National Program 302 Progress Report:

Plant Biological and Molecular Processes

I. CONTEXT

Doubling of the World’s population between 1960-2000 (from 3 to 6 billion people) required dramatic increases in food production. The Green Revolution that created this increase was based in large part on more productive crop varieties and intensification of fertilization, irrigation, and pest management. All of these changes – including the breeding of better varieties – would be unachievable, and unsustainable once achieved, without advances in the fundamental knowledge of plant genetics and biology.  These advances in understanding of plant function are the building blocks for improvement of productivity and production efficiency. For example, increased understanding of the principles of plant growth and development led to gains in harvest index and stress tolerance.  Also, breeding for resistance to pests and pathogens has been greatly stimulated by knowledge of the resistance mechanisms and of the genes responsible for resistance.  Many other examples can be cited. Defining the mineral elements required for plant growth and seed development resulted in improved plant nutrition. Knowledge of the role and significance of plant hormones helped to identify the dwarfing phenotype as a potential target for crop improvement programs. In addition, defining hormone involvement in fruit set allowed for significant enhancement of harvestable fruit yields and post harvest stability. Knowledge of carbohydrate partitioning contributed to higher yielding sugar beets and sugar cane.

The battle is not won.  Continued advances such as these will be required to meet the food security needs as Earth’s population increases to 8 billion by 2030.  Moreover, as arable lands and fresh water available to agriculture diminish, the intensification of production on a static land base with existing resources will be more important than ever.  At the same time, reduction of off-farm effects has emerged on the world stage as a major driver of research.  The “global village” will no longer tolerate pesticides or fertilizers leaking into its water supplies, and it demands a food supply of increasingly high quality.  All of these changes will require knowledge of how plants function, so that rational strategies can be devised to enhance those functions.

National Program (NP) 302 was established with a mission to conduct fundamental research on plants, to develop knowledge that forms the basis for greater crop productivity and efficiency, better product quality and safety, improved protection against pests and diseases, enhanced tolerance to abiotic stress, and sustainable practices that maintain environmental quality. The rationale for NP302 is based on the fact that plant growth and development is the result of the coordinated expression of genes and gene networks within a given environment which gives rise to a multiplicity of phenotypes. Progress in crop improvement requires that agricultural scientists understand the genetic, biochemical, and physiological principles governing phenotype. As such, NP302 was intentionally constituted differently from most other National Programs by its emphasis on fundamental knowledge of biological and molecular mechanisms underpinning long-term advances in crop production, protection, product value, and food safety.  The centrality of the NP302 mission is supported by the engagement of our research within the mission of many other National Programs to identify innovative possibilities that utilize the outcomes of fundamental research in support of solving agricultural problems of current importance.   Research in National Program 302 demands a highly integrated approach in which the experimental design scales across levels of biological organization ranging from gene ensembles to crop canopies.  As such, success often requires interdisciplinary collaborations both within and external to this National Program.  The research must also integrate across the aerial and subterranean environments requiring new collaborations, which cross traditionally separate research disciplines.

This component was founded on expectations that over time these research activities will, through disciplined focus on identified issues of agricultural  importance,  provide the enabling biological  understanding to solve difficult problems and reveal unforeseen opportunities. A primary customer base for NP302 research outcomes is agricultural research scientists engaged in solving agricultural problems of national and international importance.  Stakeholders in our research include commercial industries involved in crop improvement, farmers and producers, and post-harvest processors and handlers, because this fundamental research underlies the advances that they need to continue in business. 

As we begin planning for the second 5-year cycle of NP302 it is timely to conduct a self-assessment of our progress in meeting the program goals.  These goals grew out of a workshop held in June of 1999 in which representatives of commodity and trade organizations, food processing and life science companies, universities, and public interest groups participated with ARS scientists and administrators to define consensus priorities for this National Program. This group endorsed the appropriateness of a federal research agency with in-house funding taking on problems of a national or international scope, problems that require long-term stability of research funding, and problems that clearly promote the public good and are inadequately addressed elsewhere.  We began the task of self-assessment by asking Lead Scientists on projects in NP302 what had been accomplished, to forecast its impact, identify the most significant opportunities and needs for future research, and for their ideas on how NP302 should evolve to meet the priority research needs for the next 5 year cycle. These reports were used along with annual reports and published work to develop the synopsis of NP302 research progress that appears below.  It was neither practical nor our intent to create a comprehensive overview of progress but rather we sought to capture the scope of activity and illustrate by example evidence of accomplishment and impact.  The Action Plan of NP302 defines three research components and these are used to organize the presentation progress and impact.  This progress report will serve as a starting point for the evaluation of NP302 progress by an external assessment team as well as a resource document for the National Program 302 Assessment and Customer Workshop to be held in May 2004 in St. Louis.

