Appendix H
Research Needs in Food, Fiber, and Natural Resources

Chapter 5 of the 1989 National Research Council report, Investing in Research: A Proposal to Strengthen the Agricultural, Food, and Environmental System (available on the Web at http:books.nap.edu/books/0309041279/html/index.html), provided a detailed list of areas for fundamental research in food, fiber, and natural resources. The committee reviewed the list and found it to be as relevant now as it was 10 years ago. The years have only added to the list of concerns. As part of this study, the committee developed the following list of research needs in food, fiber, and natural resources. Although this list is not as exhaustive and does not provide as much detail as the one in the 1989 report, it is generally consistent with the 1989 conclusions.

PLANTS

Gene and genome interactions and bioinformatics. Mechanisms of interactions of genes and organisms will be identified and will provide the basis of improved growth, metabolism, development, behavior and adaptation. This information will have many applications, from increased plant yield to cleanup of environmental pollution.



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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research Appendix H Research Needs in Food, Fiber, and Natural Resources Chapter 5 of the 1989 National Research Council report, Investing in Research: A Proposal to Strengthen the Agricultural, Food, and Environmental System (available on the Web at http:books.nap.edu/books/0309041279/html/index.html), provided a detailed list of areas for fundamental research in food, fiber, and natural resources. The committee reviewed the list and found it to be as relevant now as it was 10 years ago. The years have only added to the list of concerns. As part of this study, the committee developed the following list of research needs in food, fiber, and natural resources. Although this list is not as exhaustive and does not provide as much detail as the one in the 1989 report, it is generally consistent with the 1989 conclusions. PLANTS Gene and genome interactions and bioinformatics. Mechanisms of interactions of genes and organisms will be identified and will provide the basis of improved growth, metabolism, development, behavior and adaptation. This information will have many applications, from increased plant yield to cleanup of environmental pollution.

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research Transgenic plants for improved production. Increases in plant yield, disease control, drought tolerance, and many other characteristics will be obtained by constructing transgenic plants. A major research effort will be required to identify new genes with useful characteristics, and to construct and test transgenic plants that carry these genes. Mechanisms of pest-plant and beneficial-plant interactions. Major advances in the understanding of disease mechanisms and in development of disease-control measures will be stimulated over the next few years by ground-breaking basic research now under way. In addition, there will be increased interest in the direct use of modified beneficial organisms and in identifying the relevant genes for beneficial organisms and transferring them into plants. Knowledge base for facilitating a new generation of biologically based materials. These would replace such natural products as petroleum, such structural materials as steel, and synthetic textiles. Current trends indicate that it will be possible soon to replace these environmentally sensitive commodities with plant-produced materials that are environmentally safe and renewable. It will be of great consequence to the planet if means can be devised whereby commodities produced by higher plants are coupled with plants that have greater ability to reduce the carbon dioxide load in the atmosphere. Engineering of plant biosynthetic and metabolic pathways. With the rapidly expanding pool of genes with known functions, it is possible to consider making radical changes in biochemical pathways by introducing new genes and mutating existing genes. It is widely expected that research in this field will yield major returns in development and production of pharmaceuticals and improved plant disease and pest resistance, yield, and other characteristics. ANIMALS Gene and genome interactions and bioinformatics. Mechanisms of interactions of genes and organisms will be understood over the next several years and will provide the basis of improved farm-animal growth, metabolism, development, behavior, and adaptation. These findings will permit assessment of future disease potentials in animals and humans and will allow development of diets to avoid them. Future major progress in the production of livestock species that are important to the US economy will be attainable only if we are able to map animal genomes. This information will provide the basis of regulating various aspects of animal health, growth and development, metabolism, reproduction, and behavior. For example, the ability to identify specific marker genes associated with or predictive of such traits as rate of gain, fecundity, milk production, egg production, and ovulation rate would enable the selection of superior sires and dams in a shorter time than the many years now required

