In 2001, IRRI implemented a new Medium-Term Plan (MTP) consisting of 12 focused Projects across four Programmes. Programme 1, entitled ‘Genetic Resources Conservation, Evaluation, and Gene Discovery’ contains two Projects.
The first Project, ‘Germplasm Conservation, Characterization, Documentation and Exchange’, continues efforts of IRRI to collect, conserve and exchange the genetic resources of rice, and strengthens efforts to characterize and evaluate the conserved germplasm, explore alleles for important traits, and develop integrated information systems for all rice germplasm. The broad goals of the Project are thus to protect the biodiversity of rice and to make it and related information available worldwide for the enhancement of rice productivity and scientific discovery.
The second Project of Programme 1, ‘Functional Genomics’, aims to understand the biological functions encoded by rice DNA sequences, taking advantage of investments made in the public and private sectors in sequencing and annotating rice genomes. The Project involves experimental work leading to gene discovery and developing genetic databases as international public goods, via Project 1, to assist NARS in the discovery of new genes and development of better traits via breeding.
These Projects are involved in the CGIAR Genetic Resources Challenge Programme, ‘Unlocking Diversity in Crops for the Resource Poor’.
The value of Programme 1 cannot be evaluated in isolation from the overall IRRI research agenda as it also is constructed to supply basic and supportive information and materials to the breeding activities in Programmes 2 (especially in biotic stress tolerance genes) and 3 (especially in abiotic stress tolerance genes), where some of its impact will therefore be generated.
Efficient exploitation of rice biodiversity provides the opportunity, through plant breeding, to enhance the fitness of varieties for the environments, management practices and purposes for which they are needed. The combinations of allelic variants that have emerged from natural selection and from previous selections by man cannot be reconstructed, so their collection, conservation and evaluation are an extremely important activity for the future food security of mankind. IRRI carries the major responsibility in the CGIAR for rice germplasm.
Use and sharing of such germplasm has many beneficial outcomes including:
a) conservation of the biodiversity of rice species as public goods;
b) production of new high-yielding rice varieties;
c) discovery of the genes and their products related to desired traits, such as resistance and tolerance to many biotic and abiotic stresses;
d) development of improved varieties adapted to variable and fragile environments;
e) knowledge of allelic variation, haplotypes, population structures and the evolution of rice;
f) elucidation of QTLs and the isolation of the genes related to QTLs; and
g) enhancement of information linking the genetics of cereals in general.
This Project covering the conservation, documentation, analysis and dissemination of rice germplasm and its associated knowledge is therefore central to IRRI’s and the CGIAR’s mission. The budget of this Project was US$1.86 M in 2002 and is projected at US$2.64 M in 2004. The 3.4 IR FTEs (full time equivalents) comprise germplasm management and biosystematics experts, statisticians, bioinformaticists, molecular biologists, breeders and a GIS specialist.
Collection and conservation of wild and cultivated rice accessions have been a key underpinning activity at IRRI from its beginning. The collections have grown over the years and they have gained appropriately high status. They are maintained as public goods, and most of them are held in trust as designated germplasm under the auspices of FAO. Huge numbers of organizations and individuals have requested and been supplied with seeds over the years for breeding and research purposes. In IRRI, The Genetic Resources Centre is responsible for the collection, conservation, curation and distribution of the International Rice Genebank Collection (IRGC) that currently contains over 108,000 rice samples. IRRI’s germplasm collection is believed to represent a large fraction but certainly not all the biodiversity of rice.
In 1993, the Convention on Biological Diversity declared that nations have sovereignty over plant genetic resources held in their territory. This resulted in the need to agree on terms under which germplasm essential for food and agriculture could continue being freely exchanged amongst researchers and breeders. The International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) was adopted in 2001 and is soon expected to come into force. The IARCs will join this through re-signing an agreement with FAO. Under the ITPGRFA, the entire Oryza genus is included in the multilateral system of exchange, which secures access to germplasm, subject to a Material Transfer Agreement (MTA). To comply with the spirit of the agreement, IRRI and other IARCs concerned with genetic resources will apply similar conditions to the exchange of materials bred at IRRI, which already is subject to an MTA, now being revised.
There has been growing concern within the CGIAR and the larger stakeholder group, of the sustainable funding of the CGIAR’s germplasm collections, which currently are dependent on core resources. In response, the CGIAR with the leadership of IPGRI and together with FAO, launched a campaign to attract financing for an endowment fund. An independent Global Crop Diversity Trust has now been founded and eventually any genebank globally will be eligible for funding, providing that they fulfil certain quality criteria related to maintenance. The trust’s objectives are to provide a permanent source of funds for the long-term conservation of the ex situ germplasm, including characterization, documentation and evaluation, and sharing information, knowledge and technologies to enhance the use of these resources. This is an important development for IRRI and other Centres in a situation of declining core funding.
