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United States Department of Agriculture

Agricultural Research Service

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2004 Annual Performance Report
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The Agricultural Research Service (ARS) was established on November 2, 1953, pursuant to authority vested in the Secretary of Agriculture by 5 U.S.C. 301 and Reorganization Plan No. 2 of 1953, and other authorities.


ARS is the principal in-house research agency of the U.S. Department of Agriculture (USDA).  Congress first authorized federally supported agricultural research in the Organic Act of 1862, which established what is now USDA.  That statute directed the Commissioner of Agriculture "...  To acquire and preserve in his Department all information he can obtain by means of books and correspondence, and by practical and scientific experiments..."  The scope of USDA's agricultural research programs has been expanded and extended more than 60 times since the Department was created. 


ARS research is authorized by the Department of Agriculture Organic Act of 1862 (7 U.S.C. 2201 note), Agricultural Research Act of 1935 (7 U.S.C. 427), Research and Marketing Act of 1946 (P.L. 79-733), as amended (7 U.S.C. 427, 1621 note), Food and Agriculture Act of 1977 (P.L. 95-113), as amended (7 U.S.C. 1281 note), Food Security Act of 1985 (P.L. 99-198) (7 U.S.C. 3101 note), Food, Agriculture, Conservation, and Trade Act of 1990 (P.L. 101-624) (7 U.S.C. 1421 note), Federal Agriculture Improvement and Reform Act of 1996 (P.L. 104-127), and Agricultural Research, Extension, and Education Reform Act of 1998 (P.L. 105-185).  ARS derived most of its objectives from statutory language, specifically the “Purposes of Agricultural Research, Extension, and Education” set forth in Section 801 of FAIR.


The ARS mission is to conduct research to develop and transfer solutions to agricultural problems of high national priority and provide information access and dissemination to:  ensure high-quality, safe food, and other agricultural products; assess the nutritional needs of Americans; sustain a competitive agricultural economy; enhance the natural resource base and the environment; and provide economic opportunities for rural citizens, communities, and society as a whole.


The Agency’s research focuses on achieving the goals identified in the USDA and Research, Education, and Economics (REE) mission area Strategic Plans.  The Government Performance and Results Act (GPRA) mandates each agency to establish general goals that will contribute to achieving beneficial societal outcomes that shape and drive the work of the Agency during the five years covered by the plan.


Verification, Validation and Program Evaluation:  ARS conducts a series of review processes designed to ensure the relevance and quality of its research work and to maintain the highest possible standards for its scientists.  This process involves customer input to help keep the research focused on the needs of the American food and agricultural system.  Each of the approximately 1,000 research projects, which are organized into 22 National Programs, undergoes a thorough external peer review conducted by the Office of Scientific Quality Review (OSQR) before new or renewed activities are begun.  All ARS employees, including the scientific workforce, are subject to annual performance reviews.  Senior scientists undergo a rigorous peer review (Research Position Evaluation System-RPES) on a 3- to 5-year cycle.  These processes ensure the continuing high quality output of the ARS research addressing the needs of American agriculture.


ARS has also recently implemented two program evaluations that are included in the President’s Management Agenda (PMA).  The PMA is designed to strengthen the management of Federal programs and increase program accountability.  In the FY 2005 budget cycle, ARS conducted a “pilot” Program Assessment Rating Tool (PART) analysis on its Food Safety National Program.  During the FY 2006 budget cycle, the PART Analysis was applied to all the research conducted under Strategic Plan Goal 1, Enhance Economic Opportunities for Agricultural Producers.  This Goal includes research on new and improved high quality value added products and processes, livestock production, and crop production.  The PART assessment seeks to measure four aspects of a program: program purpose and design, strategic planning, program management, and program results/ accountability. 


In preparing the FY 2006 budget submission, ARS’ National Program Leaders (NPLs) and Area Directors reviewed more than 1,000 research projects by applying the Research and Development (R&D) Investment Criteria of relevancy, performance, and quality.  The information gained from this review helped the Agency to identify low performing and/or low priority research.  This information was used in shaping the FY 2006 budget; it will also be used to make future program management decisions.  The R&D investment criteria were applied as follows:


For relevance, the NPLs assessed whether ARS’ research is consistent with the Agency’s mission and relevant to the needs of American agriculture, as identified by the Administration and ARS’ customers and stakeholders. 


For performance, the NPLs reviewed the annual project reports submitted by each research unit.  Beginning with FY 2004, these reports provided information on how well each research project did in achieving the milestones in its Project Plan.  First year data identified over 5,400 milestones, of which 59 percent were “fully met,” 26 percent were “substantially met,” and 15 percent were “not met.” 


For quality, the Area Directors relied on data from the ARS OSQR reviews of each research project at the beginning of its 5-year program cycle.  OSQR conducts rigorous reviews of ARS’ research projects by independent external peer panels to ensure their quality.  In addition, the Area Directors used information from the RPES reviews of individual scientists in making this assessment.  RPES conducts rigorous peer reviews of ARS’ scientists on a regular schedule (i.e., every three, four, or five years).  The Area Directors also assessed the capacity (i.e., facilities, human and fiscal resources, equipment, etc.) of each project to meet its research objectives, an important consideration for intramural programs.


The National Programs focus the work of the Agency on achieving the goals defined in the ARS Strategic Plan 2003-2007.  The research priorities for each National Program are established with extensive input from customers, stakeholders, and partners, which is received, in part, at a series of National Program Workshops.  A detailed Action Plan developed for each National Program is available on the ARS home page,; open “Research” and select the National Program of interest.  The Annual Performance Plans, the Annual Performance Reports required by GPRA, and the National Program Annual Reports all serve to keep the work of the Agency focused on achieving the goals established in the ARS Strategic Plan.  The aggregate effect of these processes is a strengthened research program and an accountability system that measures more effectively the progress made towards achieving established goals and outcomes.


Key External Factors that Affect the Ability of ARS to Achieve its Goals and Objectives:  The future of American agriculture depends on its ability to respond to critical external factors.  Effective planning within ARS will take these factors into consideration when establishing and executing the Agency’s research programs.


Globalization:  The globalization of all aspects of the food and fiber system is having a major impact on American agriculture.  Profound changes are seen worldwide from competitive markets around the world, from diseases not limited to national boundaries, to population growth and evolving diets.  These changes have led to a dramatically new trade environment, threats of exotic diseases and pests to domestic production, and international controversies over the use of biotechnology.  To remain competitive, the food and agriculture sector needs to respond to these developments.


Information Access and Communication:  The explosion of information technology, the worldwide use of the Internet, and the major advancements of cyberspace communications are changing the way private industry, government, and individuals conduct daily business.  Vast amounts of information soon will be available in “real time,” more people from around the world will be able to retrieve the information, and advanced computer software will make the information more useful and meaningful.  Advancements in communication technology offer benefits and opportunities for everyone involved in the American food and agriculture sector.


Workforce:  A very important employment issue is the need to recruit and retain a highly skilled and technically well trained Federal workforce.  The relatively low U.S. unemployment rate makes recruitment highly competitive.  This competitive environment is expected to require more employer emphasis on recruitment, retention, student employment, upward mobility, and training/retraining programs.   The public sector will need to recruit a diversity of people and to maintain a highly qualified and technically competent workforce.  Expanding job opportunities for women and minorities in science and engineering will help to tap the Nation’s human potential.


Technology:  Advances in technology--such as bioengineering, precision agriculture, remote sensing, and decision modeling--enable agricultural production to enhance nutrition, protect the environment, and continue to make the food supply safe.  Biotechnology offers great promise for increasing production efficiency, improving food quality, and enhancing nutritional value.  However, concerns about genetically modified organisms (GMOs) have had a marked impact on international exports of affected commodities, and prompted questions about the potential benefits and risks.  Precision agriculture, remote sensing, and decision modeling will both increase production efficiency and mitigate adverse environmental impacts of agriculture.  Public concern about food safety has led to new rapid detection technologies that, when fully implemented, will make the food supply increasingly safer. 


Changing Demographics:  Growing global populations, demographic changes, and economic growth will substantially increase the demand for agricultural products, thus creating new markets for U.S. products. At the same time, however, increased agricultural competitiveness from other countries will force U.S. agriculture to become more efficient.  Because arable agricultural land is limited, the growing demands will increase pressure to maximize yields, protect marginal areas from unsustainable development, and minimize the harmful effects of agriculture on the environment and the natural resource base.


Changing Structure of Agriculture:  The structure of the food and fiber system--from farm to market--changed dramatically in the last decades of the 20th century, and is likely to continue.  Change can be seen all across the food and agriculture sectors.  An increasing share of U.S. food and fiber is being produced on fewer, larger, and more specialized farms.  Production and marketing are more vertically and horizontally integrated.  Concentration is greater causing sharp declines in the number of buyers and sellers of a product.  Consumer preferences, new technologies, and global markets bring about continuing changes that affect farmers, processors, marketers, and consumers.


Congressional Support:  The ability of ARS to respond to the diverse needs of producers and consumers is determined by the level of Congressional support.  As a consequence of inflation and higher operating costs associated with advances in research equipment and technology, the ARS scientific workforce, which reached a maximum of about 3,400 scientists in 1970, decreased by almost 40 percent during the ensuing 25 years.  More recently, appropriations have allowed the Agency to expand its research program and hire additional scientists to bring the current number of scientists to almost 2,200.


Drug-Free Workplace:  ARS will continue to use the applicable contract clauses and regulations to ensure compliance with drug-free workplace debarment and suspension requirements in all of its acquisition programs.


General Comments:  In January 1998, ARS requested permission from the Office of Management and Budget (OMB) “to describe specific and tangible products, steps, intermediate goals, and/or accomplishments that will demonstrate that the Agency has successfully met each Performance Measure/Goal in a given fiscal year.”  With OMB’s concurrence, ARS is able to use narrative descriptions of intermediate outcomes and indicators of progress instead of numerical metrics as specified in GPRA.  The FY 2004 accomplishments reflect actual achievements against the FY 2004 indicators previously identified.  The research and technology transfer activities listed in this report are not all inclusive of the Agency’s work.  The reported accomplishments reflect, but do not adequately capture, the broad range of basic research that underpins the Agency’s work. 


Only Federal employees were involved in the preparation of this report.

Table of Contents

Strategic Goal/ Management Initiative


ARS FY 2004 Annual Performance Report


Goal 1:  Enhance Economic Opportunities For Agricultural Producers



Performance Measure 1.1.1:  Develop cost effective and functional industrial and consumer products from agricultural and forestry resources.


Performance Measure 1.1.2:  Provide higher quality, healthy foods that satisfy consumer needs in the United States and abroad.


Performance Measure 1.1.3:  Improve efficiency and reduce cost for conversion of biomass to energy.


Performance Measure 1.2.1:  Provide producers with scientific information and technology that increase production efficiency, develop improved germplasm, safeguard the environment, improve animal well-being, and reduce production risks and product losses.


Performance Measure 1.2.2:  Develop needed information on the relationships between nutrients, reproduction, growth, and conversion to and marketability of animal products.


Performance Measure 1.2.3:  Identify genes responsible for economically important traits, including animal product quality, efficiency of nutrient utilization, and environmental adaptability.


Performance Measure 1.2.4:  Maintain, characterize, and use genetic resources to optimize and safeguard genetic diversity and promote viable, vigorous animal production systems.


Performance Measure 1.2.5:  Provide producers with scientific information and technology that increase production efficiency, safeguard the environment, and reduce production risks and product losses.


Performance Measure 1.2.6:  Improve the understanding of the biological mechanisms that influence plant growth, product quality, and marketability to enhance the competitive advantage of agricultural commodities.


Performance Measure 1.2.7:  Identify genes responsible for plant product quality and resistance to diseases, pests, and weather losses.


Performance Measure 1.2.8:  Maintain, characterize, and use genetic resources to optimize, safeguard, and enhance genetic diversity and promote viable and vigorous plant production systems.



Goal 3:  Enhance Protection and Safety of the Nation’s Agriculture and Food Supply





















Performance Measure 3.1.1:  Develop new on-farm preharvest systems, practices, and products to reduce pathogen and toxin contamination of animal- and plant-derived foods.


Performance Measure 3.1.2:  Develop and transfer to Federal agencies and the private sector systems that rapidly and accurately detect, identify, and differentiate the most critical and economically important foodborne microbial pathogens.


Performance Measure 3.2.1:  Provide scientific information to protect animals from pests, infectious diseases, and other disease-causing entities that affect animal and human health.


Performance Measure 3.2.2:  Identify, develop, and release to the U.S. agricultural community genetic markers, genetic lines, breeds, or germplasm that result in food animals with improved (either through traditional breeding or biotechnology) pest- and disease-resistant traits.


Performance Measure 3.2.3:  Develop and transfer tools to the agricultural community, commercial partners, and Federal agencies to control or eradicate domestic and exotic diseases that affect animal and human health.



Performance Measure 3.2.4:  Develop and release to potential users varieties and/or germplasm of agriculturally important plants that are new or provide significantly improved (either through traditional breeding or biotechnology) characteristics enhancing pest or disease resistance.


Performance Measure 3.2.5:  Provide fundamental and applied scientific information and technology to protect agriculturally important plants from pests and diseases.


Performance Measure 3.2.6:   Provide needed scientific information and technology to producers of agriculturally important plants in support of exclusion, detection, and early eradication; control and monitoring of invasive insects, weeds and pathogens; and restoration of affected areas.  Conduct biologically-based integrated and areawide management of key invasive species.



Goal 4:  Improve the Nation’s Nutrition and Health


Performance Measure 4.1.1:  Scientifically assess the efficacy of enhancements to the nutritional value of our food supply and identify, conduct, and support intramural and extramural research to develop, test, and evaluate effective clinical and community dietary intervention strategies and programs for modifying diet, eating behavior, and food choices to improve the nutritional status of targeted populations.  A special emphasis is to prevent obesity and promote healthy dietary behaviors.


Performance Measure 4.1.2:  Define functions, bioavailability, interactions, and human requirements (including effects such as genetic, health status, and environmental factors) for known, emerging, and new classes of nutrients.  Determine the abundance of known, emerging, and new classes of nutrients in the food supply and provide that information in databases.


Performance Measure 4.1.3:  Determine food consumption patterns of Americans, including those of different ages, ethnicity, regions, and income levels.  Provide sound scientific analyses of the U.S.  food consumption information to enhance the effectiveness and management of national and community food and nutrition programs.



Goal 5:  Protect and Enhance the Nation’s Natural Resource Base and Environment


Performance Measure 5.1.1:  Develop ecologically-based information, technologies, germplasm, and management strategies that sustain agricultural production while conserving and enhancing the diverse natural resources found on rangelands and pasture lands.


Performance Measure 5.2.1:  Develop the tools and techniques required to maintain and restore the physical, chemical, and biological integrity of the Nation’s watersheds and its surface and groundwater resources.


Performance Measure 5.2.2:  Develop agricultural practices that maintain or enhance soil resources, thus ensuring sustainable food, feed, and fiber production while protecting environmental quality.


Performance Measure 5.2.3:  Develop approaches that mitigate the impact of poor air quality on crop production and provide scientific information and technology to maintain or enhance crop and animal production while controlling emissions that reduce air quality or destroy the ozone layer.


Performance Measure 5.2.4:  Develop agricultural practices and decision support strategies that allow producers to take advantage of beneficial effects and mitigate adverse impacts of global change.


Performance Measure 5.2.5:  Develop management practices, treatment technologies, and decision tools for effective use of animal manure and selected industrial and municipal byproducts to improve soil properties and enhance crop production while protecting the environment.


Performance Measure 5.2.6:  Develop agricultural and decision support systems that assist in increasing the efficiency of agricultural enterprises and achieve economic and environmental sustainability.




Goal 6:  Management Initiative 0.1:  Ensuring the Quality, Relevance, and Performance of ARS Research (covers all research objectives)


Performance Measure 6.0.1:  Relevance—ARS’ basic, applied, and developmental research programs are well conceived, have specific programmatic goals, and address high priority national needs.


Performance Measure 6.0.2:  Quality—ARS research projects are reviewed by National Program by external peer review panels at the beginning of the 5-year program cycle.


Performance Measure 6.0.3:  Performance—ARS will monitor and measure the performance of each research unit and National Program.



Goal 6:  Management Initiative 1:  Provide Agricultural Library and Information Services to USDA and the Nation via the National Agricultural Library


Performance Measure 6.1.1:  Develop and deliver content for the NAL National Digital Library for Agriculture (NDLA).


Performance Measure 6.1.2:  Integrate the NAL AGRICOLA database into the NDLA.


Performance Measure 6.1.3:  Ensure long-term access to the resources of the NAL NDLA.



Goal 6:  Management Initiative 2:  Provide Adequate Federal Facilities Required to Support the Research Mission of ARS



Performance Measure 6.2.1:  Complete priority buildings and facilities projects on schedule and within budget.


Goals 1 and 2



Analysis of Results:  This goal is related to production agriculture, adding quality and value to agricultural products, new products, biobased products, and biofuels.  Under Goal 1, 24 Indicators are aligned under 11 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2004.  Ninety-three significant accomplishments are reported below.


OBJECTIVE 1.1:  Provide the Science-Based Knowledge and Technologies To Generate New or Improved High Quality, Value-Added Products and Processes To Expand Domestic and Foreign Markets for Agricultural Commodities.