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research through regular genetic approaches. However, mapping the genome of just one species is a time-consuming and costly endeavor. Unless additional funds are made available to the NRI to ensure support for genome mapping, it is unlikely that this aspect of animal research will be carried to completion in a timely manner. Nutrition research. Devising ways to approach human and animal nutrition in novel ways will become increasingly important. We need research on devising delivery mechanisms and studying their efficacy. Transgenic and cloned animals. These approaches will greatly increase the efficiency of farm-animal production. It is expected that animals will function as bioprocess reactors to facilitate the introduction of improved nutrients into meat, improved and altered milk composition, and other developments. Research will provide many additional avenues for using the basic advances offered by the ability to clone farm animals and produce transgenic animals. Animal Reproduction. There is a need to examine the basic physiologic, genetic, and molecular mechanisms that underlie reproductive events that ultimately dictate productivity of economically important livestock and aquatic species. There is also a need to develop improved and new methods of cloning superior livestock. Reproductive failure continues to be a major cause of revenue loss to livestock producers. Much needs to be learned about the effects of disease and environment on the reproductive system of our livestock species. Much research is needed to identify the underlying causes of embryonic mortality, cystic ovaries, inferior sperm quality, poor conception rate, abortion, and reduced hatchability in poultry. Many of the future research approaches to these problems will of necessity be molecular. Animal Nutrition. There is a need to examine the potential of genetically engineering rumen microbes that use dietary nutrients effectively for production of meat, milk, and fiber and to research the effects of diet on the evolution and survival of pathogenic rumen and intestinal microorganisms. It is unlikely that conventional methods of research will yield progress in animal nutrition. Yet, there is the potential for increasing the ability of the animal to use feedstuffs as a source of energy or to use nutrients that now remain undigested. This can be accomplished by using genetically engineered rumen or intestinal microorganisms with specific digestive enzymes. This is a challenging subject that is not being investigated. Land areas now available for grazing or production of forage crops will decline, and livestock might have to be fed foodstuffs that by today’s standards are considered to be of poor quality. However, appropriate genetically engineered microorganisms that are deemed nonpathogenic when introduced into livestock species might enable these animals to use poor quality foodstuffs efficiently. Such research will require a concerted effort by several laboratories, will take time, and will be expensive.

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research Animal-Rangeland Interactions. Western livestock producers are gradually forced out of existence because of various restrictions imposed on the use of riparian areas and western rangelands. Many current environmental issues targeting livestock producers are not based on solid scientific evidence. There is a dire need for research to be conducted to provide well-controlled data on the impact of cattle, sheep, and horses on stream quality under various conditions and on the vegetation and ecology of desert and forested rangelands. There is no concerted effort in the NRI to fund this type of research, which ultimately will affect the economy of the eleven western states. Animal Health. The US research community must continue to research the organisms that now lay waste to the health of our livestock species. The US should be at the forefront of research on potential emerging diseases, such as BSE, that are or can be transmitted to humans. We need a better understanding of virology as it pertains to infection of livestock by foreign viruses; this is essential not only to develop appropriate vaccines, but also to identify the etiology of viral infections in humans. Animal Growth and Development. Consumers of meat and meat products are demanding a lean, virtually fatfree product. There is also a growing demand for organically grown animal products, such as meat, milk, and eggs free of hormone residues and antibiotics. The European meat market is closed to American beef producers because of concern about hormones in meat. To provide this type of consumable product, extensive research will be required to define the underlying mechanisms of growth in general and the development of muscle and fat specifically. The identification of specific marker genes that are associated with enhanced meat, milk and egg production can provide an excellent starting point for this research. However, muscle and fat formation involves innumerable complexities which are only tangentially known. This is an area of animal production that can have a serious effect on livestock producers and on the American economy and should be supported by the NRI to a greater extent than it is now. Aquaculture and Mariculture. Aquaculture and mariculture constitute the most rapidly growing sector of animal agriculture; many new species are added each year. A broadly expanded research program in genomics, nutrition, and reproduction of domestic aquatic species is essential to the health and well-being of these newly emerging industries. Consumable Animal Products. Research is needed to improve and develop methods of processing, packaging, and marketing of animal products for national and international markets. Immunology. With today’s global travel, diseases are exchanged more rapidly than prophylactic drugs can be devised. We need more basic research on the