The International Network for Genetic Evaluation of Rice (INGER) is a formal network among the NARS of the world’s main rice growing countries and three IARCs, IRRI, WARDA and CIAT, established in 1975. In the early 1990s, as a consequence of a long-term donor pulling out the funding, INGER’s operations were seriously threatened by a funding crisis. The 5th EPMR Panel recommended that the Council for Partnership on Rice Research in Asia (CORRA) take action to reinvigorate this partnership for the common good of NARS and IRRI breeders. Since 1999, CORRA has been serving as INGER's Steering Committee, guiding its broad policies and overall direction, namely the safe international exchange and evaluation of elite germplasm. INGER is managed by the Plant Breeding, Biochemistry and Genetics Division at IRRI. Key NARS scientists serve as technical advisers of INGER.
The 5th EPMR also recommended that IRRI evaluate carefully the developments in bioinformatics and develop a new strategy to secure in-house capacity in this evolving field. IRRI consequently reformed its former biometrics unit into the Biometrics and Bioinformatics Unit (BBU), which has developed a comprehensive data management system to link, for example, germplasm and bioinformatics information, nursery performance, pedigrees, and field performance of varieties. The BBU is therefore an essential ingredient for Programme 1 but it also provides the biometrics needs for all IRRI's research programmes. In addition to undertaking statistical research and consultation, scientific computing and database development, it provides consultation and training support to other groups, including the functional genomics Project. Its vision encompasses the need to ensure global public access to high quality informatics technology and information in support of rice agricultural research and to promote long-term capacity building in biological informatics including residential and outreach training in statistics, information management and bioinformatics for the NARS.
The IRRI genebank is the world’s largest and most important collection of rice genotypes. It was cited in a recent external review as "best in the CGIAR system" and "a model for others to emulate". The staff at The Genetics Resources Centre were awarded the 2003 CGIAR prize for ‘Outstanding Scientific Support Team’.
The rate of germplasm collecting has been reduced in recent years in the belief that the Oryza sativa collection is relatively complete and in order to target resources to other activities related to germplasm curation. This was probably a reasonable decision but the Panel suggests that attempts to stimulate projects to get as complete a collection as possible should be sustained. This makes practical sense because, as molecular marker technologies increase in efficiency, it will be possible to assay new material efficiently for new segments of chromosomes and new combinations of alleles not previously included in the collections. Also, the IRRI collection is biased towards indica types. It appears that japonica acreage could increase in the future and therefore acquisition and evaluation of japonica germplasm should also be considered a priority.
Despite the slowing down in collecting activity, a substantial number of new accessions has been deposited with the IRGC over the past five years including some 4,000 O. sativa and 200 wild rice samples. Wild rice accessions have already been shown to be useful sources of traits not found in cultivated accessions (e.g. resistance to rice tungro virus). In collaboration with NARS, two genotypes (Matatag 9 in the Philippines and AS996 in Vietnam), with genes from Oryza rufipogon were released and have been grown on over 100,000 ha. These provide tungro virus and aluminium toxicity tolerance respectively. Another success is the introgression of genes conferring resistance to African gall midge via an IRRI-WARDA collaboration. Due to the high potential utility to breeding of wild species of rice, their curation is important.
Special emphasis has been placed on understanding the biosystematics and classification of the wild rice species using a variety of cytogenetic, biochemical and molecular technologies. Wild rice has been shown to be a useful source of genes that have not been found in cultivated rice accessions and so this activity seems very worthwhile. There has been continued devotion of resources to in situ and ex situ conservation of rice cultivars from and in Laos. The in situ conservation activities are integrated with participatory development of improved varieties from traditional varieties.
There is some backlog in the management processes in the genebank, including documentation of accessions, which require attention in order to make the material available. The emphasis on maintenance of the accessions is important. New seed has been produced for over 40,000 samples and, overall, germination rates remain high. In the last 5 years, over 1,000 batches of seeds, representing over 70,000 samples have been sent to over 59 countries. Information on over 2,000,000 germplasm samples has been distributed to over 450 recipients in response to specific requests. These numbers reflect the interest and value of the IRGC and also the scale of the continuing task of curating the world’s rice germplasm and serving the various user communities. These tasks increasingly need to be carried out with compliance to international standards and policies.
The IRGC activities have included necessary improvements in data management, quality control, databases and on-line accessibility. The conversion from the old IRGCIS database to IRIS, to allow many more data streams to be combined and be accessible on line, is necessary and IRRI has been devoting substantial resources to the transfer. Web development is a continuous process to do justice to growing expectations, standards and new data. IRRI continues to make data available on CD ROMs for those without convenient Internet access. Partners are being encouraged to develop better non-English interfaces.