II. PROGRESS

Component I.  Analysis and Modification of Plant Genomes

Component I concentrates on the discovery of genes controlling important agronomic traits in crops, the functional role of such genes, how genes are regulated both individually and as networks, and how gene expression in crops can be modified.  This component provides the framework for plant scientists to take advantage of the current genomics, proteomics, and metabolomics revolution in biology to understand and improve crops.  Two problem areas were identified in this component: (a) molecular characterization of plant genetic systems which considers genes and gene action from chromosome location to genotypic diversity; and (b) plant transformation systems and influence of transgenes on genome structure and function which focuses on extending and improving genetic transformation efficiency in crop species.  A more recent area of emphasis, and one that is expanding, involves research on biotechnology risk assessment.

Research areas identified for Component I came out of the genetic and technological breakthroughs with model species that resulted in vast amounts of information about genome sequence and gene structure (genomics).  Yet a disconnect between model and crop species as well as between gene sequence and function has limited translation of information into crop improvement.  Advances in understanding the molecular underpinnings involved in controlling complex agronomic traits and biochemical pathways as outlined in this component will lead to the translation of genomic knowledge into improved plant productivity and quality.  Translation of biochemical and genetic information will require both highly efficient classical selection methods as well as newer approaches based on molecular markers and transgenic technology.

Ia.

ARS scientists associated with Component I have been instrumental in extending functional genomics to crop species.  Not only have they deposited thousands of ESTs into GenBank for a wide range of crops but ARS personnel have also played a key role in the development of the Arabidopsis, barley, tomato, soybean, and Medicago truncatula microarrays (all now currently available to the public).  Transcript profiling has become a standard approach in several crop species due to ARS advances.  Transcript profiling research by ARS scientists at several locations is being used to identify genes and gene networks important in mineral nutrition, disease resistance, pollen and seed development, root architecture, and carbon/nitrogen metabolism.  To understand how gene expression is regulated and to specifically target transgene expression in organs and/or tissues, ARS scientists have characterized and made publicly available gene promoter elements that control expression.  Examples include promoters specific for gene expression in seed hull and endosperm, pollen, stomates, roots, root hairs, cotton fibers, root nodules, apical meristems, disease responses, and abiotic stress responses.  Along those same lines transcription factors, which play key roles in regulating expression of gene cascades, have been characterized. Robust single nucleotide polymorphorisms (SNPs) have been developed for soybean and are providing an abundant source of molecular markers for high resolution mapping of the soybean genome.  Moreover, the SNP technology has been extended to wheat, corn, rice, vegetable crops, and fruit crops.  ARS research has been key to developing an integrated physical/genetic map of maize.  Collaborative research across the country between ARS researchers led efforts to develop a physical/genetic map of soybean and assess its synteny with Arabidopsis.  Computational biology (bioinformatics) is pivotal for integrating genomic information and bench biology research.  Although access to computational biology limits research of some ARS programs, bioinformatics expertise has been added to at least four locations. More readily available access to bioinformatics expertise is crucial to future ARS functional genomics research.

Ib.

In order to fully take advantage of gene discovery arising from plant functional genomic research, it is important to enhance our ability to more effectively and efficiently transfer these genes into a wider range of crop species.  ARS scientists have made significant progress in the transformation of new crop species.  For example, blueberry is an important horticultural crop that has been very difficult to transform. ARA led the development of a regeneration system for blueberry that has paved the way for introducing cold hardiness and disease resistance genes into blueberry.  ARS efforts have also made improvements in strawberry transformation and progress towards developing a transformation system for roses. Stably transformed hard red winter and durum wheat cultivars were obtained for the first time through ARS efforts, thus opening up opportunities for improvement of these economically important wheat genotypes.  With regards to improving the transformation process itself, ARS scientists have made progress in a number of different areas including the development have of a new selection procedure for identifying transgenic cells, embryos, and plants without the use of antibiotics, and this has great promise for developing transgenic plants without the use of antibiotic resistance marker genes.  A novel recombination system that holds promise for directing transgene integration into more specific regions of the genome, thereby facilitating site-specific DNA integration into eukaryotic genomes, is being evaluated by ARS scientists. ARS researchers have also developed a new technology to more effectively introduce multiple genes into plants as a single unit so they can more readily be under the same genetic control

