation, a critical commodity priority ranking within the CGIAR system should aid in guiding the allocation of funds.R.4. Accelerated genomics research programs are recommended for gene discovery (functional genomics), mapping of the B genome, whole-genome BAC-based physical mapping, and mapping of functional genes identified by expressed sequence tags (EST).R.5. To conserve landraces of banana and plantain, it is recommended that the practicality and acceptability of introducing useful genes by transformation be explored. For example, introducing genes for pest resistance into landraces will make them more valuable to farmers, thus providing incentive to conserve locally desirable landraces.R.6. It is recommended that INIBAP assume a leadership role in promoting national policy on the safe introduction and evaluation of transgenic plants in selected countries, especially Nigeria, for example, where IITA and KUL are ready to do field studies of transgenic plants.R.7. INIBAP is commended for its role making PRO Musa an effective networking consortium. It is recommended that INIBAP take a leadership role through PRO Musa network to clarify intellectual property rights for developers and users of protected germplasm and molecular tools, especially for providing access and benefit-sharing to local users.R.8. There is a disconnect between public and private organizations in banana breeding, especially with respect to molecular-based plant breeding. It is recommended that INIBAP intensify its role in creating effective collaboration of large plantation holders who produce and export bananas in world trade with public sector research programs.R.9. It is recommended that INIBAP explore new modes of collaboration of national programs with advanced research labs.List of AcronymsProteinAMP AntimicrobialArtificial ChromosomeBAC BacterialB&P Bananas and PlantainsReviewExternalCCER Center-CommissionedCGIAR Consultative Group on International Agricultural ResearchCIRAD Centre de Coopéracion Internationale en Recherche AgronomiqueCRBP Centre for Research in Bananas and PlantainsEMBRAPA Empresa Brasilera de Pesquisas AgropecuariasEPMR Externaland Management ReviewProgrammeSequence TagsEST ExpressedFHIA Fundación Hondureña de Investigación AgrícolaIGM Integrated Gene ManagementIITA International Institute of Tropical AgricultureMusa Testing ProgramIMTP InternationalINIBAP International Network for the Improvement of Banana and Plantain IPGRI International Plant Genetic Resources InstituteCenterITC InternationalTransitKUL Katholieke Universiteit LeuvenNARS National Agricultural Research SystemsOrganizationNGO Non-GovernmentalFragment Length PolymorphismRFLP RestrictionRepeatSequenceSSR SimpleTAC Technical Advisory CommitteeToR Terms of Reference。