A new commitment has also been made to characterize the phenotypes of the accessions. This is being done through specific in-country evaluations, as well as in Los Baños. This is a special challenge given the complexities of phenotypes being dependent on the environment.
A core set of O. sativa accessions has been carefully selected for establishing the first round of genotype-phenotype studies. It is expected that DNA from all the core set accessions will have been made by the end of 2004. Various very good approaches are being adopted to carry out the analyses both in house and in state-of-the-art laboratories in ARIs, as described in Project 1. Specific mapping populations have also been chosen for special study, especially to locate drought QTLs. Alternatively, molecular genetic loci have been chosen and correlations of their map positions with known traits and QTLs have been studied. IRRI’s strategies for linking traits and genes are well conceived and have influenced those subsequently adopted by the Challenge Programme ‘Unlocking Diversity in Crops for the Resource Poor’.
During the review period, IRRI and other IARCs contributed 1,687 and 344 elite materials respectively to INGER. The number of contributions from NARS declined from the mid nineties until 2002, the total being 93 only. The decline may have resulted from the uncertainty of the rules applying to germplasm exchange and the trend is now starting to change positively as evidenced by the 139 NARS varieties contributed in 2003. In 1998-2003, INGER distributed 53,200 seed packets representing 11 ecosystem-based and 9 stress-oriented nurseries to 45 countries. INGER also distributed more than 2,000 seed packets of INGER entries to scientists at request. Thirty-three INGER lines were released as varieties in 6 countries in this period. In China, the restorers of 8 recently released hybrids are INGER lines. Release of INGER lines saves around 5 years in research time and resources, and hastens the flow of materials from research stations to farmers' fields[7]. Some 20 NARS utilized INGER materials originating from 39 countries and from 3 IARCs as parents in 1,700 crosses for improving the yield potential, pest resistance, abiotic stress tolerance, or grain quality of local varieties. NARS reported 30 released varieties where an INGER line was one of the parents. The impact of IRRI and INGER in contributing to variety production by NARS partners is clearly significant but more perhaps would have been expected. It is difficult for the Panel to form an accurate opinion of what kind of an impact the volume of exchange described above eventually leads to. However, a recent impact study[8], which included a section on rice breeding at IRRI, confirms that the use of both advanced and landrace materials from IRRI have had significant impact on NARS breeding success. No doubt, an exchange mechanism such as INGER has been and continues to be vital to facilitate this exchange.
A major thrust of the last five years has been the integration of germplasm information from different sources. IRRI has continued the design of the International Crop Information System (ICIS) in collaboration with CGIAR Centres, advanced research institutes and NARS partners. The rice version of ICIS, the International Rice Information System (IRIS), integrates information on all accessions in the IRGC with germplasm improvement and evaluation data from IRRI and numerous NARS collaborators. The integrated information comes from germplasm collections, breeding projects, and testing programmes, and uses unique germplasm identifiers and common trait descriptors so that rice researchers can implement knowledge intensive crop development strategies. IRIS is also being developed to integrate genealogical and phenotypic information with genetic and molecular characterization contained in local databases and in international bioinformatics resources. For the first time it is now simple to trace pedigrees back to their original sources, and also to trace the flow of genetic resources to released varieties around the world. The BBU has developed a stand-alone breeder's interface with read and write access and has also provided web access. Now BBU is designing an interface for genetic resources specialists so that genebank collections can be managed directly through ICIS. New web-based technologies are being adopted to deliver full, distributed read and write access to IRIS in the future.
The EPMR wishes to draw special attention to this Project because the opportunities to use the conserved germplasm are now entering a new era that will increase enormously its value and widespread use. It should therefore be recognized again, by all, as a resource of incalculable value and the investments necessary to enhance its near-term value for the world should not be spared. The goals and vision of IRRI in connection with the rice germplasm collection are excellent and strongly supported by the Panel. In the next few years, the genetic diversity in the genebank can be and should be characterized in increasing detail using molecular biology fingerprinting technologies, and database innovations introduced so that all this information is made available to the world at large in user-friendly searchable forms. Such advances usher in a new reason to appreciate the whole of rice germplasm worldwide as a single pool to be sampled in a directed way. The information in individual chromosome segments should be linked to all other data on rice germplasm - phenotypes, genotypes, yield trials, tolerance to stresses, adaptation to particular environments, preferences of consumers and use by farmers, and therefore be selected in breeding programmes to achieve defined goals. This will fulfil the dreams of collectors, breeders, geneticists, farmers and consumers. The power of gaining all this information and making it available to all should not be underestimated. It is now within reach.
