Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology (2008) / Chapter Skim
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3 Recommendations and Goals: New Horizons in Plant Genomics
3 Recommendations and Goals: New Horizons in Plant Genomics
Pages 53-108
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From page 53... ...
The key to understanding those principles is basic research done in the context of the revolution of genome-based science. The committee strongly recommends that the next wave of National Plant Genome Initiative (NPGI)
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From page 54... ...
• The committee strongly endorses the conclusions of the 2002 NRC report, The National Plant Genome Initiative: Objectives for 2003–2008, that studies aimed at defining core concepts of molecular and developmental plant biology are best undertaken rapidly and efficiently in model plant systems. Basic discov ery that can be most rapidly and efficiently done in these systems should receive high priority.
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From page 55... ...
Each recommendation has a set of goals on three different time horizons: The 5-year goals represent immediate, pragmatic "next steps" in plant genome science, 10-year goals require significant development of new tools and resources to en able transformative solutions to real world problems, and 20-year "achievements" reflect the committee's desire to define some admittedly long-range, high-risk, high-reward areas that would significantly alter society's ability to understand how plants work. TOOLS FOR PLANT GENOME RESEARCH IN THE 21ST CENTURY One of the most remarkable impacts of genomics projects is the development and application of facile technologies that allow the global analysis of cellular components, including genes, proteins, and metabolites.
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From page 56... ...
empowering individual principal investigators or col laborative groups to access and utilize next generation sequencing technologies for a broad spectrum of genomics and metagenomics discovery. RECOMMENDATION 2: Develop "omics" resources and toolkits at high resolution in a few, carefully chosen plant species, including expansion and deeper investment in currently lead ing model species.
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From page 57... ...
These technologies are now sufficiently wide spread that they are accessible to most researchers for individual experiments. In plant sciences, the accessibility of these technologies can be largely attributed to NPGI and the Arabidopsis 2010 Project of the National Science Foundation (NSF)
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RECOMMENDATION 1: Expand plant genome sequencing, plant-associ ated microbial sequencing, and plant-associated metagenome sequencing, and associated high quality annotation by (a) using the Department of Energy's Joint Genome Institute's sequencing capacity to generally serve plant sciences and (b)
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From page 59... ...
Although there are several high-throughput genome centers devoted to the missions of NHGRI, only JGI has plant biology as a central component of its mission. JGI has established a peer-reviewed policy for high-impact reference plant genome sequencing, which it has implemented suc cessfully (see Chapter 2)
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From page 60... ...
It seems reasonable that the JGI would take the lead on generating a broad swath of new plant genome sequences, because plant science still requires many high-quality draft sequences to serve as reference sequences for those species and branches of the evolutionary tree. In addition, other existing large-scale sequenc ing centers could be recruited to participate in NPGI activities.
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From page 61... ...
• Tens of thousands of plant genomes, or more, will exist as annotated resequences. "Omics" Resources and Toolkits RECOMMENDATION 2: Develop "omics" resources and toolkits at high resolution in a few, carefully chosen plant species, including expansion and deeper investment in currently leading model species.
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From page 62... ...
crop that is highly sensitive to frost. Genome sequencing could aid genetic improvement for cold resistance.
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From page 63... ...
Useful, integrative, Web-based computational resources that allow the broader community of scientists to derive high value and to form testable hypotheses are a critical component of a full omics effort. For example, what good is an omics project to assemble a deep catalog of molecular and metabolic responses to drought stress if plant biologists working on important problems of drought stress cannot access, synthesize, understand, and analyze the data?
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• Extensive bioinformatics resources. Well-developed, community stan dards-based bioinformatics resources for a plant species are critical to place omics data in context.
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Therefore, omics tools and resources are best developed and tested in plant species that have served as model systems for basic experimental science. Broadly applicable model systems have several common features, including well-established and easily managed ge netic properties (for example, the ability to self- and cross-fertilize, and abundant genetic markers)
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From page 66... ...