Component II:

Biological Processes that Determine Plant Productivity and Quality

Component II of National Program 302 addresses fundamental research that underpins the improvement   and sustainability of crop productivity. Issues pertaining to the efficiency of resource utilization, regulation and control of photosynthate partitioning, tolerance to environmental challenges including those associated with global climate change, and the biological determinants of nutritive and other value-added traits are central to this component.   The three national problem areas identified for Component II are:  (a) plant productivity and efficiency of resource use; (b) plant tolerance to environmental stress; and (c) biological bases for expression of value-added traits.

 The horizons of research within this component have been launched forward by the emergent genomic era of biology and the ready application of these powerful technologies is seen as one important metric of progress toward the component’s long-term goals.  Across the three problem areas within Component II there has been extensive adoption of new and emerging technologies and a willingness to invest in establishing a molecular foundation on which future progress will be built.  Molecular phenotyping has been area of particular activity in which DNA markers for wide range of phenotypic traits of interest have been identified. Improved methods for genetic transformation of the nuclear and chloroplast genomes of higher plants are conspicuous advances.   These and other advanced technologies have helped achieve numerous outcomes projected for Component II and helped make substantive progress toward others. 

IIa.

Foundation research into the biological processes that underpin crop production and resource utilization efficiency were seen critical within the action plan because of world’s need to simultaneous improve yield potential and agricultural sustainability.   Both the environmental and economic sustainability of agriculture and the capability of producers to keep pace with increasing demand on decreasing cultivated land area will require crops that are more stress tolerant, utilize water and acquire soil nutrients more efficiently, and provide improved ecological services to agricultural lands and watersheds.

The control and regulation of assimilate partitioning within crop plants is the biological basis for harvest index, an important determinant of yield.  The discovery by ARS researchers that expression of the sucrose transporter responsible for loading sucrose in the phloem within the source leaf is regulated by sucrose provides insights into the molecular determinants of export capacity and sink strength.  That increasing atmospheric carbon dioxide often leads to increased source leaf sucrose levels, has produced a collaboration with other ARS scientists investigating the acclamatory response of photosynthesis to carbon dioxide fertilization. The identification of genes involved in the control and regulation of vegetative meristem development, which are critical determinants of growth and phenotype development, is another avenue of work on partitioning within ARS which in this case contributes to the understanding of molecular controls over plant architecture including stem strength, inflorescence size, and seed size. ARS research underway on the binding of sucrose synthase to multiple cell membranes revealed an important role for sugar regulation of enzyme localization and may provide a new approach to control how plant cells partition carbon among different pathways during growth and development. Transcript and protein profiling are identifying genes involved in carbohydrate and storage protein synthesis in wheat grain. These ARS projects, along with other work such as that investigating cellulose synthase genes and the identification of fiber specific promoters  in cotton,  exemplify the many and varied  aspects of assimilate partitioning that are relevant to the improvement of agricultural productivity and the quality of food and fiber.

A clear understanding of the mechanisms and capacity of nutrient and ion uptake by roots from the soil is fundamental to the development of environmentally responsible soil nutrient application recommendations, to the development of phytoremediation strategies, as well as for altering or tailoring the nutrient  and ion selectivity and uptake capacity of roots.  ARS research on nutrient uptake in woody horticultural crops has lead to improved application strategies for growers and helps reduce the environmental impact of growing these crops.  Microarrays are being employed by ARS researchers to identify genes that control iron use efficiency in soybean.  Although still in early stages this work has the potential to define the complex genic interactions involved in the intricate process of iron uptake, mobilization and utilization.                                                                                                                                          

IIb.