IRRI has a large comparative advantage to empower this global germplasm analysis initiative because it has built up the germplasm collection and knows it better than anyone else. It has the molecular genetics expertise to understand and inspire a global programme, and with its partners is organized already to perform the vital, but challenging, phenotypic evaluations in multiple environments and under biotic and abiotic stresses and to centralize the results. IRRI is well connected with the ARIs who will also provide advice, leadership, results and resources. In addition, few institutions can come close to providing guaranteed safe long-term storage of these genetic resources together with the level of expertise that is required to co-ordinate, analyse, exploit and manage the data for the poorer countries. IRRI is, without doubt, with its international status, the best organization to provide open access to the germplasm and information under the international conventions.
The Panel therefore strongly supports the ongoing conservation of rice germplasm in the GRC, the aim of the GRC to stay at the forefront of germplasm curation, research and management and its collaborative ethos with its NARS and other partners to characterize the germplasm in multiple environments. Its prioritized research programme of improvements in data management and quality, revision of the molecular systematics of rice adding GIS data, removing backlogs and upgrading of the facilities should be supported without interruption. It must continue to foster the strongest working relationships with NARS, ARIs and other CGIAR Centres to realize the extraordinary opportunities that are now available for germplasm characterization worldwide in all crops. Links between the databases of IRRI and its partners, with all the associated training, need to be improved. It will be necessary to have the highest levels of quality control and systems in place to ensure that all the links between the seed accessions and other data have the highest accuracy. This will require very special attention.
IRRI with other stakeholders should continue development of a global informatics network integrating information on rice genetic resources, germplasm improvement, evaluation and utilization networked to similar networks for other crops and to other bioinformatics resources through public sequence databases. This network will provide the comparative biology platform and the very important means of making discoveries and transferring knowledge from one crop to another. Geographic Information and crop modelling data bases should be added to the networked data to help unravel the interdependent environmental, socio-economic and other factors that underlie the adaptation and use of rice genetic diversity. Database design and development are now sufficiently advanced in the world, and developed extensively in the past few years at IRRI, as part of the CGIAR initiatives that designing to communicate with each other readily is feasible and necessary. This should be a major investment, in collaboration with specialist database scientists elsewhere, ARIs, NARS and other IARCs.
As part of this initiative, and for many other reasons, IRRI should create an in-house database that allows linkage of any and all scientific and management information. This will facilitate the kind of scientific and management strategies that are essential today. For example, managing germplasm and genetic reagents is intimately involved with IPR and MTA management that needs to be done with diligence and accuracy. Such a database would help manage the absolutely essential quality control checks, tracking all germplasm accessions and observations on them, in all experiments in-house and by others, by bar coding or other such foolproof systems.
All of this visionary Programme should be continuously evaluated, technically, bioinformatically and comparatively with state-of-the-art methodologies as the subject is very fast moving. Many other institutions have comparative advantages and funding to generate particular types of information and will be leaders in parts of the endeavour. IRRI must be a significant and exemplary contributor but its major role must be to champion the global goals, empower others to use the germplasm and screening reagents for their own purposes and to coordinate availability of all the outputs for the world, but especially the NARS of the poorer countries.
In this Project, the tools of genomics are applied to find the genetic linkages between genes, functions and traits relevant to the problems confronting rice production. The Project includes the discovery of genes relevant to IRRI’s short-term breeding objectives and also a contribution to the global effort to find the functions of as many rice genes as possible over the coming decade. It is essential that IRRI takes advantage of the worldwide advances in functional genomics to find valuable, breakthrough genes and gene combinations in rice germplasm.
The value of molecular genomics to IRRI can also be illustrated by the following. Major fundamental constraints make the characterization and evaluation of germplasm difficult. First, most traits of high agronomic relevance have low heritability and high G x E, necessitating multi-location, multi-season, multi-treatment traits for fully comparative analyses. Second, breeding and research targets change, necessitating changes in the evaluation protocols, and repeated evaluation of old germplasm for new targets. A solution to the frequent mismatch between heritability and usefulness in traits is now emerging due to the recent advances in molecular genetics. From combinations of easily scored molecular markers that link chromosomal physical features to traits in a selected collection of germplasm accessions, it is possible to predict attributes of agronomic performance in other germplasm. This is achieved by scoring the DNA polymorphisms and applying the principles of association and linkage genetics.
The time is right, given the publication of near complete rice genome sequences and the high level of activity in generating the tools and markers and applying them to rice in the public and private sectors of numerous countries, also those in the developing world. These tools offer the opportunity not only to recognize and genetically map variation in genomes, but also to discover the expression patterns of thousands of genes under different environmental conditions. These tools are an essential part of plant breeding research today and must continue as an established part of IRRI’s and CGIAR’s plant breeding research for the NARS.