Performance Measure 1.1.1:    Develop cost effective and functional industrial and consumer products from agricultural and forestry resources.




During FY 2004, ARS will


develop new or improved, or more environmentally friendly, processing technologies.


ACCOMPLISHMENTS:  To meet the needs of the military for wool fabrics that will not burn, scientists at Wyndmoor, Pennsylvania, processed wool with a heat-resistant synthetic polymer which exhibited burning behavior similar to blended wool and Nomex (synthetic fiber known to resist burning). 


IMPACT/OUTCOME:  Participating wool mills are anticipated to include this new technology in their existing product lines, thereby increasing the demand for domestic wool fiber and apparel for traditional and new uses.


ACCOMPLISHMENTS:  Industry is searching for a biobased process to produce mannitol (a low-calorie sugar alcohol widely used in foods, pharmaceuticals, medicines, and chemical industries) to replace the problematic low yield chemical process currently used.  Researchers at Peoria, Illinois, developed a fermentation process for production of mannitol from sugars using a lactic acid bacterium obtained from the ARS Culture Collection.  The process has been scaled up to 30 liters and the purity of the product has been established.


IMPACT/OUTCOME:  The private sector partner in this project has applied for FDA approval of the process and the product.  The new process offers an attractive alternative to the chemical production process and utilizes inexpensive corn-derived sugars.


develop new or improved methods to measure or predict quality.


ACCOMPLISHMENTS:  Moisture is typically added back to cotton during ginning and spinning, but too much moisture can adversely affect fiber quality and processing.  In trials on a commercial gin with a commercially available moisture restoration system, researchers in Clemson, South Carolina, in partnership with researchers at Lubbock, Texas, found that restored moisture above 8 percent resulted in deteriorating fiber quality and poor yarn properties.  In related work, engineers at Lubbock, Texas, developed a novel low cost microwave-based cotton bale moisture sensor with high accuracy and precision. 


IMPACT/OUTCOME:  Based on the work at Clemson, the National Cotton Council established a level of 7.5 percent moisture as the highest level of restored moisture acceptable at ginning.  Based on the work at Lubbock, a U.S. patent application has been initiated.  Reliable moisture measurement will limit excessive moisture application to the bale, which results in lint deterioration and lower grades for the end user.


ACCOMPLISHMENTS:  Non-destructive sensing of fruit quality attributes, such as firmness and soluble solids content (SSC), will allow the fruit industry to deliver superior, consistent quality fruit to the marketplace and better meet consumer demands for high quality fruit.  Researchers at East Lansing, Michigan, developed a light-based multispectral imaging prototype which was able to inspect individual apples for firmness and SSC in real time for up to two fruit per second. 


IMPACT/OUTCOME:  Initial evaluation demonstrated that the prototype is promising for sorting and grading individual apples and other fruit for firmness and SSC.   


develop technologies leading to new or improved products from renewable resources and agricultural residues and wastes.


ACCOMPLISHMENTS:  A soy oil-based elevator hydraulic fluid technology was developed by scientists at Peoria, Illinois, in response to a request from the National Park Service (for the Statue of Liberty).  The fluid was independently evaluated by an industrial partner and scaled up and retrofitted in the Statue of Liberty elevator; it has been successfully operating for nearly two years. 


IMPACT/OUTCOME:  A leading lubrication company has applied for a product license for commercial production of the fluid.  This work resulted in a 2004 “Excellence in Technology Transfer” award from the Federal Laboratory Consortium.  Potential exists for expanded utilization of this biobased, biodegradable fluid in place of petroleum-based fluids.


ACCOMPLISHMENTS:  Scientists at New Orleans, Louisiana, developed products from cottonseed and its derivatives to control fire ants and termites.  A patent has been approved by the U.S. Trade Mark and Patent Office.  Field tests with the cottonseed-containing baits in Mississippi have been conducted for almost three years with good results. 


IMPACT/OUTCOME:  A Japanese company is interested in the technology and is currently evaluating the bait system.  This development offers a possible new market for cottonseed and a biobased biocontrol technology.


Performance Measure 1.1.2:    Provide higher quality, healthy foods that satisfy consumer needs in the United States and abroad.




During FY 2004, ARS will


develop new or improved methods to measure or predict quality, or to sort by quality.


ACCOMPLISHMENTS:  Aflatoxin and fumonisin are carcinogens found in corn.  Rapid detection means are needed to ensure a safe food and feed supply.  Researchers at Manhattan, Kansas, in cooperation with scientists at Peoria, Illinois, developed a high speed sorting machine to remove corn kernels that are contaminated with aflatoxin- or fumonisin-producing fungi.  The sorter, which uses near-infrared detectors, removes as much as 80 percent of these toxins in a single pass. 


IMPACT/OUTCOME:  This technology will help ensure the safety of the U.S. food and feed supply and could save the corn industry millions of dollars.


ACCOMPLISHMENTS:  The mechanical harvesting of billeted (9-15cm long) sugarcane is now more predominant than the harvesting of whole stalk cane in Louisiana, but the billeted cane deteriorates faster so there is now a more urgent need to have a reliable test of the extent of cane deterioration at the factory.  Deteriorated cane contributes to sugar losses and processing problems in the factory.  Researchers in New Orleans, Louisiana, demonstrated that mannitol (a sugar alcohol) is an excellent predictor of sugarcane deterioration, and they developed a quick, easy, reliable, cheap enzymatic method to measure it in cane press juices from individual loads of sugarcane. 


IMPACT/OUTCOME:  This new method will allow factory staff to determine if a shipment load of cane can be economically processed or not.   


develop functional food ingredients and/or products.


ACCOMPLISHMENTS:  New fruit and vegetable products and processes and their consumption can help to combat the rising obesity epidemic in the United States.  Researchers at Albany, California, in cooperation with an industrial partner developed and tested novel fruit- and vegetable-based films for use in wrapping food products. 


IMPACT/OUTCOME:  A patent was filed on the final products and processes.  The cooperator is building a food manufacturing plant in a rural area of California and expects to begin commercial production in 2005.  As a result of ARS; research new jobs will be created in an area of high unemployment, and new healthy food products for consumers and novel value-added outlets for fruits and vegetables will be provided.


ACCOMPLISHMENTS:  Scientists at WRRC in Albany, California, in collaboration with a large commercial food manufacturer, found that food processing can improve the ability of legume proteins to lower blood-serum cholesterol in lab animals, ostensibly due to certain peptide fractions in the processed products. 


IMPACT/OUTCOME:  This discovery provides the legume industry with critical scientific knowledge necessary for the development of more heart-friendly foods.


ACCOMPLISHMENTS:  Fantesk(TM) is a patented technology developed at the NCAUR in Peoria, Illinois, which uses cornstarch and soybean oil, surplus products of U.S. agricultural production, or other crop-based materials, which has both food and non-food applications.  A starch-based Fantesk gel was developed that has many of the desirable properties of a solid fat.  This gel is blended into low fat ground beef produced hamburger patties with improved flavor, texture, and juiciness. 


IMPACT/OUTCOME:  The licensee of the technology is currently working with food processors to produce and market Fantesk containing low fat meat products.  Improving the sensory properties of low fat foods, to make them more closely resemble their full fat analogues, will encourage consumers to purchase these low fat, healthier alternatives.     


ACCOMPLISHMENTS:  Current rice starch processing requires extensive soaking of rice in dilute caustic solutions prior to separation of its starch and protein.  These processes involve water and energy, and are time intensive and require costly wastewater treatment.  The process uses high pressure supplied by a microfluidizer (homogenizer) to separate the starch from the protein.  Scientists at New Orleans, Louisiana, working through a Cooperative Research and Development Agreement with a private sector partner and partially supported by a Small Business Innovative Research grant, developed and successfully scaled up a process for commercial production of rice starch.   


IMPACT/OUTCOME:  This technology has the potential of reducing imports of rice starch and increasing profits for the U.S. rice industry.    


develop improved or new methods to maintain quality of food products.


ACCOMPLISHMENTS:  Scientists at Fargo, North Dakota, in cooperation with the Wheat Quality Council and Federal, State, and commercial bakers, evaluated quality traits of spring wheat experimental lines, resulting in the identification of the most promising lines and the release of four new commercial varieties with superior agronomic, disease resistance, and end use quality traits. 


IMPACT/OUTCOME:  This research could result in a higher net income for producers, and a greater marketing potential of higher quality wheat to domestic and overseas buyers.


ACCOMPLISHMENTS:  Engineers at Manhattan, Kansas, found that little co-mingling of different corn varieties occurred in elevators. 


IMPACT/OUTCOME:  The results of this study, the first of its kind, will be used by elevator operators to better segregate grain with desirable characteristics into separate channels for delivery to end users.  This information is also useful to grain processors for improving their handling of specialty grains.


ACCOMPLISHMENTS:  Researchers at Beltsville, Maryland, demonstrated that ‘Goldrush’ apples possessed better quality attributes for fresh cutting than traditional cultivars. 


IMPACT/OUTCOME:  This finding is important since repeat sales of fresh cut apple products is driven by consumer satisfaction with product taste, including texture, sweetness, acidity, and aroma.  ‘Goldrush’ apples can be refrigerated for 12 months in air before processing and for three weeks as the cut product.  Once “Goldrush” becomes more commercially available, these findings will enable fresh cut processors to provide a better testing product and enhance fresh cut apple sales.


ACCOMPLISHMENTS:  Fruity fermented off flavor is a significant economic problem for producers in areas where peanuts are exposed to high temperature during initial curing.  Scientists at Raleigh, North Carolina, discovered that sandwich windrow construction (plants placed in windrows with one up and one down providing shade for the peanuts) and a sprayed coating of white kaolin powder on normal inverted windrows reduced peanut pod temperatures and decreased intensity of fruity fermented off flavor. 


IMPACT/OUTCOME:  Because these findings occurred in one of the worst years (2003) for the off flavor, this information has been instrumental in changes by producers toward use of sandwich diggers as standard practice.


Performance Measure 1.1.3:    Improve efficiency and reduce cost for conversion of biomass to energy.




During FY 2004, ARS will


develop improved biomass plants, sustainable biomass production systems, and efficient handling and storage technology for biomass feedstocks.


ACCOMPLISHMENTS:  Sustainable management technology was developed for growing switchgrass as an energy crop on marginal cropland in the western Corn Belt and was demonstrated to produce biomass amounts with the potential to yield more ethanol per acre than corn while providing environmental benefits similar to that of the Conservation Reserve Program.


IMPACT/OUTCOME:  Provides the technology for and demonstrates the potential for large quantities of ethanol producing crops to be grown while avoiding soil erosion and protecting soil quality.


ACCOMPLISHMENTS:  Genetically modified switchgrass, an herbaceous energy crop, by Agrobacterium mediated transformation to successfully provide plant material that is more readily converted to ethanol by existing technologies.


IMPACT/OUTCOME:  Provides the technology to improve the characteristics of crops grown for liquid transportation fuel production.


ACCOMPLISHMENTS:  Developed hybrid cultivars of switchgrass and demonstrated their potential to increase yields of biomass for use as bioenergy feedstock.


IMPACT/OUTCOME:  Increased potential of switchgrass as an energy crop.


develop technology and systems that improve the efficiency, economics, and sustainability of energy production from agricultural biomass.


ACCOMPLISHMENTS:  Enzymatic wet milling, a process previously demonstrated to avoid the need to use hazardous sulfur dioxide, was optimized to reduce by a factor of ten the amount of enzyme needed.  These findings reduce the cost while maintaining a production level similar to that of conventional wet milling.


IMPACT/OUTCOME:  Improved commercial potential for this environmentally favorable bioprocessing technology.


ACCOMPLISHMENTS:  Enzymes were selected and processes developed to efficiently convert beta-glucan, a material in barley that limits its suitability for fuel ethanol production, into fermentable sugars.


IMPACT/OUTCOME:  These developments increase ethanol production from barley, improve the economics of the process, and provide an additional market for farmers where barley can be grown.


ACCOMPLISHMENTS:  Developed an aqueous enzymatic process that avoids the need to use the flammable, toxic solvent hexane to extract corn oil from oven dried corn germ produced during wet milling. 


IMPACT/OUTCOME:  Development of an environmentally friendly process for extracting valuable oil from corn.


ACCOMPLISHMENTS:  Described an adaptive response of yeasts to fermentation inhibitors that are byproducts of dilute acid hydrolysis of lignocellulosic biomass, and developed adapted strains that were shown to be able to convert these inhibitors into forms that are less toxic.


IMPACT/OUTCOME:  Provided fundamental guidelines for further development of industrial yeasts to alleviate the stress factors associated with commercial dilute acid hydrolysis of lignocellulosic biomass.


ACCOMPLISHMENTS:  Identified binary mixtures of oxidation inhibitors (antioxidants) exhibiting synergistic effects when applied to improve oxidative stability of biodiesel.


IMPACT/OUTCOME:  A lower cost method has been identified to protect biodiesel fuel from oxidative degradation and maintain fuel quality.


develop renewable energy technology and systems to meet on-farm and remote rural needs and to enhance the rural economy.


ACCOMPLISHMENTS:  Demonstrated that a new submersible pump powered by wind or solar energy can pump water from a deep well while requiring little maintenance, that is less costly to install than a mechanical windmill.


IMPACT/OUTCOME:  A more economical method has been identified for farmers and ranchers to provide water for livestock in remote locations.


OBJECTIVE 1.2:  Contribute to the Efficiency of Agricultural Production Systems.


Performance Measure 1.2.1:  Provide producers with scientific information and technology that increase production efficiency, develop improved germplasm, safeguard the environment, improve animal well-being, and reduce production risks and product losses.




During FY 2004, ARS will develop scientific information that contributes to improved efficiency and environmental stewardship of food animal production systems.


ACCOMPLISHMENTS:  Previous work by ARS researchers at Ithaca, New York, has shown that Clostridium sporogenes, the primary detrimental bacteria involved in the fermentation of silage for dairy cattle, could be inhibited by a specific bacteriocin that is produced by the ruminal bacterium S. bovis.  The research team has now shown that the activity of the bacteriocin is at least tenfold higher under the relevant conditions experienced during silage production.


IMPACT/OUTCOME:  The dairy industry relies heavily upon the use of silage as a feedstuff, but silage preservation is often inadequate to ensure quality.  One of the critical control points impacting silage quality is the control of detrimental amino acid degrading bacteria during the ensiling process.  These results suggest that the bacteriocin producing bacteria S. bovis, has the potential to improve silage quality.


ACCOMPLISHMENTS:  Research conducted at the Grazinglands Research Laboratory, El Reno, Oklahoma, demonstrated that producers can substitute perennial cool season grasses for wheat, or use a combination of these grasses with wheat, to buffer highly variable wheat forage production and simultaneously meet the nutritional demands of stocker calves.


IMPACT/OUTCOME:  These farm scale studies of stocker calf weight gains indicate that a variety of grasses can be grazed a full month later in the spring than wheat pasture, extending the marketing date of stocker calves past the seasonal lows in beef prices associated with the end of the wheat pasture grazing season.  These findings allow livestock producers to more consistently meet the forage needs of stocker calves and reduce the economic losses associated with livestock production in the southern Great Plains.


ACCOMPLISHMENTS:  ARS scientists developed advanced oxidation processes for controlling and mitigating microbial populations and critical water quality parameters within a re-circulation fish production system.  They developed a disease challenge model for a rainbow trout pathogen (Yersinia ruckeri) at Leetown, West Virginia, and developed and applied for U.S. patents on fish vaccines against the fish pathogens, Flavobacterium columnare, Edwardsiella tarda, and Streptococcus agalactiae at Auburn, Alabama.


IMPACT/OUTCOME:  These health management accomplishments will reduce the risk of losses from diseases and improve profitability of warm and cold water aquaculture.


ACCOMPLISHMENTS:  ARS researchers developed a technique for measuring the palatability of shrimp feeds needed to implement the use of plant protein sources in their diets at Hilo, Hawaii.  Also, scientists showed that poultry byproduct meal supplemented with two amino acids could replace fish meal in diets for hybrid striped bass at Stuttgart, Arkansas.


IMPACT/OUTCOME:  This research will help demonstrate the feasibility of replacing fishmeal in aquaculture diets.  Replacing fishmeal in aquaculture feeds improves the sustainability of aquaculture and reduces the cost of the feed.


ACCOMPLISHMENTS:  ARS showed that stressing pregnant sows carried over to their off-spring an altered physiology, demonstrated that dopamine and serotonin are useful indicators of stress in chicken genetic improvement, and demonstrated an alterative to forced molting (feed removal).  A patent application is being pursued at West Lafayette, Indiana.


IMPACT/OUTCOME:  This information provides livestock producers with methods for reducing stress in swine and chickens.


Performance Measure 1.2.2:    Develop needed information on the relationships between nutrients, reproduction, growth, and conversion to and marketability of animal products.




During FY 2004, ARS will


identify underlying genetic and physiologic mechanisms impacting reproductive efficiency, nutrient conversion, and growth in food animals.


ACCOMPLISHMENTS:  Research work conducted in the Breeding and Genetics Unit at the U.S. Meat Animal Research Center, Clay Center, Nebraska, has determined that variation in the thyroxine-binding globulin gene causes a 30 to 40 percent reduction in the size of the mature testes with a concomitant reduction in average backfat thickness. 


