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The National Plant Genome Initiative: Objectives for 2003–2008 Executive Summary Plant life plays important and diverse roles in our society, our economy, and our global environment. Research on plant biodiversity, development, physiology, and evolution is needed to understand plant biology in those roles and to increase our ability to use plants beneficially. The National Plant Genome Initiative (NPGI) was launched in 1998 to advance national objectives in plant biology, agricultural, and energy research. In addition to the instrumental role that NPGI played in accelerating the completion of the first plant genome sequence, that of the model plant Arabidopsis thaliana, it has supported the development of genomic resources, such as bacterial artificial chromosome libraries, physical and genetic maps, comparative genetic maps, and novel germplasm resources for a broad array of crop species. Functional-genomics tools enabling high-throughput screening for mutations have been developed for some crop species. And NPGI support has led to the generation of a wealth of DNA sequences deposited in public databases, mostly in the form of expressed sequence tags (ESTs), the short segments of DNA that represent gene-coding regions. That investment is creating a distributed infrastructure of experimental and database tools for plant genomics in a variety of crop species. The NPGI has, in fact, brought genomics to crop-plant biology, resulting in important new knowledge, for example, about the function of plant centromeres and kinases, and the basis of plant responses to the environment. This
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The National Plant Genome Initiative: Objectives for 2003–2008 capability can now be leveraged to accelerate the translation of basic discovery to agriculture. The predictive manipulation of plant growth will affect agriculture at a time when food security, diminution of lands available for agricultural use, stewardship of the environment, and climate change are all issues of growing public concern. The Office of Science and Technology Policy and the federal sponsors of the NPGI—the National Science Foundation, the Department of Energy, and the Department of Agriculture—approached the National Research Council for help in determining goals for the NPGI in the timeframe 2003–2008. In response to the request, the Research Council established a committee to study the future directions of plant biology and genomics and to recommend priorities for the 2003–2008 phase of the NPGI. The work of the committee was informed by a 2-day workshop held at the National Academy of Sciences on June 6–7, 2002. On the basis of discussions at the workshop and additional information, the committee developed a set of recommendations, which are summarized below and detailed in the full report. The recommendations rest, in part, on: Progress of the NPGI to date. The availability of data, software, methods, tools, biologic, and other genomics-related resources for various plant species. The ability of research and development user communities to absorb and rapidly exploit gene-sequence information and other genomics tools. The potential for international collaboration in new plant-genome activities. The need to advance a variety of efforts in plant research and applications as rapidly as possible was balanced with the desire to proceed as economically as possible.
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The National Plant Genome Initiative: Objectives for 2003–2008 Recommended Goals for the National Plant Genome Initiative in 2003–2008: Focus the NPGI portfolio on a small number of key plant species for in-depth development of genome-sequence data and development of functional-genomics tools. Candidate species for detailed analysis and investment should be individually evaluated and selected by using science-based criteria that recognize: rapid and economic scientific development, the need for temporal ordering of investments to achieve economies of scale, and application to crop improvement. The criteria include genetic tractability, genome size and complexity, and the potential for translation of data and tools to agronomically important relatives. The availability of a sufficient population of researchers, including international partners, working on both a candidate species and its relatives is vital to ensure use of DNA sequence and functional-genomics tools by a coherent community (Appendix C of the report provides information on the number of publications on the 50 most-cultivated crops and a few reference species in 2000–2001). Species for this level of large investment should be chosen from the families of Poaceae (grasses), Fabaceae (legumes), and Solanaceae (including tomato and potato) to maximize translational opportunities for the greatest number of economically important plants. Rice, maize, Medicago truncatula, and tomato would be examples of species that meet most criteria for immediate expanded emphasis. Because the species would be sequenced to near completion, and because their sequences will inform research and crop development for all the related crop species, we refer to them as reference species. Concentrating DNA sequencing efforts on a small number of carefully selected genomes is greatly preferred over a diffuse effort on many plant species because it focuses research on identification of genes and key biologic functions in experimental contexts in which those goals can be achieved economically.
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The National Plant Genome Initiative: Objectives for 2003–2008 Enable translation of basic findings from the reference species to related crops. To leverage the investment suggested for the reference species, essential tools for comparative genomics need to be developed, including large-insert DNA-clone libraries, physical maps, and mapping tools for their agronomically relevant relatives within the Poaceae, Fabaceae, and Solanaceae. These tools should be explicitly developed with applied goals in mind, including acceleration of plant breeding, mapping and deployment of quantitative-trait loci in breeding programs, and molecular identification of beneficial alleles of any particular gene. These tools will facilitate further genome sequencing of a variety of crops in the future as sequencing costs drop. We recognize that soybean and wheat are key crop species and thus anticipate that draft sequencing of the gene-rich regions of these genomes could commence during the 2003–2008 time frame, as the cost of sequencing declines, or funding increases. Begin dissection of the evolutionary diversification of plants using genomics technologies. The more than 250,000 species of plants have a wide variety of growth habits, adaptive responses, and useful traits. The diversity and complexity of plant genomes is increasingly recognized as a reflection of the evolutionary forces driving plant speciation. Genome comparisons across great evolutionary distances provide insights about the similarities and differences among organisms. To begin exploring and potentially harnessing that information, the NPGI should make an investment in evolutionary genomics. The investment would enable the participation of the evolutionary-biology community in the genomics revolution, thus expanding the intellectual expertise in plant biology as a whole. A broader understanding of plant evolution will also increase the palette available for crop improvement.