The average yield of all major grain crops grown in the United States is less than 25% of the genetic potential as estimated from record yields. The explanation for the remarkable difference between the genetic potential for crop production and the production actually realized by farmers lies in part with the prevalence of biological pests but much more in the limitations imposed by physicochemical factors, which are often collectively termed environmental stresses.  The fact that in many cases closely related non-crop species survive and reproduce in environments that would be lethal to crop plants suggests that substantial genetic and physiological acclimation to environmental stresses is possible and that tolerance may be enhanced in crops if the underlying mechanisms of susceptibility and tolerance can be elucidated.

Among the environmental factors that most limit agricultural production, temperature extremes and drought are economically the most significant. Assessing the genetic basis for freezing tolerance was advanced when ARS research groups identified quantitative trait loci for cold tolerance in rice and the first DNA markers that correspond to freezing tolerance in oats were identified.  A role for fructans and fructan metabolism in the development of freezing tolerance in oats extends our knowledge about the types of carbohydrates now known to participate in freezing acclimation.  The discovery by ARS researchers that chilling temperatures interfere

with the circadian regulation of carbon and nitrogen metabolism has provided insight into the mechanism of chilling susceptibility in warm climate crops.   A mechanistic overlap between freezing and drought tolerance was revealed by ARS work that demonstrated a role for dehydrins as an antifreeze protein in cold hardiness of peach trees.  ARS work assessing and selecting for improved water use efficiency has lead to new water-use efficient peanut varieties.

IIc.

Improved animal and human nutrition, post-harvest stability, resistance to pests and pathogens, tolerance to stress, and novel products produced in plants are at the forefront of national and international interest and simultaneously present enormous challenges and opportunities for agriculture. Foundation research in support of metabolic and genetic engineering of value-added traits was deemed a priority area in Component II.

Avid interest in chloroplast genetic transformation and engineering derives in equal parts from the potential to contain transgene drift through pollen owing to the maternal inheritance of the chloroplast genome and the relative freedom from silencing that can limit foreign gene expression in genetic transformations of the nuclear genome.  In collaboration with university partners, ARS researchers are using chloroplast transformation to introduce an alga rubisco into higher plants that would allow plants to perform better in the higher carbon dioxide containing atmospheres of the future.  The development of more efficient plastid transformation technologies that can be used on a wider range of plant species will be a critical enabling technology for the production of high-value specialty materials in crops. Moreover, this approach to generating transgenic plants is primary in reducing the risk associated with genetic engineering of crops. 

One important goal of agricultural genetic engineering is to tailor natural metabolic processes within crops to improve quality and expand the scope of uses. ARS research has identified regulatory genes that control lignin biosynthesis.  Finding a transcription factor that globally regulates lignin biosynthesis has potential in the development of  bio-fuels as well as for improving the digestibility of grasses for ruminants.  Transgenic manipulation of wheat glutenins is underway to manipulate the mixing and baking properties of flour. Successful metabolic engineering requires an in-depth understanding of enzymatic reactions and control sites within the metabolic process of interest.  ARS scientists, employing their knowledge of rubber transferase and other biochemical factors regulating rubber yield and quality, have transformed guayule to up-regulate the production rubber precursor substrates in order to increase rubber yield and molecular weight.

Component III:  Mechanisms of Plant Interactions with Other Organisms

The broad focus of research objectives in Component III of National Program 302 is to discover the plant biological and molecular processes that affect crop plant associations with microbes both symbiotic and pathogenic and to define the underlying bases for interactions that lead to the synthesis of toxins and other natural products that impact crop plant nutritional safety and ecological competitiveness.  The three national problem areas identified for Component III include:  (a) crop plant interactions with beneficial organisms such as rhizobia, mycorrhizae, and endophytes; (b) biological interactions that impact food safety and secondary products particularly as related to mycotoxin accumulation; and (c) biological interactions that reduce environmental pollution particularly as related to herbicides and pesticides.

The long-term goals of research in Component III are to enhance the sustainability of the Nation's agricultural base, reduce the environmental footprint of production agriculture, and improve profitability for farmers.  Strategies to achieve these goals revolve around increasing our knowledge of the fundamental mechanisms involved in:  crop nitrogen (N) and phosphorus (P) acquisition and use particularly as related to symbiotic interactions, thereby reducing agriculture's dependency on N and P fertilizers; plant resistance to fungal and insect pests thus alleviating overuse of pesticides and improving crop nutritional quality; and the mode of action of herbicides and naturally occurring allelochemicals moving toward a biological basis for controlling pests and weeds. Several projected outcomes as outlined in NP302 were achieved through research in Component III.