IMPACT/OUTCOME:  This discovery has identified a new biochemical pathway regulating testes size, a trait that is directly related to the number of sperm cells that a boar produces in a day.  Since the swine industry relies heavily upon artificial insemination, maximizing the number of sperm cells produced daily by a boar will minimize the number of boars required in boar studs.


ACCOMPLISHMENTS:  Research conducted by ARS scientists at Athens, Georgia, is seeking to understand the functional relationships between the numerous proteins associated with the growth and development of fat tissue in pigs.  Over 30 genes that code secreted proteins were reported for the first time in pig adipose tissue including agouti, nerve growth factor, several interleukins, brain derived neurotrophic factor, and IFNA2. 


IMPACT/OUTCOME:  One of the major goals of swine improvement is to change the proportion of lean to fat content of pork while maintaining eating quality.  This information provides a better understanding of the molecular mechanisms controlling fat tissue secretory function that in turn provides opportunities for genetic improvement in body composition.


ACCOMPLISHMENTS:  ARS completed two early growth evaluations of five different genetic stocks of North American Atlantic Salmon at Franklin, Maine; established broodyear lines of top performing families of rainbow trout for breeding at Leetown, West Virginia, and Hagerman, Idaho; and refined the protocols to produce all reproductively-sterile rainbow trout at Leetown.


IMPACT/OUTCOME:  These accomplishments increase the probability of improving the economically important traits for farmed salmonids, and provide a method to nearly eliminate risk of escapes to the environment.


ACCOMPLISHMENTS:  ARS conducted aquaculture research on the mechanisms of stress response and performance, important information on fish health.


IMPACT/OUTCOME:  This knowledge will be used to develop superior genetic lines of fish, effective nutrient conversion, and health management and production systems to reduce operating costs.


ACCOMPLISHMENTS:  ARS developed a technology for artificial insemination spawning of southern flounder and pompano at Stuttgart, Arkansas.


IMPACT/OUTCOME:  This technology is critical for making fingerlings available to producers.


develop technologies leading to improved marketability of animal products.


ACCOMPLISHMENTS:  Retail yield of beef carcasses in the beef industry is predicted through the assignment of a visually determined yield grade by a USDA official grader prior to carcass fabrication.  Due to the inherent subjectivity of this system, ARS researchers at Clay Center, Nebraska, in collaboration with the National Cattlemen’s Beef Association and Tyson Fresh Meats, have developed an image analysis system for use on-line in commercial packing plants to predict boneless, closely trimmed sub-primal cutout yields. 


IMPACT/OUTCOME:  One of the targeted areas to increase production efficiency in the beef industry is improved lean retail yield of carcasses.  Application of this on-line instrument allows more objective and accurate prediction of beef retail yield under commercial conditions.  Two of the four major beef processors have now implemented this system with others considering it for future implementation.


ACCOMPLISHMENTS:  ARS scientists demonstrated that a previously thought harmless alga caused fish kills.  They developed a management remedy at Stoneville, Mississippi.


IMPACT/OUTCOME:  The management remedy was communicated to fish farmers; has the potential for saving thousands of dollars in losses.


ACCOMPLISHMENTS:  ARS identified a natural algicide in laboratory screening.  Tests in field evaluations confirmed its capability to control algae-related off favors in catfish.


IMPACT/OUTCOME:  A U.S. patent application has been filed, and a Cooperative Research and Development partner has been identified to commercialize the discovery.  The product has the potential to be more economical and environmentally sound than the two provisional controls being used.


Performance Measure 1.2.3:      Identify genes responsible for economically important traits, including animal product quality, efficiency of nutrient utilization, and environmental adaptability.




During FY 2004, ARS will


identify genes and their function leading to DNA tests for use in food animal genetic improvement programs.


ACCOMPLISHMENTS:  Advances in cattle genomics have enabled scientists to identify genes affecting a wide array of traits of economic importance (so-called Quantitative Trait Loci (QTL)).  ARS researchers at Beltsville, Maryland, working collaboratively with scientists at the University of Illinois, have recently reported the first QTL detected affecting the pregnancy rate in U.S. holstein germplasm.  Additional QTLs were also detected for somatic cell score, an indicator of mastitis incidence.


IMPACT/OUTCOME:  One of the most critical issues facing the U.S. dairy industry is a decline in fertility, thought to be associated with a gradual accumulation of in-breeding depression over the past forty-five years, largely due to widespread use of genetically superior sires through artificial insemination.  Discovery of these QTLs will lead to improved efficiency of genetic selection for fertility traits in dairy and beef cattle. 


ACCOMPLISHMENTS:  Swine and beef reproduction research over the past 20 years at the U.S. Meat Animal Research Center, Clay Center, Nebraska, has been focused on identification of physiological mechanisms contributing to increased reproductive capacity.  Researchers have validated that a previously identified genetic marker for the pig erythropoieten receptor gene is associated with a two to three pig difference in ultimate litter size, and for the first time, two QTLs for male reproductive traits in cattle (testes size and follicle stimulating hormone). 


IMPACT/OUTCOME:  One of the primary selection criteria in genetic improvement programs in the livestock industry is reproductive rate.  By increasing the total production per female in the breeding herd, profitability is enhanced significantly for the individual producer through increased output over static fixed costs.  Identification of these QTLs will lead to enhanced efficiency of genetic improvement programs for reproductive rates in swine and cattle germplasm.


ACCOMPLISHMENTS:  Research in the Growth Biology Laboratory at Beltsville, Maryland, has involved the study of the chicken proglucagon gene that produces five different peptide hormones functioning in tissue growth, gastrointestinal function, regulation of insulin and blood glucose levels, and appetite control.  This work has recently led to the cloning and sequencing of the gene, and to the identification of four distinct protein transcripts produced by this one gene through alternative splicing and alternate promoter usage.  The types and levels of specific proglucagon transcripts were determined in pancreatic, intestinal, and brain tissues collected from chickens that had been deprived of feed and/or refed to induce changes in energy status. 


IMPACT/OUTCOME:  Development of a more complete understanding of the biological mechanisms regulating feed intake in poultry and livestock is needed in order to better tailor production systems to available genetic lines to improve production efficiency.  This research provides new information necessary to understand how the peptide hormones are produced and what impact changes in the expression of this gene might have on glucose metabolism and appetite regulation in poultry.


ACCOMPLISHMENTS:  ARS researchers identified genes expressed in rainbow trout oocyte using a successfully constructed cDNA library from rainbow trout oocyte, identified immune genes of rainbow trout, and identified genes that expressed calpain protein in rainbow trout.  They also identified genes expressing toll-like receptors believed to be involved in disease resistance of catfish.  Insulin–like growth factors I and II showed promise as markers for selection of channel catfish broodstock for superior growth.


IMPACT/OUTCOME:  Gene identification and marker development are important steps in integrating molecular technology and genetic selection in breeding of superior performing fish.


ACCOMPLISHMENTS:  ARS was issued a patent for a diagnostic test to detect bacterial kidney disease in rainbow trout at Aberdeen, Idaho.


IMPACT/OUTCOME:  This diagnostic test will be commercialized and useful to trout producers in identifying sick fish.


develop genomics infrastructure and tools that will enhance efficiency and speed of gene identification, and utilization of DNA data in genetic improvement programs of food animals.


ACCOMPLISHMENTS:  ARS researchers at the U.S. Meat Animal Research Center have:  1) added 800 genes to the integrated bovine map via single nucleotide polymorphism (SNP) mapping in introns; 2) increased the number of microsatellite markers in the bovine linkage map from 1,500 to 3,800; 3) deposited 680 sheep, 4,429 cattle, and 5,445 swine SNPs in the public database, GenBank, at NCBI (prior to these submissions no more than 100 SNP had been deposited for any of the species); 4) deposited 13,922 bovine and 65,866 porcine expressed sequence tags (ESTs) in GenBank; 5) developed a set of 14,000 ESTs with unique 3-prime end sequences for use in developing a commercial cattle microarray; and 6) developed and tested a pipeline for identification, complete sequencing, and annotation of full-length cDNA clones for livestock genes through which 500 bovine full length cDNAs were identified.


IMPACT/OUTCOME:  2004 was a milestone year in livestock genomics with the completion of the chicken genome sequence and the release of the first draft of the bovine genome sequence.  ARS research has laid much of the path for this development and in the past year has significantly enhanced the information contained in the livestock genetic maps. These tools are enabling the more rapid discovery of genes and their functions, required to build genomic tools to improve production efficiency, animal health, and well-being of beef and dairy cattle, swine, and sheep.


ACCOMPLISHMENTS:  When the first case of BSE, more commonly referred to as “mad cow disease,” was reported in Washington State in December of 2003, it became one of the first major applications of genomic technology in providing a valuable and rapid solution in a crisis situation in animal agriculture.  Records identified the sire and other relatives of the BSE index case and their tissues were available for genetic analyses.  ARS scientists at Clay Center, Nebraska, used a panel of single nucleotide polymorphism DNA markers, under development for animal identification, to quickly verify the pedigree of the affected cow, which was traced back to a Canadian origin.    


IMPACT/OUTCOME:  Using this genotyping test, scientific evidence was made available to show that the affected animal was one of a group of 81 females that had crossed the U.S. border from Canada several years earlier.  This provided the missing link in the traceability of this female to verify that she was born prior to the 1997 implementation of a full ban on animal protein feeding in Canada.


ACCOMPLISHMENTS:  Research conducted in the ARS Bovine Functional Genomics Laboratory at Beltsville, Maryland, has resulted in the development of bioinformatic software called EST-PAGE.  It allows researchers to easily process large volumes of data on ESTs and more importantly, to submit their data to the public databases for worldwide application and use. 


IMPACT/OUTCOME:  The volume of data being generated from analysis of DNA sequence and downstream applications in functional genomics and proteomics research is growing exponentially as the genomes of the major livestock species are being added to the sequence infrastructure.  This software will facilitate ease of transfer and access to such data by researchers worldwide working across many species, especially the 25 groups around the world who have already requested and received the source code.


ACCOMPLISHMENTS:  A new normalized cDNA library has been synthesized from lactating dairy cow and calf intestinal tissue to facilitate gene discovery in ruminant metabolism by researchers at Beltsville, Maryland.  The library, called 8BOV, has been synthesized, sequenced, and characterized.  It is having a direct impact as evidenced by the 19,110 new ESTs which have now been deposited in the public database GenBank.  A total of 1,123 sequence elements from the ESTs represent genes encoding proteins in other animal systems that can now be exploited in the bovine.


IMPACT/OUTCOME:  The production of meat, milk, and wool products is considered to be relatively inefficient due to the fact that upwards of two-thirds of the input costs are expended for feed energy required for maintenance of body tissues largely attributable to energy expended by the visceral tissues (liver and gut).  This library will facilitate the search for specific metabolic pathways, transporters, growth factor receptors, and growth factors that have profound effects on ruminant visceral energy and protein metabolism, paving the way for improvements through precision management and genetics.


ACCOMPLISHMENTS:  ARS characterized a rainbow trout bacterial artificial base chromosome library made up of about 135,000 base pair DNA segments for use in constructing physical maps.  Subsequent sequencing evaluations and measures of stress are being studied for use in development of biomarkers and strategies to manage disease.


IMPACT/OUTCOME:  This accomplishment has great potential to expedite the genetic improvement and production efficiency of rainbow trout.


Performance Measure 1.2.4:    Maintain, characterize, and use genetic resources to optimize and safeguard genetic diversity and promote viable, vigorous animal production systems.




During FY 2004, ARS will


continue to characterize germplasm of food animals for traits of importance.


ACCOMPLISHMENTS:  ARS scientists at Miles City, Montana, have been working for a number of years to develop a framework for application of selection indexes in the beef cattle seedstock industry.  In the past year, selection indexes based on this research were made available to the American International Charolais Association, American Hereford Association, American Simmental Association, North American Limousin Foundation, the Angus Sire Alliance, and the South African Agricultural Research Council.


IMPACT/OUTCOME:  Genetic improvement programs in the beef cattle industry are complex due to the need to select a wide array of performance criteria.  This research enables beef cattle breeders to use an optimal approach to genetic improvement where breeding values for a variety of economically important traits are appropriately weighted according to their economic value, genetic variation, and genetic relationships into an aggregate “overall” index breeding value.


ACCOMPLISHMENTS:  The beef cattle industry has widely capitalized upon the characterization of germplasm representing 34 breeds through the Germplasm Evaluation Project conducted at the U.S. Meat Animal Research Center.  Results from the project provided evidence that the genetic variation observed amongst Continental European and British breeds for growth performance has significantly decreased over the past decade.   


IMPACT/OUTCOME:  These results are critically important to beef cattle breeders as they design selection objectives within breeds and crossbreeding systems using multiple breeds to make genetic improvement.


ACCOMPLISHMENTS:  Research conducted at the U.S. Meat Animal Research Center, Clay Center, Nebraska, has concluded that ewes sired by Romanov rams were 59 percent more productive than ewes sired by traditional sheep breeds used for out of season breeding (Dorset and Finnsheep).  Greater use of Romanov-crossbred ewes in maternal roles of terminal crossbreeding systems would contribute to enhanced profitability of sheep production.


IMPACT/OUTCOME:  Length of seasonal fertility largely determines the effectiveness of accelerated lambing systems and annual systems that breed females in the spring of the year.  Efficiency of commercial sheep production could be markedly improved through the use of Romanov germplasm in maternal line development to enhance seasonal fertility. 


ACCOMPLISHMENTS:  ARS researchers at Leetown, West Virginia, determined that the performance of domesticated strains of rainbow trout were not different in flow-through versus recirculation systems.  Also, researchers at Stoneville, Mississippi, demonstrated with performance evaluations of blue catfish and blue x channel catfish crosses the benefits of improved growth and survival.


IMPACT/OUTCOME:  This information was made available to fish producers to aid in their decisions about which strains or lines of fish to grow.


ACCOMPLISHMENTS:  ARS researchers developed a large scale facility for genetic evaluation of oysters.  They established a collaborative genetic project to reduce cadmium in oysters, a long-term objective toward breeding improved oysters for the Pacific Coast.


IMPACT/OUTCOME:  The large scale rearing facility will enable more rapid progress of the genetic selection project.  A discriminatory factor in international trade will be eliminated for Pacific Coast oysters, if a trait for lower cadmium is found.


improve cryopreservation technology for storage of animal germplasm and continue to increase the stocks of germplasm stored within the National Animal Germplasm Program repository.


ACCOMPLISHMENTS:  The National Animal Germplasm Program, located at Fort Collins, Colorado, was formally established in 1999 to better protect the U.S. livestock industry.  The number of germplasm and tissue samples in the collection was increased by 114 percent and the number of breeds represented by 50 percent in the past year.  This growth is far ahead of original plans and expectations.  Two breeds of dairy cattle, four lines of chickens, and one line of pigs were increased to a level considered as secure in the collection.  Additionally, six important fish species were added to the collection for the first time.


IMPACT/OUTCOME:  Breeding populations of livestock have narrowed considerably in their genetic diversity over the past several decades prompting concerns regarding adequate levels of genetic variability and biosecurity.  This progress provides increased security of farm animal genetic resources and maintenance of animal genetic variation.


ACCOMPLISHMENTS:  Scientists in the ARS Biotechnology and Germplasm Laboratory at Beltsville, Maryland, have exploited the recent release of the chicken genome sequence applying proteomics techniques to identify 40 proteins that are expressed in the turkey sperm storage tubule epithelium.  Four proteins were uniquely expressed when sperm were absent while three additional proteins were only expressed when sperm were present. 


IMPACT/OUTCOME:  The commercial turkey industry relies exclusively on artificial insemination (AI) for production.  Due to low success of cryopreservation of semen, these AI procedures rely on the use of fresh semen, which requires costly maintenance of male populations on production farms.  A unique aspect of turkeys is that they have the ability to store live sperm in the oviduct of the hen for extended periods of time in sperm storage tubules.  These results are the first step in identifying novel proteins for maintenance of poultry sperm viability and provide one of the first examples of the power of having a whole genome sequence available from the chicken.


ACCOMPLISHMENTS:  ARS confirmed that ghrelin, a hormone involved with growth and feed intake in terrestrial animals was in rainbow trout, tilapia, and catfish.  It was identified as a new regulatory pathway for controlling growth hormone secretion.  Researchers found that feed efficiency of groups of related fish was adequately large to use in improving performance.


IMPACT/OUTCOME:  These accomplishments will be used for developing more efficient strains of finfish for aquaculture.


Performance Measure 1.2.5:    Provide producers with scientific information and technology that increase production efficiency, safeguard the environment, and reduce production risks and product losses.




During FY 2004, ARS will


develop technologies and strategies to manage or mitigate pests, pathogens, weather damage, and/or improve crop quality to strengthen the U.S. agricultural production base and provide higher value products.


ACCOMPLISHMENTS:  Demonstrated that post-plant application of a hydrophobic kaolin clay mulch provided excellent weed control during the establishment year of blackberries with no adverse effects.


IMPACT/OUTCOME:  An environmentally safe and economical weed management technique for small fruit and horticultural crops was identified.


ACCOMPLISHMENTS:  Papaya and plum trees have been genetically engineered to resist virus pathogens (papaya ring spot virus and plum pox virus) that otherwise threaten to eliminate the production of these fruits.  In both cases there is no other known method available to generate resistance to these devastating diseases.