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The National Plant Genome Initiative: Objectives for 2003–2008 Expand investment in bioinformatics to fully leverage the wealth of plant genomics data now being generated. The large amount of information housed in genomics databases and the expected explosion in data place huge pressures on the organization of research to effectively mine that data. The plant-research community will have to place greater emphasis on integrating bioinformatics approaches into its work. We propose a national strategy for bioinformatics that includes training, collaboration with large data centers, and bioinformatics-oriented research, such as the creation of specialized databases and new analytic tools. Create new interdisciplinary training opportunities for doctoral and postdoctoral researchers. To fully exploit genome-based data, the plant-biology community needs to expand training opportunities into disciplines that are not traditionally associated with plant biology and crop sciences, such as computer science, mathematics, chemistry, and engineering. In addition to continued support for students and postdoctoral fellows on single-grant applications, increased support for interdisciplinary training grants is needed to develop a scientific workforce capable of using the tools that multiple scientific fields offer to plant genomics. All of those goals are important, and it is equally important that they be pursued logically and efficiently, with funding decisions determined by stringent peer review. Some will require more effort and support than others, and different technical approaches will be needed, depending on the species under consideration, the objectives of the research, and the genomic information available from other projects. The following recommendations constitute a strategy for implementing the 2003–2008 goals. The strategy assumes that the current trend of funding for the NPGI, and for the necessary complement to NPGI provided by the Arabidopsis 2010 Project to exploit the model plant species, will continue or increase.
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The National Plant Genome Initiative: Objectives for 2003–2008 Recommended Strategy for the National Plant Genome Initiative in 2003–2008: Support two categories of DNA sequencing: Genomic sequencing. Sequence to the level of a “deep draft” the genomes of appropriately selected and ranked reference species from Poaceae, Fabaceae, and Solanaceae. By deep draft we mean sequencing of the gene-rich regions of a genome so that each DNA base is represented, on average, 6 times. This is termed 6-fold coverage. Finishing implies filling gaps and increasing the sequence accuracy to no more than one error per 10,000 base pairs. This sequencing effort should be buttressed by sample genomic sequencing (at ~2x coverage) of related and progenitor species of these families and Arabidopsis (in Brassicaceae). Because having a complete sequence is fundamental to all other activities, we recommend that roughly 40% of the entire 5-year budget be used for this activity. Transcript sequencing. We recommend that roughly 12–15% of the budget be used to support sequencing of transcripts, as full length cDNAs or ESTs, as follows: First, sequence full length cDNAs of all the Arabidopsis genes to generate a baseline “plant Open Reading Frame reference set"—the ORFeome—that represents the set of genes from which protein is made. Second, based on the EST data sets and unigene assemblies now available via NPGI, sequence full-length cDNAs for those genes of the other reference species that are either not found in, or are most diverged from, relatives in Arabidopsis. This hierarchical approach to full-length cDNA sequencing will eventually yield a plant ORFeome that incorporates many aspects of plant evolution, as well as having very high value for functional studies. Sequence ESTs from specialized plant cell types and organs in species from which specific novelties in the expressed gene sets can be expected. We expect roughly 25 such projects of various size determined by the specific biological question. Sequence ESTs from carefully normalized cDNA libraries of each of about 50 species chosen with reference to current programs in evolutionary
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The National Plant Genome Initiative: Objectives for 2003–2008 genomics. This activity is aimed at facilitating an understanding of the events leading to plant diversification (see item 5, below). Translate genomics data from the model species, Arabidopsis, and the reference species to agricultural improvement. The public and private communities of applied plant biology should be included in efforts to translate basic discoveries to crops. In addition, assuming that prerequisite resources are developed and sequencing costs continue to drop, genomic sequencing of the gene-rich regions of soybean and wheat could be initiated. We suggest a 10% budget investment to hasten the fulfillment of translational agriculture. Support efforts to enable and deploy whole-genome functional analysis to determine the function of genes and gene networks in Arabidopsis and the reference species. The efforts should be ordered over time to ensure maximal leveraging of sequencing activities proposed above. These activities will require roughly 20% of the budget. Support the construction of integrated databases and analytic tools to manage plant-genomics data and make them available to the worldwide research and development community. This should include a large training component and will require about 15% of the budget. Enable plant evolutionary genomics, systematics, and population biology, through the analysis of EST sequences generated in this program as suggested in item 1, above. Support the creation of a national plant-genomics initiative steering committee. To maximize the nation’s return on its investment in plant genomics, there is a need to continually strategize and coordinate research efforts on all fronts. A committee broadly representative of the plant-biology community that would take a long-term view of plant genomics could provide essential advice to the NPGI Interagency
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The National Plant Genome Initiative: Objectives for 2003–2008 Working Group on critical community needs, logical next steps, and specific research or technical objectives. If implemented, the strategy proposed here will substantially affect plant biology. Furthermore, results from the NPGI will generate insights for all of biology and its applications. At the end of this decade, the plant-genome community will have made major inroads toward a more complete understanding of plants and gained new abilities to use them in productive and helpful ways.
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