The goals of this Project include activities in 3 CGIAR Challenge Programmes. The budget for the Project was US$4.40 M in 2002 and has increased to US$4.6 M in 2004. There are 11.56 FTEs comprising approximately 7 IRS and 4.5 PDF statisticians, bioinformaticists, physiologists, geneticists, molecular geneticists and plant breeders
IRRI has addressed the relevant opportunities for molecular genetics over the past 10 years by gaining internal competencies, hiring some senior scientists with very good experience and establishing collaborative projects with ARIs. In the 5th EPMR, the Panel raised items relating to genomics and IRRI’s role and strategy. Since then, IRRI’s competencies and commitment have increased substantially as the value of the applications has become clear, transgenic plants have entered commerce in developed and developing countries and NARS have sought leadership and training in the technologies.
Externally, the near complete genome sequences of an indica and a japonica variety have been published and a huge number of useful molecular genetic markers derived. The technologies for designing unique features of tens of thousands of genes and putting them on to chips and hybridising with RNA extracted from plants, or plant parts, grown in defined conditions have been developed together with analytical methods to infer how and which genes are regulated in concert with developmental and environmental adaptation. Applications of these technologies have progressed rapidly. Methods to locate genes and to find which are responsible for QTLs have also developed. There are many examples in the literature today of map-based cloning of defined genes from rice as well as other plants and other organisms. Thus many of the technologies appreciated 5 years ago have now been reduced to practice to a considerable extent.
IRRI has developed a functional genomics strategy and many of the technologies and skills in-house, as described below, and added them to its arsenal of genetic skills for producing mutants, introgression lines etc. The pace of development of IRRI’s activities in functional genomics has been noteworthy.
A new laboratory was opened in 2002 to carry out some of the high throughput molecular biology techniques, especially those for chip array and marker applications. This laboratory, impressively equipped for present needs, provides a research and training lab for IRRI and its NARS partners. Extensive bioinformatics software programmes as well as drafts of the complete genome sequence have also been introduced into IRRI to design and manage the analyses of these sorts of experiments.
One way to identify the function of individual genes is to mutate them and observe the effects on the phenotype, providing the functions are not duplicated in the chromosomes. IRRI has produced such a mutant bank of about 30,000 lines, containing deletions and other chromosome aberrations. These are being distributed to the scientific community worldwide, to help in programmes to identify genes responsible for specific traits. IRRI was particularly motivated to create this set, using its facilities to handle and maintain the large numbers of plants involved, for its own interests and to contribute something very useful and tangible to the rice molecular genetics community worldwide, including the ARIs. Once screened, it is hoped to be relatively straightforward to find which genes have been changed and are responsible for the new traits. IRRI will, of course, be able to benefit from the discoveries made using these lines.
To help discover the genetic location on chromosomes of genes conferring specific traits, IRRI has substituted indica rice chromosomes one at a time into a japonica background. It has also created other specialized genetic stocks, mapping populations, near isogenic stocks and backcrossed lines. All these lines are to be disseminated to NARS and ARIs to facilitate the mapping and identification of gene-phenotype linkages. IRRI is also interacting and collaborating with labs in the USA that have specialized technologies for identifying plants with mutations in known genes and with other technology leaders. IRRI is commended for taking these initiatives.
There is now an International Rice Functional Genomics Consortium (IRFGC) led by IRRI involving the leading labs worldwide, with the mission to discover as many gene-trait linkages as possible. This is built upon and continues to attract resources from other major funding agencies including agencies in the US, China, Japan, Korea and India. Many students are being trained in the participating laboratories. The IRFGC provides a formal structure to share resources and develop collaborations between ARI and NARS. Again, IRRI is highly commended for taking this leadership position to stimulate and leverage knowledge from worldwide efforts for its clients and partners.
IRRI established an in-house micro-array facility for high-throughput screening of germplasm to find polymorphisms and haplotypes linked to desirable agronomic traits. This approach is very powerful. Using similar approaches, IRRI has established the means and carried out analyses to find out the expression patterns of a large proportion of the known rice genes and is collaborating in the IRFGC to enhance this knowledge. Some of the chips carrying 65,000 segments of rice genes are obtained from China. IRRI has selected sets of genes that respond to stresses for internal studies and has created chips to study the behaviour of these in detail in different lines, environments and stages of plant development. It is hoped that the results will lead to genes that can be deployed and combined to help in the control of stresses in future varieties. Training workshops focused on the chip technologies have been held for NARS and for the Asian Rice Biotechnology Network.
IRRI functional genomics and bioinformatics staff have won grants to be significant players in three Challenge Programmes, because of their leading skills and resources for tackling complex problems through molecular and database/computational biology technologies. This is a very significant achievement and is resulting in new staff and investments for IRRI in these very high priority areas of the CGIAR.