IMPACT/OUTCOME:  The resistant papaya tree has restored papaya production in Hawaii to pre-disease levels, and ARS (Hilo, Hawaii) is cooperating with scientists from many other countries to develop their own locally adapted resistant varieties of this fruit, a dietary staple with excellent nutritional value in much of the tropical world.  The pox-resistant plum variety developed by ARS (Kearneysville, West Virginia) is undergoing biosafety evaluations, and when approved for distribution, will provide the only source of virus resistance for fruit breeders.


ACCOMPLISHMENTS:  ARS scientists at Raleigh, North Carolina, have led a cooperative project to develop high yielding soybeans with low phytate content.  When plants were grown with excess phosphorus, seed phytate concentrations in normal soybeans doubled whereas levels in the low phytate line remained constant.  This result led to the discovery that two different genes control phytate concentration in soybeans.


IMPACT/OUTCOME:  In southern States, there are many large poultry and swine feeding facilities which are sources of phosphorus pollution from livestock waste.  Soybeans that are naturally low in phytate (a major cause of phosphorus in animal wastes) are a great advantage in reducing pollution.  The new information makes it possible to devise efficient plant breeding methods to transfer the low phytate genes to soybean varieties.


ACCOMPLISHMENTS:  ARS scientists at Beaumont, Texas, have developed “Neches,” a new sweet or waxy rice cultivar.  The rice can be used as dessert rice and has novel starch and flour properties.  ARS researchers at Lincoln, Nebraska, in cooperation with the University of Nebraska have released two new hard white winter wheat varieties for Asian noodles.


IMPACT/OUTCOME:  These new varieties will help diversity and expand markets for U.S. producers.


ACCOMPLISHMENTS:  ARS researchers at Mississippi State, Mississippi, have identified new molecular markers for aflatoxin resistance and released an inbred line of corn with improved aflatoxin resistance.  ARS scientists at Raleigh, North Carolina, discovered that resistance to fumonisin contamination is highly heritable and linked with ear rot resistance. 


IMPACT/OUTCOME:  Contamination of corn grain with mycotoxins (aflatoxin and fumonisin) can cause food safety problems and major losses to U.S. corn producers.  These new genetic resources will expedite the transfer of fungal mycotoxin resistance into superior corn hybrids for U.S. producers.


maintain genetic and genomic databases and make information accessible via standard software from the Internet.


ACCOMPLISHMENTS:  ARS researchers at Albany, California, and Ithaca, New York, have developed a new web site, “GrainGenes 2.0.”  Large scale genomics and genetic data are provided to cereal researchers from this web site along with new bioinformatics software tools and genetic mapping information.


IMPACT/OUTCOME:  This central site ensures that the most recent genetics and genomics discoveries are rapidly deployed to wheat, barley, and oats genetic improvement programs.


Performance Measure 1.2.6:    Improve the understanding of the biological mechanisms that influence plant growth, product quality, and marketability to enhance the competitive advantage of agricultural commodities.




During FY 2004, ARS will


describe in model plants and crop plants the structure, function, and regulation of agriculturally important genes that control plant composition and yield.


ACCOMPLISHMENTS:  ARS scientists in Columbia, Missouri, have identified three soybean genes that control the enzymes that are responsible for linolenic acid production.  Two of these genes have mutations, bringing the total number to five mutant alleles.  The mutations in four of these genes are the result of single nucleotide changes, and a fifth allele actually has lost a significant part of its sequence, a natural genomic deletion.


IMPACT/OUTCOME:  This information enables the construction of very specific molecular markers that will facilitate the selection of very low linolenic acid germplasm from breeding populations.  Genetic reduction of linolenic acid in soybean oil is a major step that enables the manufacture of more healthful foods with low levels of ‘trans’ isomers.


ACCOMPLISHMENTS:  All aspects of plant biology hinge on their ability to perceive light.  Phytochrome is the major light receptor for plants.  ARS scientists at the Plant Gene Expression Center in Albany, California, have discovered genes that control the process called “phytochrome signaling.”  This gene encodes an intermediate signal that regulates red light induced changes in seedling growth (photomorphogenesis), by functioning as the central circadian oscillator of the plant biological clock.


IMPACT/OUTCOME:  The research may provide insight into the molecular mechanism by which light controls agriculturally relevant responses, such as floral induction.


ACCOMPLISHMENTS:  ARS scientists at Lubbock, Texas, have mapped a gene that is essential for signaling cold stress in plants.  At Raleigh, North Carolina, ARS scientists have developed methods to isolate specialized cells in winter wheat seedlings that survive extreme freezing temperatures.  Those cells can now be used to identify genes that confer freezing tolerance in winter wheat.  Scientists at the University of California, Davis, and ARS scientists at Albany, California, have identified the “vernalization” gene, which ensures that wheat plants will not flower and form grain until the greatest danger of killer frosts has passed. The ARS scientists successfully inserted the gene into wheat plants to test its effect, proving the essential role of the gene in freezing protection. 

IMPACT/OUTCOME:  Winterkill and cold temperatures cause major losses every year to horticultural plants and field crops.  These studies advance the science of freezing protection and identifying genes and methods that can be used to improve crop resistance.


ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland; Ithaca, New York; and Albany, California, are characterizing the effects of genetic engineering on plant metabolism and environmental fitness and developing methods to reduce or eliminate identified risks.  Targets include changes in plant metabolic competency, spread of transgenes to sites where they are unwanted, and limiting expression of transgenes to non-harvested plant parts.


IMPACT/OUTCOME:  As a result of the research, we will be able to identify the risks associated with genetic engineering that need to be prevented or ameliorated.  The data is essential to regulatory agencies charged with oversight of agricultural biotechnology.  Consumers in the United States and in overseas marketplaces must have confidence in the genetically engineered products from U.S. agriculture.


improve plant genetic transformation systems to expand their usefulness and improve exploitation of genome sequence information to identify valuable genes in raw germplasm collections.


ACCOMPLISHMENTS:  Scientists at the USDA-ARS Plant Gene Expression Center, Albany, California, have developed a strategy that will help prevent gene spread from genetically engineered crops.  The revised strategy incorporates three site specific recombination systems, one to insert the DNA precisely into the plant genome, a second to remove selectable markers (such as antibiotic resistance genes), and a third to remove transgenic DNA from pollen.


IMPACT/OUTCOME:  The three systems, when working together, will provide an unprecedented level of control over the potential environmental spread of transgenic DNA, one of the chief concerns voiced repeatedly by consumers.


ACCOMPLISHMENTS:  ARS scientists within the Plant Stress and Germplasm Development Unit in Lubbock, Texas, have identified a novel gene that is essential for heat tolerance in plants.  This finding advances ARS’ understanding of how cellular components impact the expression of heat tolerance.  The scientists used positional cloning to map the mutated gene within the thermo-sensitive mutant AtTS244.


IMPACT/OUTCOME:  Plant productivity in arid climates often is reduced by temperature stress.  This discovery will improve the ability to develop more heat tolerant crops.


ACCOMPLISHMENTS:  Identified the true sex pheromone of the female dogwood borer, an increasingly important wood-boring pest of apple, and developed pheromone lures for the capture of male moths.


IMPACT/OUTCOME:  A technology for mating disruption was identified that could control the pest insect of apples and reduce or eliminate the need for use of insecticides.


Performance Measure 1.2.7:    Identify genes responsible for plant product quality and resistance to diseases, pests, and weather losses.




During FY 2004, ARS will


develop new genetic methods and tools to identify specific genes that affect end-product traits desired by consumers, such as oil and grain quality, disease resistance, and stress tolerance in agricultural crops.


ACCOMPLISHMENTS:  ARS scientists are very active in identifying, characterizing, and transferring genes that provide resistance to pests and pathogens, combining modern genomic methods with traditional breeding, for use in developing resistant crop varieties.  Examples include:  resistance to reniform nematode in cotton (College Station, Texas; and Mississippi State, Mississippi); resistance to soybean cyst nematode (Beltsville, Maryland); resistance to Fusarium wilt in cotton (Shafter, California); resistance to soybean rust (national multi-location cooperative effort); resistance to Aspergillus flavus in cotton (New Orleans, Louisiana), corn (Mississippi State, Mississippi), and peanut (Tifton, Georgia); and resistance to Fusarium head blight in grains (Fargo, North Dakota; St. Paul, Minnesota; and Madison, Wisconsin).


IMPACT/OUTCOME:  Resistance genes, many of which are very difficult to transfer, will be the basis for improving resistance to pests and pathogens, thereby enhancing yields and quality, reducing dependence on pesticides, and improving profitability and sustainability of U.S. agriculture. 


ACCOMPLISHMENTS:  ARS researchers at Columbia, Missouri, have provided the majority of the molecular marker resources for trait mapping in corn.  More recently, these scientists, along with scientists at the University of Wisconsin and University of California, Irvine, have developed a new genomic approach to identify genes that control agronomic traits.


IMPACT/OUTCOME:  A major constraint for crop breeders is limited knowledge concerning which genes control valuable traits.  This new approach was developed to make breeding more efficient in selecting genes.  For the first time, it is now possible to exploit corn genomic discoveries to facilitate more targeted, efficient corn improvement.


ACCOMPLISHMENTS:  Genetic diversity in agricultural crops is thought to decline during their evolution from wild species to modern land races, and even more rapidly as man has selected elite cultivars from the land races for commercial production.  Recent findings by ARS scientists at Beltsville, Maryland, have shown that the loss of genetic diversity in the modern soybean genome was much less rapid than in maize or even Arabidopsis.  The decline in genetic diversity was significantly more rapid in wild soybean (the progenitor of cultivated soybean) versus unimproved cultivated soybean germplasm, typical of that in the USDA Soybean Germplasm Collection.


IMPACT/OUTCOME:  This unexpected discovery suggests that genetic association analysis using whole genome scans may be feasible for gene or QTL discovery.  This approach is based on the first application of “linkage disequilibrium” theory in a self-fertilized crop species, such as soybean, and suggests the possibility of a much more efficient approach to discover genes or QTL in the soybean germplasm collections, such as that maintained by the USDA.


ACCOMPLISHMENTS:  ARS researchers at Phoenix, Arizona, have bred Lequerella to improve seed oil content, harvest index, and seed yield.  A new germplasm line is being released this year with 33 percent oil content compared to 29 percent from the previously released line.  The new line provides high genetic diversity for future improvements to public and private researchers, and is an alternative domestic source of hydroxy fatty acids presently filled by imported castor.  Hybrid Lesquerella lines now produce above 80 percent hydroxyl fatty acid compared to 56 percent from non-hybrids.  These are significantly improved over the best lines available and will result in significantly lowering the cost for industrial use.


IMPACT/OUTCOME:  This research is being accelerated with the development of 20 single sequence repeat (SSR) molecular markers.  These tools will enable marker assisted selection for traits, such as high hydroxy fatty acids, improved oil content, and other yield related traits.  Lower oil costs for products, such as biodegradable motor oils, are needed to improve chances for commercialization of lesquerella.


ACCOMPLISHMENTS:  ARS scientists in Stillwater, Oklahoma, discovered new sources of genetic resistance to the bird cherry-oat aphid, a perennial pest of wheat.  Purdue scientists and ARS researchers at West Lafayette, Indiana, developed wheat lines that are resistant to barley and cereal yellow dwarf virus.  ARS scientists at Aberdeen, Idaho, and Stillwater, Oklahoma, developed a new barley variety, “Burton,” that is resistant to Russian wheat aphid.


IMPACT/OUTCOME:  Insects and diseases cause major losses to the U.S. wheat and barley industry.  These new lines and varieties will help U.S. producers combat serious pest and disease threats.


construct and maintain physical, genetic, and transcript maps to facilitate comparative analyses among plant genomes.


ACCOMPLISHMENTS:  ARS scientists at Fargo, North Dakota, constructed a gene linkage map with a set of 129 recombinant inbred lines (RILs) derived from the cross of 83HR4 x RHA345.  Linkage maps are desirable for the rapid location of genes governing simple and complex phenotypes or quantitative trait loci (QTLs), and for the development of DNA markers for marker-assisted breeding.  DNA samples were prepared in collaboration with A. Berville in France.  The linkage map consisted of 160 markers in 17 linkage groups plus four pairs of linked markers, and covered a total length of 1,140 centiMorgans (cM) with an average interval of 9 cM between two markers.


IMPACT/OUTCOME:  This map will be useful to define the QTLs affecting oleic acid composition in the sunflower seed oil.


ACCOMPLISHMENTS:  ARS scientists at Ames, Iowa, have developed techniques that help sort DNA fragments or ESTs.  These fragments were used to identify members of gene families and define locus defining polymporphisms that distinguish each family member.  This was followed by the identification of SNPs (alleles) between homologs in the germplasm used to construct the EST libraries.  In addition, bioinformatic software was developed to help position genes (gene ontology).  Analyses of BAC-end sequences from genetically anchored loci also provided insight into the structure and organization of the soybean genome.  BLAST analysis using BAC-end sequences revealed microsynteny between Medicago truncatual and Arabidopsis thaliana.


IMPACT/OUTCOME:  The soybean genome is composed of two duplicated sets of chromosomes.  This makes reassembly and assignment of gene sequences to the correct chromosome very difficult.  Statistical modeling of redundant BAC ‘hits’ using mapped genetic markers indicated that most soybean genes will be found in approximately 25 percent of the genome, thus making genome sequencing in soybean much more manageable and providing clues to the sequencing strategy that will save millions of dollars in sequencing costs.


ACCOMPLISHMENTS:  Relatively few breeding lines have been used in the parentage of most modern soybean varieties in commercial production.  This “narrow genetic” base does not take advantage of the great genetic diversity that exists in the soybean germplasm collection.  ARS scientists at Urbana, Illinois, have demonstrated the value of these “untapped” genes.  Four new quantitative trait loci (QTL) associated with high protein concentrations have been mapped in populations derived from three exotic sources of high protein.  Five of six putative QTLs associated with soybean seed yield were confirmed, two near isogenic line populations.  The favorable alleles at these QTLs were originally derived from exotic germplasm.


IMPACT/OUTCOME:  In the near isogenic populations the yield increases per QTL ranged from 2.9 to 4.5 bushels per acre.  A new germplasm release, LG00-3372, was the highest yielding entry in Uniform Preliminary Test IIIB in 2003.  This line is a selection from the cross of two Chinese varieties, Hui nan zi hua he jia (PI 561319A) x Fen dou 31 (PI 574477); and the pedigree is 87 percent exotic germplasm. 


Performance Measure 1.2.8:    Maintain, characterize, and use genetic resources to optimize, safeguard, and enhance genetic diversity and promote viable and vigorous plant production systems.




During FY 2004, ARS will


identify, acquire, and expand the genetic base of crops through new accessories to enhance the diversity of plant germplasm collections.


ACCOMPLISHMENTS:  The 20+ genebanks in the USDA/ARS National Plant Germplasm System (NPGS) now conserve 460,000 separate samples of over 10,700 plant species.  During the last few years, scientific interest in this germplasm has increased significantly, with more than 130,000 samples distributed last year to requesters worldwide. 


IMPACT/OUTCOME:  These materials are key to enabling continued progress in crop genetics and breeding, requisite for future food security.


ACCOMPLISHMENTS:  ARS scientists at Cold Spring Harbor Laboratory, New York, improved bioinformatic tools for comparing the genomic structure of corn and rice.  Also, they incorporated sorghum and wheat “physical maps” into the grain genome database, Gramene.


IMPACT/OUTCOME:  These advances furnish new, more powerful bioinformatic/database tools for accelerating progress in understanding the detailed genetic structure of grain genomes.  The new insights gained may aid grain crop genetic improvement.


ACCOMPLISHMENTS:  ARS scientists at Ithaca, New York, successfully applied a new statistical genetic approach, termed “association mapping,” to characterizing the genetic control of starch and protein quality in maize.  They identified new genes and alleles associated with starch pasting quality, starch to protein ratios, starch content, and the interaction of those genes with environmental variability.


IMPACT/OUTCOME:  Not only was this a successful proof-of-concept for a new method, it also identified new genes potentially valuable for breeding corn tailored to meeting specific agronomic and industrial needs.


strengthen breeding and evaluating of minor agronomic crops that have increasing economic importance.


ACCOMPLISHMENTS:  ARS scientists at College Station, Texas, established in Louisiana an innovative plantation of pecan seedstocks selected for their combined horticultural and forestry merit. 


IMPACT/OUTCOME:  The research results in the first long-term pecan test system focused on pecan genetic improvement in a major U.S. production area and on the development of large-scale pecan production systems that simultaneously improve wildlife habitat and harvest yield.


ACCOMPLISHMENTS:  Scientists at ARS genebanks developed and/or applied new genetic markers, called “SSRs,” to a broad spectrum of crops, such as peanuts, citrus, grapes, tropical legumes, mangoes, paspalum, tropical ornamental bulbs, blueberries, and hazelnuts.  They developed a means for assaying genetic variability in DNA rapidly and inexpensively. 


IMPACT/OUTCOME:  The markers are molecular tools potentially useful for accelerating progress in crop genetic resource conservation and breeding.


ACCOMPLISHMENTS:  Developed techniques to effectively identify watercore and mealiness in apples by using spectral reflection of near infrared frequencies.


IMPACT/OUTCOME:  The new technology that was developed could form the basis for sorting and removing defective apples.