IIIa.

Research on rhizobial and mycorrhizal symbioses were deemed important in Component IIIa of the action plan because of their potential to impact the use of N and P fertilizers.  The production and use of N and P fertilizers in U.S. agriculture is neither sustainable nor environmentally prudent.  Overuse of N and P in U.S. agriculture has resulted in contamination of water systems and hypoxia.  In addition, both fertilizers are produced from non-renewable resources. EST sequencing in Medicago, Glycine, Phaseolus, and Lupinus by ARS scientists resulted in several thousand cDNA sequences being deposited in GenBank.  Upon completion of contig assembly and bioinformatics analysis, more than 300 genes were identified as root nodule specific.  High-density macroarrays and microarrays confirmed the identity of nodule specific genes and identified another group of genes having either a 2-fold enhanced or reduced expression.  Good progress in legume crop transformation has laid the foundation for functional analysis of genes through gene silencing via RNAi, insertional mutagenesis, and antisense approaches.  ARS has also contributed to the development of mutagenized germ lines in legume crops and methodology for tilling in Medicago and Glycine. ARS scientists have used genomic approaches with several crop species to identify genes involved in developmental and biochemical adaptation to P-deficiency and Al-toxicity stresses. Genes important to the adaptation to P and Al include those involved in:  synthesis and exudation of organic acids, glycolytic bypass reactions, transcription factors affecting root development, and genes responsive to mycorrhizal inoculation.

Collection, identification, and curation of rhizobial and mycorrhizal strains have been focal points for research by scientists involved in Component III.  Moreover, field and laboratory inoculation trials identified those strains most effective in symbiosis.  ARS houses a large collection of rhizobial strains (maintained by NP 301).

Studies of root nodule and mycorrhizal roots utilizing both stable and radioactive isotopes have contributed to characterization of metabolic pathways involved in exchange of carbon (C) and N compounds between the host plant and microbe and aided modeling of nutrient exchange systems in these interactions. These studies have provided novel insights into metabolic pathways and new targets for genetic improvement.

While characterization of plant endophyte systems was identified early on as an element in NP 302, those projects having objectives related to endophytes (currently some nine projects) are found in other National Programs.

IIIb.

Mycotoxins and secondary metabolites produced by fungal infection of plants pose serious pre-harvest and post-harvest problems in small grain and nut crops.  These compounds can be carcinogenic, reduce palatability, and affect acceptability of products in both domestic and foreign markets.  Reduction in mycotoxins in products would improve human and animal health and improve product quality.  ARS scientists are integrally involved in the development of peanut, corn, wheat, and tree nut genotypes having greater resistance to toxin producing fungi.  Improved resistance has been achieved through both traditional and marker-assisted selection.  Another strategy for the development of resistant genotypes has been transformation with antifungal genes that produce products having potential to impede fungal infection and growth.  Research on biochemical and molecular control of toxin production in Fusarium and Aspergillus has been successful in characterizing the metabolic pathway and genes involved in fumonisin and trichothecene synthesis.  Toxin deficient fungal strains are being developed and evaluated as biological control agents against toxin producing lines of fungi.  Inoculation with selected endophytic fungi is also being evaluated as a biocontrol strategy.  The occurrence of toxin degrading enzymes and use of these enzymes to reduce either the presence or accumulation of toxin is under study as an alternative biocontrol strategy.  In addition, metabolite screening is being conducted in resistant crop species to identify naturally occurring compounds that inhibit fungal growth and mycotoxin production.  While many of the above approaches were identified in NP 302's action plan, as the reorganization of National Programs occurred significant portion of ARS' mycotoxin effort was transferred into NP 108, Food Safety.

IIIc.