IRRI has, over the years, illustrated very well the way to use molecular biology to identify important genes that then enable germplasm to be screened for novel alleles. Using the identified genes it is also possible to make transgenic plants possessing a new trait. IRRI has focused on genes conferring tolerances to biotic and abiotic stresses, in line with major priorities. Its approach is to establish phenotype-genotype correlations, by studying the genes located in chromosomal regions where relevant QTLs map and sometimes by also comparing their expression patterns, to home in on the most probable gene candidate underlying the QTL. The work has progressed well and provides models for many such endeavours in the future. For example, some 96 drought responsive genes were identified and several found to apparently co-localize with QTL regions of drought tolerant traits. 365 markers located around these on the genetic map were tested for polymorphisms in 11 parents. Specific markers were thus discovered to conveniently track these genes in breeding studies. In other studies to find genes associated with the very important broad spectrum resistance, QTLs were identified that confer resistance to brown plant hopper. The Spl 11 gene was subsequently shown to be associated with the QTL and so this was then isolated by map-based cloning. That this gene is responsible for the trait was concluded by showing that allelic mutations in the gene correlated with the trait.
Other genes showing changed patterns of expression in the presence of disease resistance genes have been identified and thus are candidates for being involved in the mechanism of trait determination. Lines of rice have been screened for having different haplotypes around these loci to find novel variation. In yet other studies, QTLs associated with submergence tolerance were mapped and markers linked to them discovered. This enabled the sub1 gene to be identified and manipulated. Genes conferring salinity tolerance and phosphorus deficiency tolerance have similarly been localized to positions on DNA fragments for use as markers and to aid verification of gene-phenotype determinations.
All these represent good progress and point the way for how the Functional Genomics Project, working in collaboration with other Projects in-house, is opening up the way to find new alleles of known function in germplasm. This should become a rapid process in the future and should greatly assist the efficiency with which new alleles can be found, tested and built into varieties as appropriate.
IRRI notes that this Project will shift in 2004 from the past resource and infrastructure building phase to one where finding and verifying gene functions predominate. There will be a two track approach. The first will aim to produce ready-to-use products via trait-validated alleles or perfectly linked markers for production and deployment of improved plants by conventional breeding. The second will aim, via the IFGRC, to play a role in characterizing the functions of large numbers of rice genes. These two tracks will enable IRRI to bring nearer term value to NARS and facilitate continuing access to the discoveries and tools made by others.
The emphasis in the near term will therefore be to discover the function of as many valuable genes as possible and then variant genes/QTLs and linked molecular markers by utilizing the power of segregational genomics, as discussed above. The focus on the selected core collection of germplasm to begin the assessment of diversity and association mapping should continue with special emphasis. Continued in-house deployment of state-of-the-art bioinformatics, experimental and data analysis systems is also essential. All of this will need to be associated with external networks and collaborations to succeed and with continuous training in-house and with the NARS.
The EPMR endorses this strategy but encourages IRRI to continue to carefully choose its priorities. Finding out what phenotype is affected by a knockout mutation is not necessarily a good guide to how a variant allele will affect the phenotype in agriculture. Furthermore, such mutations will rarely be of use in elite lines. Similarly, activation-tagged lines may not recapitulate their phenotypic variation in an elite line. Thus, even when candidate genes have been identified from the gene-phenotypic correlations, how efficiently can they be used? At best, such knowledge will guide the researcher to screen germplasm for allelic variation to find better variants, but then there is the problem that the behaviour of each allele may be dependent on the genetic background. Haplotype blocks may still also be larger than ideal and linkage of undesirable alleles may still be a problem. Finding the right, rare recombinant may be too expensive. Whatever the difficulties here, the favourable alleles/haplotypes identified will surely often be useable for agricultural improvements. Alternatively, transgenes can be designed with the intention of releasing transgenic-enhanced germplasm to the NARS.
The current complexities in developing transgenic germplasm for release into agriculture and food chains are well known. There are biosafety, regulatory and IP issues which can make costs high, even before the value of the gene is known. Nevertheless, it could continue to be the case that many of the most beneficial, breakthrough improvements in the coming years will be via transgenesis and thus IRRI needs to continue to respond to the NARS wishes to take advantage of these breakthroughs. Fortunately, the private sector and the public sectors in developed and developing countries using arabidopsis, rice and other plant species are screening large number of transgenes and moving valuable ones through field trials towards products. Drought and disease resistance genes are attractive candidates for public and private sector alike. Thus, IRRI can afford to monitor these advances and only commit itself to develop highly selected, NARS approved transgenic varieties when the value, biosafety and IP license issues can be clarified. Consequently, IRRI should not put a high proportion of its resources into this area ahead of progress elsewhere. Its position in the IRFGC enables it to adopt this stance without neglecting the NARS needs. It should also be noted that the number of transgenes that the NARS are likely to release in the next 6 years is probably very few and therefore IRRI has time to choose very carefully which ones should be carried forward to advanced trials.