The major thrusts of ARS’ mission are to conduct research that:  ensures high quality, safe food and other agricultural products; assesses the nutritional needs of Americans; sustains a competitive agricultural economy; and enhances the natural resource base and the environment.  In carrying out these research functions, ARS provides economic opportunities for rural citizens, communities, and society as a whole.  While ARS research has a large and very positive impact on rural America, the Agency has chosen to organize its research programs around the other four programmatic USDA/REE/ARS Strategic Plan goals.


Goal 3



Analysis of Results:  This goal is related to food safety and the security of the U.S. agricultural production system (crop and livestock protection).  Under Goal 3, 17 Indicators are aligned under 8 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2004.  Forty-four significant accomplishments are reported below.


OBJECTIVE 3.1:  Provide Science-Based Knowledge on the Safe Production, Storage, Processing, and Handling of Plant and Animal Products and on the Detection and Control of Toxin-Producing and/or Pathogenic Bacteria and Fungi Parasites, Mycotoxins, Chemical Residues, and Plant Toxins So As To Assist Regulatory Agencies and the Food Industry in Reducing the Incidence of Foodborne Illnesses.


Performance Measure 3.1.1:      Develop new on-farm preharvest systems, practices, and products to reduce pathogen and toxin contamination of animal- and plant-derived foods.




During FY 2004, ARS will


using new detection and quantitation methodologies, including genomic technologies, and through the study of epidemiology, ecology and host pathogen relationships, intervention strategies, and antibiotic resistance in food producing animals, develop practices, products, and information that will reduce preharvest pathogen and toxic residue contamination of animal-derived food products.  Ensure that these technologies can be utilized by regulatory agencies and/or producers to help assure safe food products.


ACCOMPLISHMENTS:  If food safety pathogens are both antibiotic resistant and also hyperinvasive, they can easily make animals sick and pose an exceedingly dangerous public health threat.  ARS scientists at Ames, Iowa, demonstrated that rumen protozoa can engulf and hold viable bacterial pathogens, such as Salmonella, and that after surviving within rumen protozoa, the Salmonella were more invasive than other similar antibiotic sensitive Salmonella. 


IMPACT/OUTCOME:  Since rumen protozoa can be a reservoir for pathogens, they could be released during bouts of illness when acidic conditions kill the protozoa.  This provides another intervention point (protozoa) for eliminating a reservoir of foodborne pathogens, thus improving the safety of meat and dairy products. 


ACCOMPLISHMENTS:  An ARS laboratory in College Station, Texas, has developed very promising candidates to kill the human pathogen, E. coli O157:H7 in cattle, and significantly help prevent contamination of beef.  In studies to satisfy FDA requirements for human safety, ARS scientists at Fargo, North Dakota, used radio-labeled compounds to demonstrate that a large proportion of chlorate residues are converted to a non-toxic metabolite (chloride ion), and are present as natural products in edible tissues of cattle.  In an earlier stage of product development, ARS scientists at College Station, Texas, demonstrated that certain other chemicals called nitrocompounds also effectively kill pathogenic E. coli, and Salmonella. 


IMPACT/OUTCOME:  The work of these two ARS laboratories with two different chemicals will help provide cattle and swine industries with practical intervention strategies that eliminate foodborne pathogens from food producing animals.


ACCOMPLISHMENTS:  ARS scientists in College Station, Texas, in collaboration with English scientists, were able to stimulate certain cells in the chicken, called heterophils, to kill enteropathogenic bacteria in the chicken’s own gut.  This is a potentially new method for increasing resistance of birds to colonization by important food poisoning microorganisms, such as Salmonella and Campylobacter, and provides information essential for highly effective new vaccines.  This same laboratory with a broiler breeder industry partner identified new immunologically efficient lines of chickens resistant to bacterial colonization by enteropathogenic bacteria.


IMPACT/OUTCOME:  These birds possessing their own genetic bacterial resistance phenomena could provide a very efficient and cost-effective means of minimizing bird colonization by food poisoning bacteria that would greatly enhance poultry food safety. 


using new detection and quantitation methodologies, including genomic technologies, and through the study of crop fungal toxin relationships, production practices and expert systems, breeding targets for resistant crops, biocontrol technologies and chemical toxicity, develop practices, products, and information that will reduce preharvest fungal/toxin contamination of plant-derived food products.  Ensure that these technologies can be utilized by regulatory agencies and/or producers to help assure safe food products.


ACCOMPLISHMENTS:  To better understand the genetic pathways required for the formation of mycotoxins, such as aflatoxins and fumonisins, ARS scientists in Peoria, Illinois, and New Orleans, Louisiana, have continued to expand the scope of their Expressed Sequence Tag (EST) libraries of fungal genes in collaboration with The Institute for Genomic Research (TIGR). The fumonisin library consists of 86,400 individual sequences that most likely correspond to approximately 11,000 unique genes, while a 7,214 element aflatoxin EST gene microarray (a technique for measuring expression of genes in mass numbers) has been constructed to significantly speed the detection of fungal genes governing aflatoxin formation.  


IMPACT/OUTCOME:  These rapid bioassays are helping identify markers and inhibitors related to reproduction/survival, virulence, and toxin formation for the fungi that produce these mycotoxins.   Already ARS scientists at Albany, California, have conclusive evidence that gallic acid levels in aflatoxin resistant tree nut varieties increases with maturity and is maintained throughout the growing season, rather than declining as in more susceptible varieties.  This research will identify those fungal genes that can be targeted for controlling mycotoxin contamination through genetic engineering or marker assisted breeding of susceptible commercial crops, thus further protecting the public health.


ACCOMPLISHMENTS:  ARS scientists in Tuscon, Arizona, and Dawson, Georgia, have led the world in the successful development of atoxigenic strain technology to prevent aflatoxin from contaminating susceptible crops.  In Georgia, development of this technology for aflatoxin biocontrol in peanuts was licensed to Circle One Global as Afla-guard®, Inc. and received Section 3 registration in May 2004, from the EPA.


IMPACT/OUTCOME:  Approximately 50 tons of Afla-guard® was commercially applied to the 2004 peanut crop in Georgia and Alabama.  In Arizona, further development of atoxigenic strain technology with the previously registered product AF 36, continued in 2004, in collaboration with many industry partners.  Product application was made to nearly 30,000 acres of cotton including 5,000 acres in south Texas, and requests were made to EPA for Experimental Use Registrations providing for expanded application to cotton in southern California and pistachios in the central valley of California. Use of this technology will help keep harmful toxins out of the food supply.


ACCOMPLISHMENTS:  An ARS laboratory in Peoria, Illinois, developed rapid, easy to perform, quickly learned fluorescence polarization immunoassays for measuring the fumonisin and zeaaralonone mycotoxins in maize and deoxynivalenol in wheat.  The reagents and labware for this immunoassay are easy to use and easily obtained. 


IMPACT/OUTCOME:  The assays offer faster, environmentally friendly alternatives to traditional instrumental methods, and ELISAs (enzyme linked immunosorbent serologic assays).  They will be useful screening tools to determine mycotoxin contamination.  Since mycotoxins are unevenly distributed in any contaminated plant commodity, there is a great need for methodology to determine the contamination of a large volume of potentially contaminated grains.  These tests help fulfill that need.


Performance Measure 3.1.2:  Develop and transfer to Federal agencies and the private sector systems that rapidly and accurately detect, identify, and differentiate the most critical and economically important foodborne microbial pathogens.




During FY 2004, ARS will


develop innovative methods and advanced technology systems that: rapidly and accurately detect, identify, and differentiate the most critical and economically important foodborne contaminants, such as bacterial, viral, and protozoan pathogens; drug and chemical residues; and pathophysiological and processing surface contamination  Ensure that the technologies are transferred to the Food Safety Inspection Service (FSIS) and the Food and Drug Administration (FDA); the Department of Homeland Security; and industry for implementation into Hazard Analysis Critical Control Point (HACCP) programs, and Good Manufacturing Practice (GMP) protocols for both large and small producers and processors.


ACCOMPLISHMENTS:  ARS scientists at the Richard Russell Research Center, Athens, Georgia, designed and constructed a second generation prototype in-line, real-time, portable multispectral imaging system that can capture images of every poultry carcass on the processing line and detect fecal contamination at a rate greater than 140 birds per minute.  This process goes well beyond the rate at which an inspector can evaluate.  A decision tree has been incorporated in the in-line system software and has virtually eliminated false positives while retaining high fecal detection accuracy (99 percent).  The next step is to integrate a new carcass washing system developed by the research team so that any contaminated carcass can be reprocessed and passed safely into the food supply.


IMPACT/OUTCOME:  Implementation of the entire system in processing plants will have enormous effects.  It will free inspectors to evaluate only contaminated carcasses, enabling FSIS to redeploy thousands of inspectors to other safety tasks.  It will also assure the increased safety and quality of the product for the consumer, thus financially increasing profits for the poultry industry.


ACCOMPLISHMENTS:  ARS scientists at various locations took the lead to develop methods and technologies that have regulatory, industry, and research use.  A variety of new, improved, and innovative methods were developed to detect, differentiate, type, and quantify numerous foodborne pathogens including: Campylobacter, Salmonella, E. coli O157:H7, and related E. coli, Listeria, Yersinia, C. perfringens, B. cereus, Cryptosporidium, hepatitis A, Noroviruses, Fusarium species, and products of their growth, such as toxins.  New sampling methods were also developed which included a method to capture cells from any sample size and type, and enumerate without, or with minimal enrichment, currently the most time limiting step.  In collaboration with Purdue University, ARS scientists developed an inexpensive, micro-fluidic and electronic bio-chip that detects cell growth, metabolites, such as toxins, and differentiates living and dead cells in very small samples/volumes.


IMPACT/OUTCOME:  The focus of development was utility and cost-effectiveness for the end user.  Technologies were transferred to the end users, mainly FSIS and FDA, who will work with ARS to refine them for (automated) day-to-day use.  Development of the microchips will allow industry to incorporate this technology into food packages before shipping.  Spoilage could be monitored (by GPS) during transportation, and/or by retailers and consumers through an enzyme-based color change.


ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, developed a variety of fast, rugged, inexpensive, non-solvent portable new methods to screen foods for drugs, chemical residues including pesticides, and bacterial toxins.


IMPACT/OUTCOME:  Development of these tests will have a significant and immediate impact for FSIS and FDA, generating savings in materials, equipment, and labor costs.  For example, in the screening of milk tankers for tetracycline, 6.4 million man hours will be saved.  In addition, $1.6 million will be saved from elimination of the solvent.  Current commercial toxin tests costing $12 – $20 per sample were reduced to less than $1 per test.


determine the microbial ecology and transmission of human pathogens during animal, plant, and seafood (shellfish) processing, and identify the critical control points to reduce contamination. Develop innovative postharvest intervention strategies for improving the microbial and chemical safety of foods while reducing the impact on quality and consumer acceptance. Ensure that these technologies can be implemented into HACCP and GMP protocols and have efficacy for approval by FSIS and FDA.


ACCOMPLISHMENTS:  ARS scientists at the Richard Russell Research Center, Athens, Georgia, examined eggs collected from commercial plants from various stages of processing and analyzed them microbiologically and for quality.  Various methods are currently used to assess microbial quality of shell eggs, but no single method has been shown to be superior to others under all circumstances.  The study showed that microorganisms on the surface of eggs were significantly reduced through washing.  The microbiological safety, interior quality of the egg, along with the functional characteristics, remained at a high level through ten weeks of refrigerated storage.


IMPACT/OUTCOME:  This research will assist egg processors and regulators providing validation of current commercial practices; providing evidence that a more effective sanitizer could potentially improve egg microbiology; and indicating that sell-by dates could potentially be adjusted allowing for marketers to reach a broader customer base.  This latter impact would be particularly beneficial to producers of specialty eggs (i.e., reduced cholesterol, high omega fatty acid, cage-free, pasteurized, etc.) who are now limited to regional marketing due to concern over additional transportation time cutting into sell-by time windows. 


ACCOMPLISHMENTS:  The 2002 Farm Bill and the Richard B. Russell National School Lunch Act allow irradiated ground beef, on a voluntary basis, to be distributed in the National School Lunch Program (NSLP) in order to prevent foodborne illness caused by bacteria such as E. coli O157:H7.  However, there were consumer concerns, based on questions from school district administrators and parents, that irradiation might change the sensory quality of the product.  ARS scientists at the Eastern Regional Research Center, Wyndmoor, Pennsylvania, examined frozen ground beef patties distributed as a part of the NSLP that had been irradiated under commercial conditions.  The study showed that irradiated ground beef could not be distinguished from non-irradiated ground beef when tested for overall liking, flavor, taste, texture, or aftertaste.  Further, irradiation did not affect palatability of frozen ground beef patties used in the NSLP.


IMPACT/OUTCOME:  Information from the study was provided to the USDA Food and Nutrition Service, which was subsequently transmitted to schools as part of the USDA NSLP educational program on food irradiation.  Orders for frozen irradiated ground beef patties have now been placed by school districts.


ACCOMPLISHMENTS:  ARS scientists at various locations including Albany, California; Athens, Georgia; Beltsville, Maryland; and Wyndmoor, Pennsylvania, in association with various university collaborators, utilized many of the new, improved, and innovative methods to obtain data on the ecology of specific pathogens on foods, within the production and processing environment.


IMPACT/OUTCOME:  The data transmitted to the regulatory agencies and commodity organizations facilitated the identification of critical control points during food production and processing; allowed development of alternative Hazard Analysis Critical Control Plans (HACCP) systems; and led to the design and validation of alternate pathogen intervention strategies.  One critical outcome was the need to balance the cost of the intervention strategy, practicality of use by the food processing industry, and the effects on food quality.


undertake genomic and proteomic analyses of pathogens affecting food safety.  Develop bioinformatic databases and tools, and predictive user-friendly models to understand pathogen behavior and acquisition of virulence characteristics under various stress conditions. Determine the key risk factors of human pathogens in foods, and evaluate systems interventions for their impact, which will allow regulatory/action agencies to make critical food safety decisions that impact public health and food security.


ACCOMPLISHMENTS:  Bacteria in Campylobacter are the major cause of human bacterial associated gastroenteritis worldwide, responsible for 500 million cases of diarrhea each year.  These bacteria can also cause special types of arthritis and the neurological disease Guillain-Barre which can result in paralysis and death.  ARS scientists, in association with The Institute for Genomic Research (TIGR), sequenced, annotated, and compared the genome of four different Campylobacter species. This information has been used to develop and produce comprehensive Campylobacter. This is important in determining the differences among human and animal isolates of Campylobacter, and for studies of gene expression of Campylobacter exposed to relevant nutrients. Microarrays provide perhaps the most complete view of strain differences and responses to environments.


IMPACT/OUTCOME:  The availability of this new genetic information will make it possible to better address food safety-related problems through the application of powerful genomic and proteomic technologies.  For example, the development of better and more rapid detection techniques, the identification of those proteins essential for bacterial pathogen survival and growth in foods, and the development of data for risk assessment, will ultimately be used by FSIS, FDA and other regulatory agencies worldwide to develop strategies to decrease the public health risk and impact.


ACCOMPLISHMENTS:  Listeria monocytogenes remains a significant national and international regulatory, industry, and public health risk, and economic burden.  However, not all serotypes and/or strains of the bacteria have the same virulence, and capacity or ability to cause disease.  In order to determine which types were critically important, ARS scientists at the National Center for Agriculture and Utilization, Peoria, Illinois, developed a robust phylogenic description for Listeria monocytogenes from a comparative DNA sequence database developed by ARS.  Analyses demonstrated that L. monocytogenes lineages most frequently and least frequently associated with human listeriosis are sister groups, and revealed for the first time that the human epidemic associated serotype 4b is prevalent among strains from both of these lineages.  In addition, a Polymerase Chain Reaction (PCR)-based test for lineage identification was developed and used in a survey of food products demonstrating that lineage prevalence among human listeriosis cases reflects rarity of exposure and not reduced virulence as has been previously suggested.  These data also indicate that lineage 3 isolates are better adapted to the animal production environment than the food processing environment.


IMPACT/OUTCOME:  This research has provided regulatory agencies and food producers genetic information, prevalence and ecological data, and molecular tools required for the development and implementation of the Hazard Analysis Critical Control Plans (HACCP) and regulations that provide maximum protection to consumers while limiting the number and size of product recalls.


ACCOMPLISHMENTS:  ARS scientists in the Center of Excellence for Microbial Modeling and Informatics, Wyndmoor, Pennsylvania, developed the next generation of the Pathogen Modeling Program (PMP) software.  The PMP will be translated into several other languages including Spanish, Chinese, possibly French, and Finnish.  Combase, developed in association with the Institute of Food Research in Norwich, United Kingdom, and the United Kingdom Food Standards Agency which is the relational database behind the models and other predictive microbiology records, was expanded to include Australasia through CSIRO-Food Science Australia.


IMPACT/OUTCOME:  The PMP is utilized by numerous national and international regulatory agencies and various food industries to assist in identifying specific food processing steps that can serve as Critical Control Points in HACCP systems.  The predictive models are an integral part of microbial risk assessment used to support food safety measures adopted by member countries of the World Trade Organization.  Combase is now a global resource for the development of new microbial models, providing the food industry with:  an efficient location of specific food microbiology data; access to improved models that consider the complex nature of pathogen-food interactions; and greater transparency to microbial risk assessment. 


OBJECTIVE 3.2:  Develop and Deliver Science-Based Information and Technologies To Reduce the Number and Severity of Agricultural Pest, Insect, Weed, and Disease Outbreaks.