Criteria for Investing in a "Partial Omics Effort" Although only a few species will fulfill the criteria for full omics treatment, a broad range of plant species will warrant development of a partial omics toolkit. There is not a strict, sanctioned list that defines which omics comprise a "partial omics toolkit," as the omics most relevant to a particular species or crop plant will vary.
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From page 67... ...
Physical resources include items such as clone and mutant collections. Information resources include DNA sequences, datasets that catalog information such as protein-protein interactions, gene expression, and transcription factor binding.
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From page 68... ...
• Begin development of, or expand existing, partial omics kits for plant species that have important economic, ecological, developmental, or biological features that cannot be fully studied in the core model species. Some examples to consider: a legume (for nodulation studies)
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From page 69... ...
• Create genome-wide knockouts and complete full-length cDNA collections; strive for accurate genome annotation, functional analysis and other omics tools for both core full omics models, and leading partial omics species. • Implement translation of discoveries in model plants to most key crop plant species, including transformation methods for all major crop species.
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From page 70... ...
. Further, the NSF Arabidopsis 2010 Project and the Interagency Working Group on Plant Genomes NPGI have defined an initial set of key pathway components required for the regulation and manipulation of plant growth and development and of plant responses to pathogens and environmental stress (see Chapter 2)
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From page 71... ...
Many of the basic intracellular algorithms can likely be determined from a few well-studied models; heterogeneous data collection and analysis will not be necessary for every plant species. As discussed in the section on omics toolkits, many of the most important basic lessons learned from the systems view of model species can be applied to other species.
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From page 72... ...
Although plant biologists have made important progress in defining components of the key regulatory modules and their hubs in plant species, a far more detailed and dynamic view is needed. Biological networks have all evolved to be generally robust -- that is, they are resistant to most stochastic changes they experience.
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From page 73... ...
Given its relatively low cost, cataloging small RNA populations in several crop species could be an initial step towards understanding the mechanisms of epigenetic change across diverse crop species. It is also now feasible to use chromatin immunoprecipitation methods together with tiling arrays or deep sequencing to describe changes to histones and DNA methylation during development and response to environment in a variety of crop species.
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From page 74... ...
The iPlant will also present novel educational paradigms, as it can be used to generate many "virtual plants" that are far smaller algorithmic clones of the iPlant, to be used for effective education and community outreach programs not only for plant science, but for biological systems in general. Goals for Research in Molecular Regulatory Networks (Recommendation 4)
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o hromatin immunoprecipitation sequence of transcription factor targets C (selected tissues, cells, and time domains)
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• iPlant algorithms will be developed and their accuracy and value will have been critically tested in many partial omics model species that represent major crop types and scientifically important species. • Synthetic biology will be in widespread use in plant science.
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From page 77... ...
Genomic analyses of genetic diver sity are needed for association studies to discover agriculturally important genes and to serve as a source of genetic polymorphisms for functional analyses of plant biology. Comparative genomics data cannot yet be fully exploited in plants, as has been done so successfully in the primate lineage for example, because of insuf ficient genome sequence coverage both within key model species and across
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From page 78... ...
As a result, understanding how plants function, and how to modify and improve their ability to carry out specific physiological processes -- the ultimate goals of plant genome research -- could have large benefits for terrestrial and linked aquatic ecosystems. Because NPGI programs improve the basic knowledge and infrastructure for understanding, managing, and breeding all plants, its environ mental impacts will be deep and far reaching.
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From page 79... ...
Because of the complexities of agroecosystems and human behavior, the over all environmental impacts from changes in plant varieties are difficult to predict. Nonetheless, new types of plants whose improvement is a direct result of genomics research either via conventional breeding or genetic engineering will likely provide substantial environmental benefits.
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From page 80... ...
In response to this recommendation, NPGI, largely under the auspices of JGI and following JGI's community-based, peer-reviewed system, undertook sequencing of reference genotypes of the plant species listed in Chapter 2. For several of these species, NPGI is positioned to take advantage of large collections of natural variation in the form of diverse cultivars, accessions, and wild relatives within each species and next-generation sequencing technologies.