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research immunology of humans and farm animals, particularly dedicated to treatment of exotic diseases. Construction of novel microorganisms. By using genes from existing microorganisms and synthetic genes, new and redesigned microorganisms can be envisioned in the near future. Such altered organisms have the potential for major impact in agricultural settings, for example, rumen microorganisms in cattle. Gene-based pharmaceuticals and gene therapy. Many experimental approaches, including the use of antisense RNAs and the transient expression of introduced genes, will greatly change how disease and nutritional problems are approached. A great deal of research will be required to deliver such approaches to the marketplace and to undercover new rationales for exploitation. Evolution of biologic systems. The several genome projects under way or expected will yield unprecedented knowledge applicable to understanding the evolutionary history of humans, animals, plants, and microorganisms. Much of this information will in turn have a major impact on agricultural processes. NUTRITION, FOOD SAFETY, AND HEALTH Research on nutrient-drug interactions. People are living longer and using alternative foods and drugs to improve quality or life. We need better information on the effects of excessive nutrient and drug use. Impact on consumers of phytochemical substances promoted as nutraceuticals. There is a need to isolate and characterize at the molecular level the active agents in traditional and alternative crops and to assess their effects on specific targeted physiologic responses and side effects. New and resurgent pathogens in foods. Greater numbers of microbial food-contamination problems are arising. We need to know more about the microorganisms in question—their biology and mechanisms for their control. Information is needed on the source of pathogens encountered in production, harvesting, processing, and distribution of plant, animal, and marine products. Pasteurizing and sterilizing of foods. New methods need be developed in food processing with regard to advanced sterilization techniques. Opportunities for the wider use of high-pressure preservation and pulsed electric-power discharges in food preservation need to be assessed. Molecular modifications of and effects on quality and hazardous microorganisms need to be carefully assessed. Identification and modification of allergens in foods. Rapid, simple, and cost-effective tests for the presence of known and unidentified allergens in foods

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research should be developed. It is also necessary to evaluate mechanisms of allergenicity and develop methods of processing to neutralize allergen hazards in foods. Probiotic development. With more antibiotics becoming obsolete, we need to develop more natural antibiotics to maintain homeostasis. NATURAL RESOURCES AND THE ENVIRONMENT Water quality. As increasing numbers of water supplies become unacceptable for human consumption or food processing, the need for research to characterize contaminants and facilitate their removal is clear. Animal-waste handling. Concentration of animal production has led to major problems with respect to odor emanation and the handling of waste products. Major research efforts are warranted. Environmental impacts. Great developments are occurring in devising methods to ameliorate toxic-waste deposits and other environmental insults. The success of American agriculture in coming decades will depend on solution of current toxic problems and seeing that agricultural practices do not produce new environmental disasters. Impact of environmental and biotechnologic modifications of plants and animals on microbial ecology of food products. There will be an increasing need to evaluate the safety and quality of foods that come from genetically modified organisms in contrast with traditional sources. Bioprocess engineering. Modifications of plants, animals, and microorganisms in the next century can be expected to have major ramifications for the production of commodities and for ecologic concerns, such as reducing waste production. We predict that major advances can be made in bioengineering of the organisms that we deal with in agricultural settings Biodiversity. Agriculture is often criticized as being incompatible with biodiversity. Yet basic research in conservation biology suggests that landscape diversity can be as important as species diversity in plant communities for maintaining diverse populations of insects and vertebrates in a geographic region. In fact, agricultural communities can benefit directly from landscape diversity in that this diversity often includes beneficial organisms that prey on crop pests, pollinate crops, and provide other ecosystem services for cropped fields that have economic benefit. The design of landscapes—for example, development and tests of theory that predicts the optimal proportion of native to cropped habitat or the best positions of such habitat within landscapes—is a basic-research question that is not now being adequately addressed.

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research Soil biodiversity is another major new branch of research that requires additional support. We have only recently acquired the molecular tools for gauging the complexity of the soil biologic community and have learned that only 3%—5% of soil microbial taxa have been identified and described. What constitutes the unknown 95%? Does it differ among ecosystems and management practices? Does it have functional significance for the forest, rangeland, or cropping system that supports it? Those are basic questions with enormous potential impact on the management and protection of agricultural resources. Understanding biodiversity also requires an understanding of basic population genetics, and many fundamental questions in population genetics that are relevant to agriculture are being insufficiently addressed. How will gene flow in native populations retard or accelerate the movement of genes from genetically modified organisms—for example, from Bt corn or glyphosate-resistant soybeans—into native plant populations? Will it matter that specific genes escape? Will they persist? How long will it take native pest populations to develop resistance to engineered traits in the genetically modified organisms? Answers to those basic ecologic and evolutionary questions will help to define the efficacy and safety of genetically modified crops. Answers to them will also help to determine strategies for protecting native and cropped communities from colonization by exotic organisms in general—an increasingly important threat to crop and forest productivity in this age of global trade. Weather and climate interactions in agricultural systems. Basic research in coming decades will uncover additional approaches to minimizing agricultural losses during weather disasters. Genes for increased cold tolerance in plants are already affecting losses from cataclysmic freezes, and many other examples can be predicted. Global change and agriculture. Agriculture both affects and is affected by many of the environmental changes that fall under the global-change rubric. Many of the practical issues that have emerged over the last decade are being addressed with mission-oriented funding from a number of agencies, including the US Department of Agriculture (USDA). These issues range from evaluating the impact of continent-scale transport of atmospheric contaminants and gauging the effects of increased climate variability and changing hydrologic cycles on crop productivity to evaluating the potential for agricultural soils to sequester atmospheric CO2. Solutions of those and the scores of other important global environmental-change problems depend implicitly on a thorough understanding of the principles that govern the patterns and processes affected by change. Such understanding is provided by basic research in such topics as soil organic matter, environmental plant physiology, and environmental modeling. Soil Organic Matter Dynamics. Cropped soils typically lose 40%-60% of their carbon after 40–60 years of cultivation. The recovery of the carbon and the potential storage of additional carbon has been widely touted as a potential