Performance Measure 3.2.1:  Provide scientific information to protect animals from pests, infectious diseases, and other disease-causing entities that affect animal and human health.




During FY 2004, ARS will


further determine partial and full genomic sequences of important animal pathogens (target four priority diseases) to better understand the evolution of new variants, determinants of virulence, host range specificity, and factors that enable evasion from host defense mechanisms.


ACCOMPLISHMENTS:  Avian influenza (AI) is one of the most feared infectious diseases.  There are already several occurrences of this virus crossing the species barrier and infecting people, resulting in mortality and high economic losses to the regions experiencing new outbreaks.  ARS scientists in collaboration with the National Veterinary Services Laboratories (Ames, Iowa), Central Veterinary Laboratory (Weybridge, England), and the Chilean Department of Agriculture (Santiago, Chile) described the first field case of recombination for an AI virus that resulted in a low pathogenic avian influenza (LPAI) virus mutating to a high pathogenic (HPAI) form of the virus.  Sequence analysis of all eight genes of a H7N3 LPAI virus and a H7N3 HPAI virus isolated one month apart in Chile showed minor differences between the viruses except at the hemagglutinin (HA) cleavage site where the HPAI had a 30-nucleotide insert.  This insertion likely occurred through a recombination event resulting in a virulence shift, demonstrating a new mechanism of how an influenza virus may evolve to a more virulent form.


IMPACT/OUTCOME:  The understanding of mechanisms for increased virulence of AI will improve our understanding of the pathogenesis of the virus and eventually may improve our ability to predict which low pathogenic viruses may become highly pathogenic.


ACCOMPLISHMENTS:  Avian pneumovirus (APV), now classified as an avian metapneumovirus (AMPV), was first isolated from commercial turkeys in Colorado in 1996.  The disease was reported in the United Kingdom in 1985 and prior to 1996 the disease was exotic to North America.  The virus causes a mild, but rapidly spreading, upper respiratory disease, with adverse effects on weight gain and feed conversion.  Secondary bacterial infections increase the severity of the disease.  APV infections continue to cause productivity losses in turkeys in the Upper Midwest particularly in Minnesota and more recently in Iowa, Wisconsin, and North and South Dakota.  The initial diagnosis of the disease in the United States was delayed because the U.S. isolates were of a different subtype than had been isolated elsewhere and serological assays to detect the new subtype had to be developed.  ARS scientists, in collaboration with scientists at the University of Minnesota, deciphered the entire genomic sequence and compared the AMPV subtype C genes SH, G, and L nucleotides and predicted amino acid sequences with those of human metapneumoviruses (hMPV).  The comparison supported earlier findings that AMPV subtype C was closer evolutionary to hMPV than the other AMPV subtypes A, B, and D.


IMPACT/OUTCOME:  This scientific information suggests that the source of the new APV serotype seen in the United States was derived from humans and not from other avian sources.  This information will be critical as control measures are evaluated to control this emerging infectious disease of poultry.


ACCOMPLISHMENTS:  Vesicular stomatitis virus (VSV) is a viral disease clinically indistinguishable from foot-and-mouth disease, one of the most devastating exotic diseases in livestock.  Outbreaks of VSV, such as the 2004 outbreak in the southwestern United States, sporadically occurs causing serious economic losses due to quarantine and the cost of associated control measures.  The natural cycle of VSV in endemic areas and the factors mediating the emergence of this disease are not understood.  VSV outbreaks occur at 8-10 year intervals.  VSV Indiana subtypes cocal (VSIV-2) and alagoas (VSIV-3) cause outbreaks in Brazil and Argentina.  Little is known about the genomes of these viruses, hindering the development of molecular diagnostic tools for rapid detection.  ARS scientists have determined the full length genomic sequences of the prototype strains of VSIV-2 and VSIV-3, and found genetically conserved areas that could serve as potential targets for rapid detection tests.  In collaboration with the PAHO's PANAFTOSA laboratory in Brazil, ARS scientists have genetically characterized representative viruses from outbreaks occurring in these countries in the last 20 years, including the latest outbreaks in southern Brazil in 1997-1998.


IMPACT/OUTCOME:  ARS has determined the extent of genetic variation among VSV isolates from Brazil and Argentina.  This information will be used to design rapid molecular diagnostic tests that will enable molecular epidemiological studies to better understand the life cycle of this important livestock pathogen.


ACCOMPLISHMENTS:  Brucella abortus, the primary Brucella species infecting cattle, also infects other animals, including humans.  Brucellosis causes abortions, significant economic losses, and is a public health threat.  This disease has been nearly eradicated from cattle in the United States after sixty years of regulatory efforts by the Animal and Plant Health Inspection Service (APHIS) in collaboration with State regulatory personnel and cattle producers.  However, a high percentage of feral swine, and elk and bison in Yellowstone National Park and surrounding areas, are infected with Brucellosis and have the potential to transmit the disease to cattle.  The completion and annotation of the genomic sequence of a field strain of Brucella abortus provided valuable data that led to the development of a molecular test to do epidemiologic tracebacks.  By comparison to the sequences of B. melitensis and B. suis, unique genetic elements were identified.


IMPACT/OUTCOME:  The discovery of unique sequences in the Brucella abortus genome provides new opportunities for developing rapid molecular diagnostic tests to identify and eradicate the different Brucellosis species that can infect our domestic and wildlife animal species.


further investigate the pathogenesis of important animal pathogens (target two priority disease) to better understand tissue tropism, disease transmission, virulence and the identification of phenotypic markers


ACCOMPLISHMENTS:  Porcine reproductive and respiratory syndrome (PRRS) virus infections account for up to 15 to 20 percent of the economic losses yearly (nearly $600 million) in the U.S. swine industry.  Methods of PRRS virus intervention (vaccines, therapeutics, genetics, etc.) are limited and new novel strategies are desperately needed.  One reason new intervention strategies have not been forthcoming is the lack of information known about the host cell response to infection by PRRS virus.  ARS scientists demonstrated that PRRS virus infection does not result in the induction of type l interferons as would be expected with most RNA viruses.  Specifically, PRRS actively suppresses the induction of Interferon-beta (IFNB) expression, which also prevents the induction of Interferon-alpha (IFNA).  These results are significant because both IFNA and IFNB are members of the innate immune system, which is typically viewed as the first response of the immune system.  Activation of this response signals other branches of the immune system to become activated and mount a protective immune response.


IMPACT/OUTCOME:  That PRRS virus is capable of suppressing the innate immune response may explain an important mechanism this virus uses to evade the immune host response, a critical step in the design of effective biotherapeutics and vaccines to control this important swine disease. 


ACCOMPLISHMENTS:  One of the major concerns with Transmissible Spongiform Encephalopathies (TSEs) is that Bovine Spongiform Encephalopathy (BSE) has been shown to cross the species barrier to cause a unique TSE in human beings.  Although there has not been a similar demonstration that Chronic Wasting Disease (CWD) could present any risk to human health, the BSE experience has raised many questions about the potential hazard CWD and other TSEs present for transmission to other animal species, especially domesticated livestock and wildlife.  ARS scientists have focused on direct experimental challenge studies to assess the relevance of the species barrier as predictive models for future risk assessments.  CWD transmission studies with cattle showed that although abnormal prion (PrPres) amplification occurred following direct CWD inoculation into the brain of cattle, none of the affected animals had classic histopathologic lesions of spongiform encephalopathy.  Furthermore, only 38 percent of the inoculated cattle demonstrated amplification of PrPres. Although intracerebral inoculation is an unnatural experimental route of exposure, it is the most severe challenge possible.  The results of these interspecies transmission studies suggests that cattle are either resistant to CWD or that CWD transmission  may require long incubation periods of up to five years. 


IMPACT/OUTCOME:  These studies provide information about the clinical and pathological disease characteristics that can be expected if a TSE crosses the species barrier; thus enabling animal health specialists to recognize such situations should they occur.  Additional transmission studies in the natural host will focus on determining the modes of transmission and disease development so that appropriate intervention strategies can be devised that will control the spread of these diseases.


further investigate the epidemiology of important animal diseases (target two priority diseases) to better understand their ecology and life cycle and provide effective disease surveillance to facilitate the development of control strategies and prevent disease transmission.


ACCOMPLISHMENTS:  ARS was one of the first laboratories to conduct poultry-related research for both the Severe Acute Respiratory Syndrome (SARS) virus and West Nile Virus in the United States.  The SARS virus emerged in Southeast Asia and infected over 8,400 humans causing over 800 deaths.  Early epidemiologic evidence suggested a zoonotic potential for the virus with animals in the live animal markets in China.  The source of the virus causing SARS is still unknown but animals may be the source or may be contributing to the spread of the virus.  ARS scientists conducted a study to determine if chickens, turkeys, ducks, geese, and Japanese quail were susceptible to the SARS virus and could spread the virus to humans.  The study failed to demonstrate that the SARS virus could grow in these birds.  These data indicate that the common five domestic poultry species were not the reservoir and will not spread the SARS virus to humans.  Similar research with West Nile Virus was conducted that showed the common poultry species could be infected with these viruses, but clinical disease seldom occurred and that with low levels of viremia, these species were unlikely to spread the virus.


IMPACT/OUTCOME:  This research contributed to our understanding of the host range (identification of susceptible animal species) of two new and emerging diseases, which is vital to our understanding of disease transmission and the epidemiology of these zoonotic diseases (diseases humans acquire from animals).


ACCOMPLISHMENTS:  Listeria monocytogenes is a bacterium capable of causing serious disease in humans and animals.  L. monocytogenes infection of cattle and sheep can lead to disease of the central nervous system and death.  Human listeriosis is a potentially fatal foodborne disease often associated with the consumption of contaminated dairy products.  ARS scientists, in collaboration with Washington State University, developed the first biologically relevant model that can be used to assess L. monocytogenes strain virulence.  Six human epidemic strains and six environmental strains were assayed for invasiveness using an oral inoculation mouse model.  Variation in strain invasiveness was observed and epidemic strains were significantly more invasive than environmental strains.


IMPACT/OUTCOME:  In order to understand the epidemiology and epidemic potential of L. monocytogenes isolates, it is important to effectively access their virulence.  The development of a validated model to assess virulence is a critical step towards understanding why some strains cause epidemics whereas others do not.  The oral inoculation mouse model will be used to evaluate the virulence potential of genes present in epidemic strains and provide valuable insight into understanding the epidemiology of this animal and human health threat, resulting in the application of early control measures at the farm level.


Performance Measure 3.2.2:    Identify, develop, and release to the U.S. agricultural community genetic markers, genetic lines, breeds, or germplasm that result in food animals with improved (either through traditional breeding or biotechnology) pest- and disease-resistance traits.




During FY 2004, ARS will continue to identify genetic markers and genes (target one marker or one gene) from food animals that can be used to identify animals with disease resistant traits.


ACCOMPLISHMENTS:  Mastitis is one of the most costly diseases in animal agriculture, with economic losses estimated to be $1 to 2 billion annually in the United States.  More than one-third of the Nation's herd of 9.5 million dairy cows experience at least one episode of mastitis during each lactation.  Increasing the mammary gland’s level of resistance to a wide range of pathogens, including coliforms and environmental pathogens, could have a significant impact in curtailing this costly disease.  A primary target is the white blood cells called neutrophils, which are considered the first line of defense against the bacterial pathogens responsible for Mastitis.  ARS scientists successfully applied a proteomics approach using mass spectrometry to determine the proteome (the entire protein profile) of the neutrophil of the cow.  Over 250 major proteins were identified.  Most are involved in glycolysis and energy transformations.  However, many proteins were also involved in the function of the phagosome and the enzymes involved in phagocytosis and killing of bacteria. 


IMPACT/OUTCOME:  ARS scientists have previously established a clear link between diseases affecting dairy cows around parturition and a poorly functioning immune system.  Efforts to boost the proficiency of neutrophils could have a major impact in controlling periparturient diseases, resulting in a major benefit to dairy producers by reducing economic losses due to culling of infected cows, discarding of affected milk, and cost of veterinary care.  In addition, consumers will benefit from reduction of antibiotic use in the food chain and increased safety of milk through reduced pathogen contamination.  The discovery of the neutrophil proteome will enable scientists to conduct experiments to identify genes associated with highly functioning neutrophils and develop genetic tests to accurately and reliably predict which cows are most susceptible to disease.


Performance Measure 3.2.3:    Develop and transfer tools to the agricultural community, commercial partners, and Federal agencies to control or eradicate domestic and exotic diseases that affect animal and human health.




During FY 2004, ARS will continue to discover and develop novel technologies (target two high priority diseases) to detect and control diseases of food animal pests that impact animal and human health, animal production, and trade.


ACCOMPLISHMENTS:  ARS played a significant role in providing the Animal and Plant Inspection Services (APHIS) with critical scientific information that enabled the USDA to take swift action when the first Bovine Spongiform Encephalopathy (BSE) case was discovered in Washington State, December 2003.  ARS very quickly applied sophisticated tests developed to inform our regulatory and action agencies that the test samples from the alleged BSE downer cow were of bovine origin (confirming the integrity of the samples), BSE-positive, and that the suspect cow in Washington State came from Canada.


IMPACT/OUTCOME:  Discovering the first BSE-infected cow in the United States had the potential to significantly impact our economy, undermine the confidence of our trade partners in our cattle industry, and curtail our export market of live cattle and meat products.  The tests developed and used by ARS to investigate the Washington State BSE Index Case enabled APHIS and other Federal agencies to move forward rapidly with a decisive action plan to protect consumers and limit the damage to our livestock industries.


ACCOMPLISHMENTS:  An ARS TSE scientist was detailed on special assignment at the request of APHIS and the Agricultural Marketing Service (AMS) to serve in a scientific advisory capacity on the U.S. - Japan BSE Technical Working Group.  This group met three times with a Japanese delegation to establish criteria regarding a return to normal U.S. beef export trade relations with Japan.  As part of this special assignment, the ARS scientist authored a critical chapter entitled "Definition of BSE and the method of Testing," for the U.S. BSE Reference Book.


IMPACT/OUTCOME:  This document is now used by AMS and the International Trade Policy group of the Foreign Agricultural Service in U.S. trade negotiations.


ACCOMPLISHMENTS:  Use of antibiotics and other drugs and chemicals in the dairy industry is one of the greatest threats to food safety.  ARS scientists demonstrated that a biotherapeutic (Poly-X) to prevent mastitis in dairy cows during the dry period was at least as effective as antibiotics.  At dry off, mammary quarters of 40 cows were injected with antibiotics and 40 cows were injected with Poly-X.  At the time of calving, cows treated with Poly-X had less mastitis than cows treated with antibiotics.  A patent application has been filed.  Dairymen and organic farmers will have available a non-antibiotic compound for use during the dry period for dairy cows.


IMPACT/OUTCOME:  The dairy industry needs new tools to overcome the problems associated with the use of antibiotics.  Surveys indicate that at least 5 percent of bulk milk shipments and 30 percent of milk sold to consumers contains detectable amounts of antibiotics and drugs. This presents a potential human health hazard.  Also, the antibiotics approved for treating mastitis are increasingly ineffective, largely due to the appearance of resistant strains.  An effective “non-antibiotic” biotherapeutics to prevent mastitis during the dry period of dairy cows provides a new tool to combat this important disease without relying on traditional drug use and their potential adverse effects on the health of consumers.


ACCOMPLISHMENTS:  Newcastle disease virus (NDV), also known as avian paramyxovirus type 1 (APMV-1), infects all known wild and domestic bird species.  Different NDV strains vary in virulence from those that caused disease and mortality during the 2002-2003 outbreak of exotic Newcastle disease (END) in California to those of low virulence that cause mild or unapparent respiratory infections with reduced flock productivity, the predominant form that occurs in the United States.  END is a reportable disease.  Its presence in commercial poultry has resulted in embargoes of poultry exports from the affected U.S. States.  Currently, there is no method beside animal inoculation to determine the virulence of NDV.  ARS scientists examined the embryonated chicken egg as a model system to evaluate virulence properties of NDV isolates.  Embryos from eggs inoculated with NDV reference and mutated reference strains were collected, formalin fixed, sectioned, and stained with a gene probe and NDV antibodies to detect virus distribution in the tissues and membranes of the embryonated eggs.  Low virulence strains were detected exclusively in the cells of the chorioallantoic membrane, whereas more virulent NDV isolates and mutated strains that were demonstrated to have acquired virulence for chickens were widely disseminated in chicken embryo tissues.


IMPACT/OUTCOME:  The research demonstrates the potential value of using, as an alternative to chicken inoculations, chicken embryos as a model system for evaluating NDV virus virulence.  As a result of ARS’ research, information is provided more quickly on the virulence potential of new NDV isolates, and the response time for implementing control measures is decreased.