Some NARS, especially in China, have been trialling transgenic plants for some years, while this has not been possible in the Philippines. This illustrates that IRRI may have constraints that others do not have and may not be viewed as the ideal vehicle to advance this technology for certain NARS. Thus, the Panel sees IRRI’s comparative advantage as lying in its first declared tactic, namely the discovery of useful alleles by combining genotyping and phenotyping of its germplasm to identify genes by association and linkage analysis, followed by detailed analysis of the allelic space around such genes in its genebank. This can be done on an extensive scale and thus hopefully deliver specific information and tools to enhance breeding to fulfil a wide range of needs. The data can be structured according to pedigrees, where possible, so that cause and effect can be inferred with high confidence.
IRRI with its partners has the capacity and network linkage opportunities to relate genotypes and phenotypes and to make the information available to the NARS. This is where IRRI should lead the world. IRRI predicts that from the investments and likely advances throughout the world over the coming 10 years, it should be possible to produce a comprehensive rice genome dictionary of alleles/chromosome segments that are valuable for meeting the needs of specific environments, consumer preferences, environmental challenges, farmers etc when introgressed via the precision of marker assisted breeding, overcoming previous difficulties associated with unwanted linkages. It will, of course, also be possible to evaluate the novel genes in novel genetic backgrounds.
IRRI and the CGIAR should make plans to scale-up molecular fingerprinting to a level that will be required in the routine breeding programmes. Selecting multiple QTLs routinely may require the necessity to examine very large numbers of plants. While marker assisted approaches will increase the costs of certain day-to-day operations the outputs may be extraordinary. Consideration should be given by IRRI and CGIAR and their partners to establish state of the art MAS breeding centres for economies of scale. It should be noted that while stacking of many QTLs to create a valuable set of phenotypes can produce outstanding results, the combination is disassembled upon further breeding, as is necessary. This is where insertion of transgenes has an advantage, providing their genetic characteristics can be optimized and regulatory and other constraints associated with these products are not prohibitively expensive.
The EPMR endorses IRRI’s plans, with the reservations above, and urges IRRI and the CGIAR to ensure that the IRRI germplasm is evaluated in the field and via molecular markers in a concerted and coordinated effort, using the public and private sectors, with all possible speed and to create the necessary infrastructure to enable high quality data to be released to all, and especially the NARS. IRRI can inspire and empower some of the best plant genetics labs in the world to focus on this goal and with the progress established via the IRFGC and the already demonstrated commitments in funding from various sources, the goal is attainable. This could be the most significant, large goal-orientated flagship Project of the CGIAR and its global partners in the coming decade. Its relevance to opening up progress in breeding methodology and utilization of the world’s germplasm resources by the NARS is without parallel in the history of science and plant breeding.
This is an extremely important Programme in IRRI’s present and future. It could be the basis of a flagship Programme for the CGIAR. Characterization of rice germplasm using the tools and intellectual approaches of genomics is a high profile subject for fundamental studies of plant evolution, of what gene combinations man has selected in different environments and phases of cultural evolution and as a platform from which to develop a new phase of crop improvement. Rice now serves as a leading model plant and the crop that feeds most people. This combination is very powerful for attracting talented people and new resources.
IRRI has made very good progress since the last EPMR and has assumed a position amongst the leading rice molecular genetics laboratories by demonstrating its comparative advantage for the challenges in this work based on the rice germplasm, by some experimental results, by international leadership, by winning competitive grants and by establishing some high profile collaborations. The formation of and leadership role in guiding the IRFGC is excellent. Staff have also kept up commitments to train scientists from NARS. Now the major investments in developing the subject and facilities for functional genomics and germplasm screening need to be recouped in terms of world-class output.
The leading IRRI germplasm collection now has additional value as molecular biologists as well as breeders seek to discover its secrets and diversity. This importance is also reflected by the international efforts to guarantee long-term funding of collections and enhance their use through global collaboration and networks. The revitalisation of INGER through CORRA is a good success, but this group must be sustained financially in some way. Its remit could be expanded to include the exchange of genes, probes and other molecular biology reagents.
Progress and vision on managing the germplasm collection and making all the associated data available to all on-line are excellent, but selective collecting should still go on to obtain as much of the Oryza genus as possible. IRRI needs to maintain the highest levels of curation and management. Its reputation will depend on it.