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research mitigator of atmospheric CO2 buildup. But fundamental mechanisms of carbon storage in soils—for example, the relative importance of physical protection by clays and microaggregates versus chemical protection by humic and other organic substances and the contribution of recalcitrant versus active fraction to total carbon stores in different ecosystems—are poorly understood. Only since the 1993 creation of the small NRI Soils Program has basic, peer-reviewed soil-carbon research had an important source of potential support in USDA. Basic soils research is in general poorly supported at the national level; soil carbon is one of many competing needs. Environmental Plant Physiology. Responses of plants to changes in atmospheric and soil chemistry are key determinants to the effects of global change on ecosystems. Many responses are interactive and require an ecosystem context in which to understand them sufficiently to suggest management solutions. But many basic ecosystem interactions are too poorly understood to gauge the effects of change. For example, increased CO2 in the atmosphere leads to changes in leaf chemistry in many tree species; do these changes affect insect herbivory or leaf-litter decomposition rates? If so, how will the changes affect other trophic levels and soil nutrient availability, and eventually plant susceptibility to insect outbreaks, fire, and drought? Is the response of forests to nitrogen saturation ameliorated by increased CO2 ? Is the response of annual plants—both crops and weeds—to increased CO2 fundamentally different from that of woody perennial plants at either the plant or the ecosystem level? Answers to those questions require fundamental knowledge that is being gained very slowly via poorly funded basic-research programs in agricultural ecosystems. Environmental Modeling. The complexity of ecosystems and differences in their responses to climatic variability suggest that process-based, quantitative models will eventually be the best way to predict the effects of human activities on ecosystem structure and function and to suggest the likely effects of different management scenarios and therefore best-management solutions. However, basic research into quantitative modeling is funded as a small part of the NRI Agricultural Systems program. To effectively link existing crop and forest models to models of soil biogeochemistry, hydrologic transport, and atmospheric chemistry—and then link these models to economic, land-use, and other social models—will require substantive basic research not now budgeted for. Nitrogen-Use Efficiency. The efficient use of nitrogen in cropping systems is essential for protecting downstream ecosystems from environmental harm while maintaining high agricultural productivity in cropped fields. Nitrogen limits crop growth, but only 50%–60% of nitrogen applied to crops is taken up by them. Most of the remainder is lost to groundwater and surface water as nitrate or to the atmosphere as dinitrogen or the greenhouse gas nitrous oxide. The

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research environmental and economic consequences can be large: an increasing proportion of drinking water, especially in rural areas, exceeds Environmental Protection Agency health standards for nitrate contamination, and nitrate in surface water eventually makes its way to coastal areas, where it has been linked to unwanted effects—hypoxic zones that can depress such populations as shrimp in the Gulf of Mexico, outbreaks of such toxic algae as those in Chesapeake Bay, and so on. Improving nitrogen-use efficiency on the field scale has been an elusive goal; efficiency has changed little since it was first measured in the 1950s. Changes in tillage practices, the application of site-specific farming methods, the introduction of nutrient catch crops in the cropped field or of riparian vegetation downstream, and increases in the efficiency of plant nitrogen uptake in the rhizosphere all depend on a better fundamental understanding of the ecologic interaction among crops, soil organisms, and the set of physical and chemical conditions that define the plant-soil environment. Opportunities for peer-reviewed, competitive funding of basic, integrated research in crop ecosystems are largely lacking outside the small NRI programs in Natural Resources and Environment. Wildlife in agricultural systems. The conflict of expanded agricultural productivity and the desire for environmental preservation, including that of wildlife, necessitates further research to devise new methods and approaches. Space. Agriculture and agricultural research will play a major part in space exploration because of obvious needs for food, fiber, and waste disposal. Engineered microbial lines and bioprocessing will have large contributions to make and need to be studied now in the context of space flight. ENHANCING VALUE AND USE OF AGRICULTURAL AND FOREST PRODUCTS Development of microtechnology for separation and analysis of biologic molecules using microfabrication and nanotechnology. These fields are progressing extremely rapidly and promise to affect approaches to use of agricultural and forest products in new ways. Impacts of organic farming. The safety and quality of organically produced products need to be compared with those of conventionally produced commodities and characterized at the molecular level. Bioprocess engineering for agricultural products. Integrated research is needed to combine molecular-biology techniques for tailoring plants to the generation of specific value-added products with postharvest processing steps that will enable cost-effective recovery of the products in appropriately located and sized bioprocessing plants.