ACCOMPLISHMENTS:  Poult Enteritis Mortality Syndrome (PEMS) is a highly infectious disease of young turkeys.  PEMS and similar disease conditions have been reported in most regions where turkeys are commercially produced, including the Southeastern United States, Texas, California, Arkansas, Missouri, and Israel.  PEMS has been called one of the most devastating emergent diseases to strike the poultry industry in recent years.  Since its emergence in the early 1990s, outbreaks of PEMS have annually cost the turkey industry millions of dollars in losses.  The major impact of PEMS is due to mortality and decreased production as turkeys are stunted and grow poorly when affected by the disease.  Currently the agent or agents that cause PEMS are unknown.  PEMS appears to be a complex disease, possibly involving multiple pathogens.  Some anecdotal evidence suggests that immunosuppression may be involved.  Real-time reverse transcriptase polymerase chain reaction (RRT-PCR), a new molecular rapid diagnostic technique, which is highly specific and highly sensitive (superior to standard RT-PCR), was developed and applied to the detection of three viruses commonly associated with PEMS, turkey astrovirus, turkey coronavirus, and turkey reovirus.  Laboratory validation for these tests with clinical samples from experimental cases was successfully completed with optimization of sample types and times determined for each of the three viruses.  This assay is superior to previous tests and will accurately identify infected turkeys.


IMPACT/OUTCOME:  Previously, no rapid or specific diagnostic tools were available for the detection of the viral agents associated with PEMS.  The development of a highly specific and sensitive RRT-PCR assay will enable scientists to decipher the role turkey astrovirus, turkey coronavirus, and turkey reovirus play in causing PEMS and may lead to the modification of management practices to minimize the impact of this disease.


Performance Measure 3.2.4:    Develop and release to potential users varieties and/or germplasm of agriculturally important plants that are new or provide significantly improved (either through traditional breeding or biotechnology) characteristics enhancing pest or disease resistance.




During FY 2004, ARS will continue to identify and characterize genes of insect resistance in crop plants, closely related non-crop species, and other species, to enhance opportunities for developing host plant resistance, and to incorporate such genes into commercially acceptable varieties.


ACCOMPLISHMENTS:  Sustainable sugarcane production in Florida is a challenge due to susceptibility of sugarcane to a wide array of disease and insect pests.  After eight years of testing, ARS scientists at Canal Point, Florida, in collaboration with researchers at the University of Florida, Belle Glade, Florida; and the Florida Sugar Cane League, Inc., Clewiston, Florida, released sugarcane cultivars CP 97-1944 and CP 97-1989.  These two new cultivars add genetic variability for disease and insect resistance while producing at sustained levels of profitability in Florida. 


IMPACT/OUTCOME:  These releases are significant since sugarcane in Florida is almost always grown as a monoculture, so new cultivars are continuously needed for resistance to intense disease and insect pressures.


Performance Measure 3.2.5:  Provide fundamental and applied scientific information and technology to protect agriculturally important plants from pests and diseases.




During FY 2004, ARS will


continue to develop fundamental knowledge about insect biology and ecology that provides the foundation for strategies to exclude, detect, and mitigate pest infestations.


ACCOMPLISHMENTS:  The pink hibiscus mealybug (PHM) can destroy more than 200 plant species by injecting them with toxic saliva while sucking their sap.  The exotic insect pest recently invaded California and Florida, and has proven difficult to track and monitor.  ARS scientists in Beltsville, Maryland, have discovered two compounds that together make up the female PHM’s sex pheromone.  The compounds provide a timely method with which to monitor and ultimately reduce infestations. 


IMPACT/OUTCOME:  Officials with the Animal and Plant Health Inspection Service (APHIS) are using the new pheromone as a sex lure to survey the degree of mealybug pest infestations in California and Florida and to track the effectiveness of biological control efforts against the pest.  ARS has applied for patent protection for the invention and already has received requests to license the technology.  The new blend of synthetic pheromones also could help crop producers manage the pests safely through either mass trapping or disruption of mating activity.


ACCOMPLISHMENTS:  Fundamental research on fungal pathogens, including how these pathogens survive and successfully infect their insect hosts in field and greenhouse environments, will foster the development of safe, effective alternatives to chemical insecticides.  Scientists in Ithaca, New York, have found that a single application of Bacillus thuringiensis (Bt) together with the fungus, Beauveria bassiana, has resulted in an 81 percent reduction in target populations of large larvae of the Colorado potato beetle. 


IMPACT/OUTCOME:  These results indicate the strong potential for using these agents as the key components of an integrated biocontrol program for Colorado potato beetle management.


ACCOMPLISHMENTS:  Enticing new lures developed by ARS scientists at Wapato, Washington in cooperation with Washington State University could make backyard gardens, fruit orchards, and crop fields places of no return for pesky caterpillars that cause millions of dollars in losses.  The lures, derived from molasses and floral odors, tantalize both male and female moths, and have been developed as an alternative to chemically controlling the pests—loopers, cutworms, fruitworms, armyworms, and corn earworms.  The insects fly into the opening of a lure-dispensing trap, never to escape.


IMPACT/OUTCOME:  The molasses-derived lure is now commercially available for garden use as the product SMARTrap.  The floral-based lures are in their second year of field tests.  So far, use of the floral lures in a “killing station” reduced the number of alfalfa loopers by 75 percent.


continue to develop fundamental knowledge about weed biology and ecology that provides the foundation for strategies to exclude, detect, and mitigate weed infestations.


ACCOMPLISHMENTS:  The winter wheat-fallow production system in the Pacific Northwest is characterized by winter annual grass weeds and wind erosion.  There are no economically viable conservation cropping systems to solve these problems.  ARS scientists at the Land Management and Water Conservation Research Laboratory in Pullman, Washington, along with two university partners, developed a system for planting facultative spring wheat in November (rather than the normal March planting) in lieu of late-planted winter wheat when conditions are dry in the Fall. 


IMPACT/OUTCOME:  During the drought year of 2002-2003, this system was used.  It was more competitive against weeds, improved grain quality, and yielded 20 percent more compared to winter wheat.  Adoption of this alternative conservation cropping system would reduce the impact of weeds and erosion susceptibility, and increase air quality.


ACCOMPLISHMENTS:  Intercrossing between rice and ecotypes of weedy red rice, a dominant weed in the southern United States, may reduce yield when herbicide resistant rice systems are used.  DNA/PCR microsatellite fingerprinting analyses were conducted to quantify rates of outcrossing between rice x red rice crosses (including imidasolinone resistant rice cultivars), foreign rice cultivars, and red seeded rice relatives from throughout the world at the ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas.  A method was developed allowing for distinguishing crosses using DNA marker analysis. 


IMPACT/OUTCOME:  These analyses may allow the rice industry to identify (or rule out) the parental lines that are responsible for development of an unwanted population of herbicide-resistant rice x red rice hybrids, a key management consideration in herbicide esistant rice systems.


continue to develop fundamental knowledge about plant disease biology and ecology that provides the foundation for strategies to exclude, detect, and mitigate pest infestations.


ACCOMPLISHMENTS:  ARS has developed rapid, reliable pathogen detection and identification procedures for accurate and timely disease diagnosis for soybean rust and other high profile pathogens on the USDA Select Agent List.


IMPACT/OUTCOME:  The detection assay was used by regulatory officials to accurately determine and identify a new outbreak of soybean rust in the southern United States in November 2004 which resulted in implementation of response planning.


ACCOMPLISHMENTS:  ARS isolated pathogenic fungi from pears shipped from China.  Pathogenicity testing was completed with other fruit-associated species.  After morphological and genetic characterization of the Chinese strains, the causal agent was determined to be a new species unknown to the United States.   


IMPACT/OUTCOME:  This research protected the U.S. pear industry from the introduction of potentially damaging exotic fruit pathogens.


ACCOMPLISHMENTS:  A unique and highly virulent strain of Fusarium oxysporum was discovered in cottonseed imported from Australia into California as a feed for cattle.  This strain devastated cotton production in areas of Australia where it occurs, resulting in 98 percent yield losses.


IMPACT/OUTCOME:  Identification of the highly virulent isolate from Australia resulted in the initiation of steps to more thoroughly disinfect cottonseed before it is allowed into the United States.


Performance Measure 3.2.6:    Provide needed scientific information and technology to producers of agriculturally important plants in support of exclusion, detection, and early eradication; control and monitoring of invasive insects, weeds and pathogens; and restoration of affected areas.  Conduct biologically-based integrated and areawide management of key invasive species.




During FY 2004, ARS will


continue to develop and demonstrate technologies for excluding, detecting, and mitigating native and invasive insect pests, including integrated pest management (IPM) and areawide approaches, and deliver IPM components and systems to ARS customers.


ACCOMPLISHMENTS:  The tarnished plant bug damages a large number of crops throughout the United States, including fruits, vegetables, forestry nurseries, fiber crops, and seed crops.  ARS scientists in Newark, Delaware, have completed a long-term study documenting that a foreign parasitoid (Persistenus digoneutis) permanently controlled and reduced the tarnished plant bug and also demonstrated that a native parasite was not eliminated by this new introduction. 


IMPACT/OUTCOME:  These findings should increase confidence in the safety of classical biological control methods used against pest insects.


ACCOMPLISHMENTS:  Many insect pests in the United States are of foreign origin, introduced accidentally with few or no natural enemies.  ARS scientists in Montpellier, France, proved that an isolate of an entomopathogenic fungus collected in China proved more virulent than the current commercially available fungus when applied to the Formosan subterranean termite colony, but not when applied to individual termites.


IMPACT/OUTCOME:  This accomplishment is important because this experimental portal (individual and grouped) and analysis suggests an effective way to compare pathogen virulence among social insects. Also, scientists in Peoria, Illinois, have shown that an application of a bioinsecticidal fungus to trees infested with the Formosan subterranean termite significantly reduces the pest numbers and foraging activities.


continue to develop and demonstrate technologies, including risk analysis, for excluding, detecting, and mitigating native and invasive weed pests, including IPM and areawide approaches, and deliver IPM components and systems to ARS customers.


ACCOMPLISHMENTS:  Invasive saltcedar (Tamarix spp.) shrubs from Eurasia infest many Western U.S. riparian areas and waterways where they cause significant economic and environmental losses.  Detailed studies on foreign exploration and host specificity testing for natural enemies of saltcedar were conducted by ARS scientists at the European Biological Control Laboratory, Montpellier, France; the Western Regional Research Center, Albany, California; and the Grassland Protection Research Unit, Temple, Texas.  The first biological control agent for saltcedar, the beetle Diorhabda elongata, was released in 1999 at 10 sites in 6 States.  The beetle has spread over 100 miles since release.  Use of aerial imagery and ground assessments shows that the beetle has totally defoliated saltcedar at many sites and is beginning to severely damage saltcedar on a landscape basis.  The impact of natural enemies is being evaluated on saltcedar and on native plant communities (cottonwoods and willows). 


IMPACT/OUTCOME:  This research is important as it interfaces with ongoing investigations of biological control, and provides revegetation strategies for land managers that are interested in removing and replacing saltcedar.  It also assists in an evaluation of the impact of the program on an endangered bird. 


ACCOMPLISHMENTS:  The invasive tree, Melaleuca quinquenervia, was introduced to South Florida in the late 19th century as an ornamental plant, but this fast growing, fast spreading tree has displaced native plants and animals, dried up wetlands, and created major fire hazards.  The spread of melaleuca is being thwarted in Florida, thanks to a cooperative program that utilizes the tree’s natural enemies in Australia.  The collaborative effort (TAME) is being carried out by ARS in cooperation with the University of Florida’s Institute of Food and Agricultural Sciences, and the South Florida Water Management District.  The purpose of TAME is to demonstrate the effective integration of biological control with other management strategies, including use of herbicides and mechanical removal of melaleuca.  The first natural enemy released against melaleuca was the melaleuca leaf weevil, oxyops vitiosa.  More than 8,000 of the weevils were released at 13 locations in 1997.   A second agent, the psyllid, Boreioglycapsis melaleucae, was released in 2002, and has spread widely since then.


IMPACT/OUTCOME:  The combination of the weevil and psyllid has been so successful that melaleuca is no longer threatening many of the natural areas in which it was dominant.


continue to develop and demonstrate technologies for excluding, detecting, and mitigating native and invasive plant disease pests, including IPM and areawide approaches, and deliver IPM components and systems to ARS customers.


ACCOMPLISHMENTS:  ARS developed the first genetic map for the Fusarium head blight pathogen, the major fungal pathogen of wheat that produces several mycotoxins harmful to humans.


IMPACT/OUTCOME:  The map has been used in genetic diversity studies, and to validate and align the genomic sequence of the pathogen. 


ACCOMPLISHMENTS:  ARS examined genetic variation in over 300 strains of Phytophthora infestans, causal agent of potato late blight.  ARS was able to demonstrate greater levels of genotypic diversity and that population structures differed from one location to another.


IMPACT/OUTCOME:  The major impact of understanding pathogen diversity will be to ensure that cultivars resistant to late blight have nonspecific resistance not limited to virulence genes in the current local populations of the pathogens.

Goal 4



Analysis of Results:  This goal is the focus of ARS’ research related to human nutrition and health.  Under Goal 4, 6 Indicators are aligned under 3 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2004.  Nineteen significant accomplishments are reported below.


OBJECTIVE 4.1:  Promote Healthier Individual Food Choices and Lifestyles and Prevent Obesity; Improve Human Health by Better Understanding the Nutrient Requirements of Individuals and the Nutritional Value of Foods; Determine Food Consumption Patterns of Americans.


Performance Measure 4.1.1:  Scientifically assess the efficacy of enhancements to the nutritional value of our food supply and identify, conduct, and support intramural and extramural research to develop, test, and evaluate effective clinical and community dietary intervention strategies and programs for modifying diet, eating behavior, and food choices to improve the nutritional status of targeted populations.  A special emphasis is to prevent obesity and promote healthy dietary behaviors.




During FY 2004, ARS will


identify dietary and lifestyle intervention strategies to prevent obesity and promote healthy food choices and eating behaviors.


ACCOMPLISHMENTS:  ARS researchers compared weight loss efficacy of four popular diets – Atkins, Zone, Weight Watchers, and Ornish – in 160 overweight and obese adults for 12 months.


IMPACT/OUTCOME:  The research indicates there are no special metabolic differences from high protein, low fat, or other composition diets.  The results emphasize that adherence to a diet is the most important factor in weight loss, not the amount of fat, protein, or carbohydrate.


ACCOMPLISHMENTS:  ARS scientists showed that consumption of a diet containing whole grains, in contrast to one containing refined cereals and grains, elevates satiety and shifts metabolism from using dietary fats to using body fat for energy needs.


IMPACT/OUTCOME:  The findings provide new science-based information for developing food-based strategies for preventing unhealthy weight gain in adults.


ACCOMPLISHMENTS:  Research demonstrated that men regulate weight primarily through physical activity while women regulate weight primarily by changing their diet. 


IMPACT/OUTCOME:  Based on the research, public health policy for maintaining a healthy body needs to take into account gender differences in adults.


ACCOMPLISHMENTS:  ARS researchers showed that poor rural residents of the Lower Mississippi Delta eat less protein, fruits, vegetables, vitamins, and minerals, but the same calories as the rest of the population and have a higher incidence of obesity and chronic health problems.


IMPACT/OUTCOME:  These data show that both diet and physical activity differences are likely to account for obesity and its related complications. 


conduct research that enhances the nutritive value of the food supply.


ACCOMPLISHMENTS:  Researchers demonstrated in a long-term human feeding study that whole grain barley, rich in soluble fiber, can lower blood cholesterol levels and reduce diastolic blood pressure in adults.


IMPACT/OUTCOME:  The barley industry has filed a petition with the Food and Drug Administration for a health claim based upon ARS’ research.


ACCOMPLISHMENTS:  Researchers found that strains of beneficial bacteria from yogurt colonize the intestine of pigs and activate their immune system.  This had the effect of reducing an allergic reaction to an experimental parasitic infection.


IMPACT/OUTCOME:  The findings suggest that healthful bacteria can help prevent infections by disease-causing organisms.  This may benefit sales of fermented dairy products that contain cultures of these bacteria.


ACCOMPLISHMENTS:  ARS scientists established a dose of cinnamon fed to humans that improves blood glucose and lipids in volunteers with type 2 diabetes.


IMPACT/OUTCOME:  Proof of concept establishes that isolation and synthesis of the active factor in cinnamon could be used to treat diabetes.  A CRADA partner has been identified and is subsidizing this research.  If commercialized, the financial impact is substantial since 12 million Americans have been diagnosed with diabetes and the annual economic burden is more than $132 billion.


Performance Measure 4.1.2:  Define functions, bioavailability, interactions, and human requirements (including effects such as genetic, health status, and environmental factors) for known, emerging, and new classes of nutrients.  Determine the abundance of known, emerging, and new classes of nutrients in the food supply and provide that information in databases.




During FY 2004, ARS will


determine the functions, bioavailability, interactions, and requirements for known, emerging, and new classes of nutrients across the life cycle.


ACCOMPLISHMENTS:  ARS scientists showed that vitamin E supplements given to elderly nursing home residents for one year significantly reduced the incidence of upper respiratory infections.


IMPACT/OUTCOME:  Since morbidity and mortality are greatly increased in the elderly following occurrence of common colds, this study has the potential to reduce the severity of illness and attendant medical costs which are often borne by Federal programs for this group.


ACCOMPLISHMENTS:  ARS researchers determined the rate of utilization in humans of two carotenoids, lutein and beta-carotene, by feeding isotopically labeled kale.  Lutein was much more effectively used than beta-carotene.  Bioavailability of carotenoids was also studied using juice from purple carrots developed by ARS.


IMPACT/OUTCOME:  These studies inform scientists about how effectively different pigmented carotenoids are used by the human body.  It also is important for understanding the bioavailability of plant components and whether increasing these components will make crops nutritionally superior.