Approximately 20-25% of annual crop production is lost to diseases and pests.  Synthetic pesticides, derived from petroleum, are the primary means used in agriculture to control diseases and insects.  An unintended consequence of chemical pest control is environmental degradation.  Furthermore, the fact that pesticide production is petroleum based means that global political issues that affect oil also affect U.S. food security.  ARS has a long history of fundamental and applied research aimed at reducing diseases and pests and controlling weeds. Genes responsive to fungal infection and insect feeding were identified via EST analysis in a wide range of crop species including but not limited to:  soybean, alfalfa, wheat, oats, corn, potato, sugarcane, apple, rice, strawberry, and grapes.  ARS scientists made significant contributions to the development of high density gene chips for many crop species and these chips are being used to evaluate plant responses to biotic and abiotic stresses.  Resistance gene analogs have been identified and mapped in soybean, wheat, and barley.  Quantitative trait loci affecting pest resistance have been identified and are being mapped in wheat, rice, soybean, potato and corn.  Research by ARS scientists in IIIc has been crucial for developing transformation systems for wheat, apple, bean, and several small fruit species.  Resistance to disease derived via transformation with antifungal genes and viral coat protein genes has proven effective in developing disease resistant lines. This approach has saved the papaya and pineapple industry in Hawaii.  Transgenic peanut lines containing antifungal genes having resistance to Sclerotinia have been developed and these lines showed enhanced resistance to fungi and less aflatoxin accumulation.

Biological control of weed pests has received significant attention from ARS scientists.

On-farm weed control is primarily through application of synthetic herbicides.  The occurrence of herbicide resistance in weed populations as well as herbicide build-up in soil has necessitated new strategies for weed control be investigated.  ARS has conducted research to identify biological agents and plant natural products as alternative weed control agents.  The biosynthetic pathway involved in synthesis of the potent allelochemical sorgeolone has been characterized and enzyme assays developed for selected reactions.  Large numbers of naturally occurring benzoquinones have been evaluated as biocontrol compounds.  To better understand Pseudomonas syringae as a biocontrol for Canada thistle, environmental factors affecting tagetitoxin were evaluated.  Reanalysis of the structure of the toxin showed original structural studies were incorrect. The biosynthetic pathway and the biological activity of several novel plant secondary metabolites, flavonoids, terpenoids, coumarins, and tannins are being evaluated for biological activity towards weeds and plant pathogenic fungi.

III. IMPACT and LEVERAGE

Although the long-term impact of discoveries made since the recent inception of NP302 is difficult to assess, evidence of the vitality and quality of the science in this Program is presented in Table I, documenting success in extramural funding, peer-reviewed publications, and mentoring students.  The success rate, including extramural funding not just from basic science agencies but also from groups more interested in applications of science, reflects the importance and central role of this Program.  Invited and elected service to professional societies and grant panels shows that input from NP302 scientists is highly valued by the larger agricultural research community. 

Creative and successful use of base funding by scientists in NP302 has resulted in greater competitiveness for attracting grant support from both peer evaluated and commodity sources, thus increasing their research capacity (Table I). NP302 scientists routinely compete well for NSF, DOE, NRI, and BARD grants. This has enabled ARS scientists to leverage base funding to participate in collaborative enterprises that, for example, have resulted in the development of important genomics tools such as publicly available microarrays for different crop species. In addition, NP302 scientists are frequently requested to chair and serve on grant panels. NP302 scientists are also very active in seeking and attracting grant support from commodity boards representing the diverse U.S. agricultural economy. Research funded by grants is frequently collaborative and involves multi-location efforts with non-ARS scientists.

NP302 scientists frequently publish in high impact peer reviewed journals such as Science, Nature, PNAS, Plant Physiology, Plant Cell, and Genetics. Inclusively, their yearly publication rate averages greater than two. They serve as editors and on editorial boards of many high profile journals. Notably, NP 302 scientists serve as leaders (officers and/or board members) in the American Society of Plant Biologists, the American Association for Advancement of Science, Crop Science Society of America, and American Society of Agronomy.

Even though ARS’ mission is research oriented and driven, its scientists also make substantial contributions to graduate education and the mentoring of postdoctoral associates. During the first five-year action plan scientists associated with NP302 were involved in the training and mentoring of 167 graduate students and 120 postdoctoral associates (Table I).

IV. THE NEXT FIVE YEARS – How Should NP 302 Evolve to Maximize Its Impact?

Because genomics and molecular genetics approaches and technologies are advancing and changing rapidly, it will be important in the NP302 Workshop to give careful thought to how NP302 will be structured for the next 5 years to help facilitate cutting edge fundamental research that is at the heart of this program. The hope is to retain the best aspects of the current NP302 program and merge these with new components that have arisen to address the rapidly changing research landscape. Based on the responses of ARS scientists in NP302 to our questionnaire, three broad topics for discussion were identified regarding the next NP 302 Action Plan. Within each of these three topic areas, a number of possible talking points were also identified to help initiate discussion during the Workshop.