The internal developments in bioinformatics are good and the design and adoption of IRIS and the transfer of data from IRRI to IRIS so that all can access it on line are particularly noteworthy. The challenge is to integrate IRRI databases with others including different NARS from different countries. IRRI is developing an open source system for accessing databases and considers itself a leader in the CGIAR in database development and networking.
The publications from staff associated with this Programme are reasonable, given that many new things have had to be started in-house. However, the overall rate of 1.8 refereed papers per year and 0.5 book chapters per international staff member (including IRS and PDFs) in subjects covering molecular biology, bioinformatics, breeding and genetics is too low to capture and sustain a high status in the subject of rice germplasm analysis and trait genetics. Scientists working on rice genetics/genomics in many other institutions will exceed this regularly. However, the proportion of papers published in molecular biology, genetics and bioinformatics in high impact journals is reasonable. IRS staff should endeavor to get sufficient, high profile papers associated with IRRI so that the status of the institution in the field is maintained. If this is lost, then the credibility and the opportunity to serve the NARS with leading information and to sustain funding may be compromised. The Panel also suggests that IRRI staff consider very carefully what is worth publishing and where it will have the biggest impact so that all the time spent writing (and attending conferences) is optimized. This is especially important now that additional burdens of Challenge Programmes are being carried by some of these same IRS staff members. The Panel expects that publications will increase in the future as the subject moves on and IRRI’s experience grows.
The scale of the opportunities and responsibilities of this Programme are far beyond IRRI. The EPMR is pleased to see that IRRI knows that partnerships are absolutely essential. It can never be done without INGER, ARIs and other CGIAR Centres. IRRI has made a good start in building on its strengths to ensure that these linkages and networks are in place. IRRI must continue to drive the global vision and inspire and empower others, wherever and for whatever reason, to join in the big push to make disseminated knowledge on rice as second to none on the planet. The value of what will flow from this is beyond the minds of us all.
With this position IRRI and the CGIAR assume much responsibility. The standards required in the molecular biology, germplasm annotation, database and bioinformatics to fulfil the expectations are very challenging. IRRI must therefore adopt very high quality control standards and systems. It should take the opportunity to learn from the leading private sector laboratories and those leading the field in human genotyping and mapping. Careful management of IP matters and MTAs is very important as expressed elsewhere.
Because the scale and scope of the opportunities are so extensive and attractive, IRRI should be ruthless in selecting what it does internally in functional genomics. It must focus on discovery of QTLs that will help address bottlenecks and the needs of the poor and methods to make plant breeding more successful. The choice to explore first stress and disease related genes makes sense, and progress to identify them has been very good. Genes that enhance grain yield in valuable ways, and also quality, are also good selections in principle. The EPMR is pleased to see the interactions with Programmes 2 and 3 and considers that such interaction and commitments are essential to extract the value out of Programme 1 to fulfil IRRI’s mission. IRRI should plan to adopt larger scale marker assisted breeding technologies as progress makes this justified. Consideration should be given to establishing a state-of-the-art lab for handling the very high throughput needs of several CGIAR Centres or simply outsourcing to specialist organizations where this is cost effective and reliable.
Overall, the conclusion is that IRRI has made good progress to help stimulate the global challenge to understand rice germplasm diversity and to develop methods and information to help improve breeding successes. However, the challenge is a global one and fortunately a large number of specialist institutions are already involved but their outputs need to be coordinated to maximize the value of their efforts. IRRI can continue to contribute to this role with the right sensitivities and sustained scientific standing.
It will take a relatively large amount of money to achieve the long-term extended goals of the Programme. Fortunately, many governments, companies and ARIs outside the CGIAR have a similar vision and are spending much more money and training people, and are therefore also contributing to the IRRI vision.
Five major priorities for action stand out:
Maintenance of the IRGC;
Phenotyping and genotyping of the selected set of accessions;
Continuing careful selection of the QTLs and genes for improving germplasm selection by IRRI and NARS breeders;
Dissemination of information on rice for the NARS; and
Planning of high throughput facilities for application of marker-assisted breeding as required by the breeders in the future.
The Panel recommends that IRRI stimulate the global community to establish gene-phenotype linkages in carefully selected germplasm in a targeted way, as rapidly as possible, for purposes of plant improvement, making results available to all. IRRI should report to the Board of Trustees by April 2005 on its progress in implementing this initiative with its partners.
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[7] Evenson, R.E. and D. Gollin
1997: Genetic Resources, international organization, and improvement of rice
varieties. Economic Development and Cultural Change. pp. 431-500. [8] Hossain, M. et al. 2002: International Research and Genetic Improvement in Rice. In: Evenson, R.E. and D. Gollin, 2003: Crop Variety Improvement and its Effect on Productivity. The Impact of International Agricultural Research. CAB International. FAO. |