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research Metabolic pathway analysis. Structure-function studies of proteins that are generated by genes discovered in the Plant Genome Project should be undertaken. MARKETS, TRADE, AND RURAL DEVELOPMENT Knowledge base to prepare for biologic terrorism or deliberate attempts to degrade the biosphere or agroecosystems. There is a great need to expand our knowledge base—for instance, on pathogenic microorganisms—to forestall attempts at biologic terrorism. Globalization of the economy. Greater broadening of economies has major effects on US agriculture. There is a need for increased research to explore the bases and ramifications of this increasing trend. Economic and social consequences of environmental regulation. Studies should assess the benefits and costs of government regulations that affect agricultural production and the environment, design and evaluate alternative policies and institutions to mitigate negative environmental impacts of production agriculture, and develop more quantitative and qualitative tools for assessing nonmarket goods. Risk-management tools and financial management. Studies should assess ways to measure and manage risk in a new, globalized, vertically coordinated food system; analyze specific risk-management strategies, instruments, and portfolios; and assist farmers and lenders in adopting improved financial accounting and reporting systems. Impacts of the changing farm and agribusiness structure. Studies should analyze the forces driving structural change and concentration and their effects on the economic performance of vertically coordinated farming and agribusiness; determine the effects of vertical coordination on market access, bargaining power, concentration, location of production, financial arrangements, rural communities, and the environment; and analyze the relationship between value-added agricultural commodities and new-product development, producer profitability, risk, and market access. Evaluate trade policies and barriers. Studies should assess the benefits, costs and other implications of trade policies, government regulation, and institutional barriers to international trade; evaluate the relationships among trade, natural resources, and the environment; and enhance understanding of the economic impacts and consequences of trade. Economic and rural community development programs. Studies should create improved information to assist local governments in cost-effectively

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National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research meeting demands for public services, financing public programs, providing infrastructure needs, and designing incentives for private-sector initiatives and involvement; improve understanding of the roles of human capital, social capital, and life-long learning in rural economic development; and ascertain the impacts of government programs on rural poverty. Effects of changes in consumer demand on health, nutrition, and food safety. Studies should assess the benefits and costs of public policies and government regulations that affect health, nutrition, and food safety; assess consumer preferences and demands and their implications for production and marketing practices in the food system; and increase multidisciplinary analysis of food-science issues. Economic and social impacts of consolidating research and extension programs. Studies should assess opportunities for regionalization of research and extension programs, change the reward systems for agricultural research to value multidisciplinary and applied work more highly, and achieve greater coordination among research and extension, including involvement by stakeholders in priority-setting, planning, and program evaluation. Information technologies and communication systems. Studies should ascertain the benefits and costs of public versus private information and the implications for delivery systems for agricultural research results and education, redesign the delivery systems of the Cooperative Extension Service for more effective and timely performance, and evaluate the value and use of precision technology and information in agricultural production. Economic and social impacts of biotechnology: Studies should analyze how biotechnology affects farm size, production efficiency, competitiveness, trade potential, and other elements of economic performance in agriculture; evaluate the public- versus private-sector roles in the development of biotechnology; and enhance the public’s understanding of the benefits and risks associated with biotechnology. Development of human capital. Studies should place greater emphasis in undergraduate curricula and public education on understanding the global economy, renew the emphasis on competitiveness as a key economic concept in agriculture and agribusiness curricula, use more “real-life” and experiential learning in the classroom.