1) What are the best strategies and tools to help promote the integration of interdisciplinary research within NP302 as well as interaction with other National Programs?

·     Are cross-location CRIS projects feasible as a means to enhance National Program integration?  What vehicles might be available for this, considering the difficulties of shifting base funds across Congressional boundaries?  Could the Headquarters’ funded postdoctoral program be a used for this?

·    Many of the activities in NP 302 are directly related to, and have an impact on, research being conducted in NP301 (Plant, Microbial, and Insect Genetic Resources, Genomics, and Genetic Improvement). Do these two National Programs need a higher degree of interaction and linkage? If so, how might this be facilitated? Should NP 302 play a larger role in the development of integrated genetic and physical maps for different crop plant genomes (currently an activity within NP301)?

·    To what degree should ARS emphasize research on Arabidopsis and other model plants with the aim of applying the discoveries to crop plant species?  Is this an alternative to extensive sequencing of many different crop plant species?

2) What strategies will best ensure access of ARS researchers to enabling technologies as they become available?

·    How will ARS scientists who work in the area of functional genomics obtain better access to the necessary computational tools (bioinformatics) as well as computational expertise in order to effectively utilize and mine the acquired data?

·     With the ever-increasing pace of progress in molecular biology and genetics, how can ARS scientists keep abreast of advances in technologies?  Many ARS researchers mentioned that that they need better access to specific genomics technologies.  Proteomics and metabolomics are increasingly necessary for proper investigations of biological and molecular mechanisms, but to acquire the capability is expensive and requires specialized training.  How can laboratories with these capabilities share their expertise to help others in ARS, without damaging the mission and fiscal accountability of the laboratory?  What is the role of the National Program is fostering these interactions?

·     How can ARS more effectively partner with universities and industry to leverage their genomics resources vis-à-vis the resources held by these other organizations?

·     Should ARS be thinking about establishing a Genomics National Program, which would be horizontally organized and cut across National Programs relating to microbes, plants, and animals?

                                                                                       
3) What emergent or re-emergent areas need to be addressed within the new NP302 Action Plan?

·    Will our biochemical and analytical chemistry expertise within the agency be sufficient to capitalize on the power of new ‘omic’ technologies, such as proteomics and metabolomics (metabolite profiling and metabolic engineering). If not, what needs to be done?

·     How can ARS scientists work in more coordinated fashion to close the gap between genomics and crop improvement?  What are the “missing links?”  Does ARS need to enhance its research efforts on developmental biology and other areas of plant science that concentrate on the organism to complement genomics efforts?

·     Biotechnology risk assessment and risk mitigation of genetically modified crops is an important new research responsibility for NP302.  This encompasses studies from fundamental genomic processes to population biology and ecology.  How can they best be linked, so that mechanistic knowledge can be used to predict traits and properties, thereby drastically reducing the number of unintended consequences of biotechnology?  

·     Also, with regards to biotechnology risk assessment, research approaches are available that could produce very different technology from that in use today.  To what extent should new and unique technology, such as plastid transformation, male sterility, management of genetic compatibility, or other novel concepts deserve greater emphasis and investment in the next action plan, despite the high-risk nature of the research (risk = failure to reach the goal, not biosafety risk)? 

APPENDIX TABLE 1:  PRODUCTIVITY AND QUALITY FACTORS OF ARS SCIENTISTS IN PLANT BIOLOGICAL AND MOLECULAR PROCESSES, NP 302

These data are self-reported by ARS scientists in response to a questionnaire.  There are 87 projects associated with NP 302; all are shown, but only 65 have data included here.  Of the other 22, 21 were initiated very recently and are without a history, or are currently not staffed, or are “pass-through” accounts (funds transferred to other institutions by Congressional mandate, with no way to retrieve information).  One project did not respond as of Friday, April 9, 2004.  The total number of Scientist-Years, or SYs (full-time equivalents) per project, and percentage of the project in NP 302 are shown in the first column.  Data are per project, with no adjustment for number of SYs or for the percentage in NP 302.