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From page 81... ...
. This trend is laudable and should continue because it provides an excellent way to leverage reference genome sequences and focus efforts using reference species to determine gene function and network operation to maximum effect.
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From page 82... ...
The aim would be to broaden the community of researchers who have access to and can effectively use plant-genomic tools and data in the future. Technologies such as low cost resequencing, initial reference genome sequencing, and association genetics greatly lower the threshold for which new species can be considered useful experi mental organisms.
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From page 83... ...
• Develop representative models to address major evolutionary issues, such as speciation, adaptive trait evolution, adaptation to environmental conditions, and evolution between and within population. • Study domestication in crop plants to understand evolutionary principles, agriculturally important genes, natural genetic variation among cultivars and landraces, adaptation to heterogeneous environments and changing climates, and phylogenetic differences among plant groups.
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From page 84... ...
In order to most effectively translate knowledge from the basic science at the core of NPGI into commercial innovation, and to accelerate the pace of translation to practical outcomes, ad ditional enabling tools and methods for enhanced transfer from model systems to crop species should be developed. Given the considerable fundamental advances in understanding plant genomes and the substantial progress in translation (discussed above)
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From page 85... ...
discovery and marker-assisted selection in crop-breeding programs, and facilitates the study of plant evolution across all taxonomic levels. The application of marker technologies has significantly advanced the study of both single- and multi-genic traits of economic importance, has become a standard tool for many plant breeders, and has been widely employed in research studying the genomic conservation among related plant genomes and the evolution of plants.
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From page 86... ...
The decrease in cost of DNA sequence acquisition, which leads to an ever increasing availability of DNA sequence for crop plants and their wild relatives, will provide a template for additional SNP discovery. In some of the major crop species, resequencing of multiple genotypes will enable massive SNP discovery, and will provide the first steps toward enabling association genetics in these important crops.
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From page 87... ...
The ability to sequence multiple isolates of a single plant pathogen species cost-effectively, coupled with the availability of dense marker maps in several crop species as well as large mapping of natural populations, allows detailed studies of the interaction of crop plants and their pathogens and their insect enemies. In addition, dissecting the genetics of traits that allow plants to perform in suboptimal environments (for example that are critically limited by water, temperature, nutrients, and light)
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From page 88... ...
Plant breeders can take advantage of the variation across the genomes of closely related populations, as well as the distant relatives of crop species. The availability of genomic resources and a clear understanding of the evolutionary divergence of various plant species can facilitate the identification of agriculturally important genes in crop species through the knowledge of its genomic location in a model species.
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From page 89... ...
On one hand, the ability to compare DNA sequences across plant species is essential to leverage information from one spe cies to another. On the other hand, plant breeders need to be able to navigate from sequences to genes to phenotypes within a single species.
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From page 90... ...
They will enable the delivery of gene stacks to improve biofuel feedstocks; to produce food crops that are resis tant to multiple diseases, pests, and abiotic stress; and to generate plants capable of synthesizing molecules useful for medicinal or pharmaceutical applications. Realizing these potentials depends on developing minichromosomes in multiple plant species that can be easily engineered and function with high fidelity.
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From page 91... ...
10-year goals • Develop novel biomarkers that accurately report the physiological status of the plant in the context of its environment in real time. • Develop crop plant genomics databases that easily access complete genotypic and phenotypic data in the field.
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From page 92... ...
It also reduces the cost and risks to plant genome research by removing the reliance on individual developers and suppliers, providing more flexibility in software development, en hancing the integration of systems, and investing the ownership of the informatics in individual members of the community. One role of NPGI will be to support standardization efforts because they benefit the entire plant research community.
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are richly described. Because the genome sequence provides the backbone resource on which all other resources depend, its utility depends on it being as comprehensive, complete, precise, and detailed as possible.
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Common syntaxes, such as extensible markup language, allow basic syntactic parsing of the data that is collected. The outstanding challenge is to interpret the data semantically, which requires the de velopment of a shared descriptive language to enable the data integration needed for plant genome research.
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From page 95... ...
The large amount of information housed in genomics databases and the expected explosion in data generate 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.
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• Data-capturing tools that are fully integrated with the knowledge generation by the researchers who collect the original data will be available; the tools will have a seamless operation from data generation to data management. EDUCATION AND OUTREACH Education RECOMMENDATION 8: Improve the recruitment of the best broadly trained scientists into plant sciences.
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From page 97... ...
Interna tional cooperation will likely continue to play a significant role in translational ge nomics, given the expanding repertoire of plant species for which genome sequence and genomic tools are available, coupled with the increasingly global nature of scientific inquiry, agricultural markets, and global concerns about sustainability. Despite the large number and expansive scope of education and outreach initiatives, metrics to measure their impact and success against their goals are essentially lacking.
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From page 98... ...
NPGI should build mechanisms to ensure that the number of graduate and undergraduate students with rigorous training in both biological and quantitative approaches to plant genomics is sufficient to support a thriving research and development job environ ment in both the public and private sectors. By leading with new opportunities for graduate support in bioinformatics and computational biology within the context of plant genomics, NPGI could bolster the image of plant science as an exciting alternative to the biomedical fields for ambitious and creative students.
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. However, undergraduate research experiences do not appear to attract significant numbers of previously uninterested students to a career that requires a postgraduate degree (Hunter et al.
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. Introductory laboratory courses that engage students in interdisciplinary in vestigations in plant sciences and genomics are another avenue to promote student interest in research at a time when their career choices are still relatively fluid.
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Outreach RECOMMENDATION 9: Promote outreach on plant genomics and related issues that are critical to educating the American public on the value of genomics-based innovations.
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For example, if one goal of workshops for K-12 teachers and summer internships for high school students is to broaden the targeted populations' understanding about plant science, genomics, and biotechnology, the conduct of rigorous surveys of participants' knowledge before and after each program is necessary to assess the impact of the workshop. Longer-term assessment could include occasional follow-up question naires to document the broader impact of participation in the workshops on the science curriculum at the teachers' home schools.
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From page 103... ...
This market sector is likely to grow, espe cially if food transportation costs rise dramatically. Philosophical interest in plant genomics among these groups is likely to benefit from clear communication that genomic research is not necessarily tied to deployment of transgenic plants, and on tangible and relevant outcomes in the form of cultivars that are well suited for particular, local, and often low technological input, agricultural niches.
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From page 104... ...
; AMS 2007) , even the most well-meaning efforts to create common ground between genomic researchers and organic farm ers could be derailed by negative grower or public perceptions that simplistically equate plant genomics with genetically engineered plants and/or proprietary tech nologies owned by multinational corporations.
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From page 105... ...
In the acrimonious GMO debate, most of the NPGI-funded genomics research community has been conspicuously quiet, even when the debate concerns substantive genomics issues. This may have helped to create space for those with strong political views, but weak knowledge of plant science, to dominate the social discourse (Vasil 2003)
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From page 106... ...
Because fundamental advances in knowledge of plant genomes are likely to empower increasingly novel, innovative uses of genomic informa tion, the opportunity cost to society from its limited ability to use transgenic approaches is likely to grow rapidly. Outreach on ELSI topics is an issue that the NPGI needs to confront.
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From page 107... ...
programs in genomics so that two courses in statistics and competence in a modern scripting language become standard requirements for advanced degrees. • Establish mechanisms to engage sustainable, organic, and small-scale farm ers in identification of specific traits for which applications of genomic tools could lead to usable varieties with enhanced performance characteristics.
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From page 108... ...
108 Achievements of the N at i o na l P l a n t G e n o m e I n i t i at i v e 20-year achievements • Integration of research and education in plant genomics will rival that of biomedical genomics in creativity, in public profile, and in the ability to attract new students. The plant genomics community will provide leadership in contributions to ward public outreach on ELSI issues, including engagement in development of sci ence-based regulatory policies at national and international levels, by NPGI-funded programs and NPGI-trained students and postdoctoral associates.
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