ACCOMPLISHMENTS:  ARS researchers found that adding meat to the diet favorably influenced blood indicators of bone growth and turnover.  Further, amounts of meat commonly consumed by the American population did not increase urinary calcium excretion.


IMPACT/OUTCOME:  Older, less well controlled studies had indicated the opposite and meat consumption was sometimes avoided by women because of believed adverse effects on bone health. This study should allay those concerns and benefit sales of meat.


ACCOMPLISHMENTS:  ARS scientists demonstrated that chronic high dietary copper levels can alter measures of immunity and oxidative stress. 


IMPACT/OUTCOME:  New knowledge on the potential health effects of long-term high copper consumption is required in order to refine the newly established upper tolerable level for dietary copper.  This information will be used to ensure that the level of copper provided in foods and supplements is safe for the American public.


ACCOMPLISHMENTS:  ARS researchers showed that children eating a low calcium diet can only partially adapt to the lower amount by increasing the proportion of dietary calcium absorbed from the intestine.    


IMPACT/OUTCOME:  Many children are not consuming sufficient dietary calcium and this increases risk of osteoporosis and fractures in later life.  This research contributed to the recommendation in the Dietary Guidelines for Americans to consume daily 2 to 3 servings of milk, milk products, or other calcium-rich foods.


develop new methods, conduct food composition analyses, and compile databases for known, emerging, and new classes of nutrients across the life cycle.


ACCOMPLISHMENTS:  ARS researchers determined that the folic acid content of fortified cereal grain containing foods is substantially higher than required by law.


IMPACT/OUTCOME:  The Food and Drug Administration mandated fortification of refined cereal grains in 1998 to prevent neural tube defects in the babies of mothers not receiving sufficient dietary folic acid during pregnancy.  However, the levels actually in the U.S. food supply are considerably higher than intended.  This new information points to the need for research on the health implications of high folic acid intakes by the American public.


ACCOMPLISHMENTS:  AS scientists developed and released special interest databases for fluoride, choline, and proanthocyanidins which are not part of the USDA National Nutrient Database for Standard Reference.


IMPACT/OUTCOME:  Information in these databases is used by industry for fortification purposes (fluoride) or by nutritionists to recommend healthy eating patterns.


ACCOMPLISHMENT:  Scientists initiated development of a new procedure to determine six B vitamins in foods and dietary supplements.  They evaluated a new method for the analysis of amino acids in foods containing sulfur and selenium.  They also developed a new analytical method to separate different forms of iron in meat.


IMPACT/OUTCOME:  These improvements in food analysis will allow more accurate information to be collected for dietary surveys and help food processors in knowing the nutrient content of their products.


Performance Measure 4.1.3:  Determine food consumption patterns of Americans, including those of different ages, ethnicity, regions, and income levels.  Provide sound scientific analyses of the U.S. food consumption information to enhance the effectiveness and management of national and community food and nutrition programs.




During FY 2004, ARS will


survey and analyze national food consumption patterns of Americans. 


ACCOMPLISHMENTS:  ARS released the “What We Eat in America” dietary intake data for 2001-2002 on the Internet in collaboration with the Department of Health and Human Services.  This yearly nationwide survey provides essential information on foods and nutrients in the contemporary American diet.


IMPACT/OUTCOME: This information is critical to understanding the role diet plays in promoting health and reducing obesity and disease throughout life.  It is widely used by government agencies, universities, and the food industry for a variety of purposes, such as, establishing dietary recommendations, setting food assistance program policies, and determining if the U.S. food supply requires enrichment or fortification.


ACCOMPLISHMENTS:  ARS researchers found that personality characteristics are associated with under-reporting food intake on dietary recall, the key tool used to assess food and nutrient intake in the United States.  Individuals with poor body image were more likely to under-report food intake.


IMPACT/OUTCOME:  This kind of information helps determine who is likely to misreport dietary intake information.  Such information is essential to improving the accuracy of national dietary survey methodology.


develop and test new dietary assessment methods and nutritional status markers.


ACCOMPLISHMENTS:  A longitudinal study of 2,000 older adults with 12.5 years follow-up was completed.  The study found blood levels of the amino acid homocysteine were a strong, independent predictor of bone fracture in addition to being associated with heart disease.


IMPACT/OUTCOME:  Levels of homocysteine are primarily affected by B vitamin status and reflect their intake and utilization.  This new information provides the basis for developing food-based strategies to prevent bone fractures in older adults.


ACCOMPLISHMENTS:  Food frequency questionnaires (FFQ) are the most cost-effective means for determining dietary intake in studies with large numbers of subjects.  New FFQ’s were developed for use in the Southern United States and for Hispanics in the Northeastern United States.


IMPACT/OUTCOME:  These new assessment methods will help improve the accuracy and reproducibility of nutrition research studies.  They point to the need for different dietary instruments for specific population groups, whether geographic or ethnic.

Goal 5



Analysis of Results:  This goal focuses on a wide range of environmental issues related to agriculture.  Under Goal 5, 14 Indicators are aligned under 7 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2004.  Fifty significant accomplishments are reported below.


OBJECTIVE 5.1:  Provide Science-Based Knowledge and Education To Improve the Management of Forest, Rangelands, and Pastures.


Performance Measure 5.1.1:  Develop ecologically-based information, technologies, germplasm, and management strategies that sustain agricultural production while conserving and enhancing the diverse natural resources found on rangelands and pasture lands.




During FY 2004, ARS will


provide increased understanding of genetic resources, genomics, and molecular processes of grasses, legumes, and other herbaceous plants that affect establishment, persistence, production and use so improved germplasm and cultivars can be released for pasture, harvested forages, turf, biofuels, rangeland restoration, and conservation.


ACCOMPLISHMENTS:   ARS plant breeders at Lincoln, Nebraska, released two new big Bluestem grass cultivars for the Midwest and Eastern Great Plains.  “Goldmine” is for hardiness zone 6 and “Bonanza” for zone 5.  In grazing trails, “Bonanza” and “Goldmine” produced, respectively 50 and 18 pounds more beef per acre than older cultivars.  During the period 2000-2002 when participation was below normal, “Bonanza” produced over 400 pounds per acre per year of cattle gains.  In an economic comparison with non-irrigated corn on marginal land during the same period, “Bonanza” averaged over $70 per acre more net profit.


IMPACT/OUTCOME:  To remain economically competitive, producers must maintain production with fewer inputs while adapting more effectively to climatic extremes.  Big Bluestem is a native prairie grass well adapted to the climate and pests of the region.  Improving its productivity gives producers more options for economic viability while creating more favorable conditions for wildlife.


ACCOMPLISHMENTS:  Bluebunch Wheatgrass is a premier native grass widely used for revegetation across the Western States.  ARS scientists at Logan, Utah, collected 565 Bluebunch Wheatgrass plants that represented 82 locations spread across 9 States and provinces.  Using multi-locus DNA fingerprinting and statistical cluster analysis, they found that the grass samples fell into 21 geographically significant genetic groups.


IMPACT/OUTCOME:  Land managers are increasingly required to conserve biodiversity within a species to ensure sufficient genetic variability to adapt to changing environmental conditions.  The Logan findings indicate that seeds for most of the 21 genetic groups identified are not commercially available.  This information is helping land managers in identifying and evaluating new seed sources that better reflect local biodiversity needs.


ACCOMPLISHMENTS:  Forage and grain legume producers sustain significant losses from diseases.  ARS scientists at Prosser, Washington, gathered information on the genetic basis of disease resistance in legumes and developed a multiplex real-time PCR assay that identifies key genes conferring resistance. 


IMPACT/OUTCOME:  Breeding resistant cultivars is an important way to reduce these losses without having to use expensive pesticides.  But breeding projects traditionally require long, expensive greenhouse evaluations to identify and evaluate disease-resistance plant materials suitable for crosses.  This new assay will greatly shorten the time and costs to breeders in selecting breeding germplasm with desirable traits and evaluating the new cultivars.


ACCOMPLISHMENTS: ARS scientists at Corvallis, Oregon, developed and made available to commercial grass seed growers a web-based decision support tool that improves the accuracy of predicting rust epidemics during the growing season.  The model also provides information that improves the timing and effectiveness of fungicide applications.


IMPACT/OUTCOME:  Stem rust is the most damaging disease in grass seed production in the Pacific Northwest.  Over 400,000 pounds of fungicide at a cost of $10 million are used annually to control this disease.  The model developed by ARS can reduce producers’ costs by increasing the effectiveness of fungicide treatments and improve the environment by reducing the amount of fungicides applied.


ACCOMPLISHMENTS:  ARS scientists at Madison, Wisconsin, demonstrated that the enzyme, polyphenol oxidase (PPO), helps to reduce the breakdown of protein while ensiling forages for dairy and other livestock operations.  These scientists working with ARS scientists at St. Paul, Minnesota, have cloned a PPO gene found in red clover and inserted it into alfalfa.  The modified alfalfa was found to produce PPO.


IMPACT/OUTCOME:  Alfalfa and some grasses have significant protein loss during the ensiling process.  This results in economic losses because additional protein supplementation for the livestock can be required.  It also results in adverse environmental impacts because nitrogen compounds are released into the environment instead of being retained in the forage.  Commercializing alfalfa with the PPO gene will increase economic and environmental sustainability.


provide forage and pasture management technologies and strategies that reduce inputs while improving livestock performance and sustaining the environment.


ACCOMPLISHMENTS:  ARS scientists at El Reno, Oklahoma, are evaluating options for providing suitable options for year round grazing.  They grazed pastures planted in tall fescue cool season grasses infected with non-toxic endophytes as a supplement to the traditional grazing system.  They found the tall fescue pasture provided producers with an additional 65 days of grazing for stocker cattle with the potential for a 145 additional pounds of gain per animal. 


IMPACT/OUTCOME:  The traditional grazing system in the southern Great Plains based on winter wheat and warm season perennial grasses has serious gaps in forage production and quality in the spring and fall.  Filling these gaps with a suitable cool season perennial grass will provide producers with new options for increasing profitability.


ACCOMPLISHMENTS:  ARS scientists at Brooksville, Florida, examined the effects of cattle stocking rates on phosphorous loadings, forage production, animal performance, and ranch economics.  When compared to the no-grazing control, they found that none of the cattle stocking rates evaluated resulted in increased phosphorus loading.  However, the higher stocking rates did result in increased net income.


IMPACT/OUTCOME:  Pasturelands were assumed to be a major source of phosphorus pollution in southern Florida.  These results indicate that with proper management there is compatibility between profitable livestock grazing and water quality goals.


ACCOMPLISHMENTS:  ARS researchers at Beaver, West Virginia, working with scientists from Virginia State University studied how crossbreeding and finishing options could improve the value of meat goats.

They found that using the recently introduced Kiko meat goat as the male sire in crosses with Spanish and Myotonic breeds produced consistently small, lean carcass more effectively than the traditionally used Boer breeds.  They also found that the offspring finished most efficiently when supplemented with daily feed at a rate between 2 and 3 percent of body weight.


IMPACT/OUTCOME:  One option for increasing profitability on small farms is efficiently serving niche markets such as the one for meat goats on the East coast.  These research results help producers select the best breeding stock and feeding supplementation rates to improve profitability.


ACCOMPLISHMENTS:  Livestock grazers in the Northeast face periods when environmental stresses lead to forage deficits that result in lower livestock production.  ARS scientists at University Park, Pennsylvania, evaluated the effects of increasing plant diversity by planting a mixture of plants in pastures instead of only one or two species.  The hypothesis was that a mixture of plants with different growth characteristics can adapt to shifting environmental conditions better than one or two species.  They found that more complex plant mixtures resulted in fewer weeds and more forage production without a significant reduction in dry matter intake or milk production in Holstein cows.


IMPACT/OUTCOME:  Maintaining profitability requires that the forage deficit periods be reduced without using fertilizers, herbicides, and other expensive inputs.  Establishing pastures with a mix of plants with different characteristics helps to maintain production without additional use of expensive inputs that often have adverse environmental impacts.


ACCOMPLISHMENTS:  Producing liquid fuels from forage biomass offers opportunities to increase national energy independence, diversify rural economies, and reduce greenhouse gas emissions.  ARS scientists at St. Paul, Minnesota, have evaluated procedures for estimating how much ethanol can be produced from biomass stocks, such as alfalfa.  They found that the common analytical system (detergent fiber analysis) used to estimate cellulose and other polysaccharides for livestock production is not adequate for biofuel estimates because it overestimates potential production.


IMPACT/OUTCOME:  This information will help public and private managers develop more accurate estimates of potential production at the farm and processing plant, and nationally so investment options can be more effectively evaluated.


provide rangeland management technologies and strategies that reduce inputs while improving livestock performance and sustaining the environment including reducing the risks of wildfires, invasive weeds and other threats by stabilizing, restoring, and monitoring degraded rangeland in an affordable and sustainable manner.


ACCOMPLISHMENTS:  The lack of basic ecological information about the sagebrush steppe limits developing and assessing management guidelines for integrating livestock grazing and wildlife habitat conservation for species like the sage grouse.  ARS scientists at Burns, Oregon, quantified vegetation cover and composition across the region on 107 Wyoming big sagebrush sites classed as being in excellent condition.  When these findings were compared to current sage grouse habitat management guidelines, they often found the guidelines to be unrealistic in estimating the habitat potential of the land.  They are now working with land managers to develop more realistic guidelines based on this new ecological data.


IMPACT/OUTCOME:  Over estimating the potential of land areas to support a wildlife species can result in poor management and regulatory decisions.  Increasing the amount of science-based information available to managers will result in more effective decisions on livestock and wildlife management.  This includes more accurately identifying ecological sites where livestock grazing was thought to be adversely affecting wildlife numbers, but in fact, is not.


ACCOMPLISHMENTS:  Because there are hundreds of millions of acres of rangelands, the cost of monitoring and assessing the condition of these ecologically diverse lands is a major concern.  ARS scientists at Las Cruces, New Mexico, working with the Natural Resources Conservation Service (NRCS) compared statistical options for analyzing data collected on the Jornada Experimental Range and data from the National Resources Inventory (NRI).  They found that the within-plot replication of data collection for monitoring and assessing at the landscape to regional scales could be significantly reduced from analytical protocols previously used.


IMPACT/OUTCOME:  Applications of these findings are expected to result in savings of as much as 25 percent in NRCS rangeland field data collection.


ACCOMPLISHMENTS:  Cheatgrass (Bromus tectorum) is a serious invasive weed that fuels wildfires and degrades rangeland ecosystems.  ARS scientists at Reno, Nevada, and Beltsville, Maryland, working with the U.S. Forest Service studied the effects of various atmospheric carbon dioxide concentrations on cheatgrass growth.  Increasing carbon dioxide levels from pre-industrial levels of 270 ppm to 420 ppm resulted in an average of 70 percent more cheatgrass biomass at 87 days.  This response to higher carbon dioxide levels could be a factor in the spread of cheatgrass into higher and lower elevations where it was not found previously.  Knowledge of this response will also help land managers identify more effective options for rangeland restoration.


IMPACT/OUTCOME:  Knowledge that increased carbon dioxide levels increase cheatgrass growth provides land managers with additional insights into the complex mix of factors contributing to the spread of invasive weeds and potential limits on restoring ecological sites, particularly to pre-industrial conditions.  Screening out excessively simplistic solutions will save managers time and resources.


ACCOMPLISHMENTS:  Mountain big sagebrush canopies can become too dense and suppress other vegetation important to wildlife and livestock.  ARS scientists at Dubois, Idaho, identified sheep with a high preference for mountain big sagebrush and compared the impacts of these animals grazing on vegetation to a group of sheep identified as having a low preference.  They found no significant difference in sagebrush canopy cover following grazing by either of the two groups.  However, the high preference group consumed significantly more antelope bitterbrush, an important component of the sagebrush steppe.


IMPACT/OUTCOME:  Using livestock to manage vegetative cover to achieve environmental objectives is an ideal management option because it provides an economic resource (livestock) while improving the environment.  However, these results indicate that using grazing to target a specific plant species should to be carefully monitored to ensure there are no unexpected impacts on other ecosystem values. 


ACCOMPLISHMENTS:  ARS scientists at Miles City, Montana, collected information on forage growth over many growing seasons with a variety of climatic conditions including droughts.  They found in the northern Great Plains that perennial grass production is closely tied to the spring rains and only loosely linked to fall precipitation.  About 90 percent of grass production happens by July 1 since summer rainfall is typically very limited.


IMPACT/OUTCOME:  Using this information, ranchers can determine if they are entering a period of drought and low forage production early in the summer and adjust their livestock grazing plans at that time instead of keeping animals through the summer, hoping for summer rain, and then finding themselves in a forage crisis.


OBJECTIVE 5.2:  Provide Science-Based Knowledge and Education To Improve Quality and Management of Soil, Air, and Water Resources.


Performance Measure 5.2.1:  Develop the tools and techniques required to maintain and restore the physical, chemical, and biological integrity of the Nation’s watersheds and its surface and groundwater resources.




During FY 2004, ARS will


develop and demonstrate the use of new irrigation and drainage management practices that improve water conservation and water quality.


ACCOMPLISHMENTS:  The application of fertilizer in irrigation water (fertigation) can be used efficiently for all irrigation methods.  Fertigation brings both nutrients and water to plants and at the same time saves money by combining two tasks into an efficient system.  ARS scientists at three locations have found different ways to improve the application of fertilizer and at the same time apply water more efficiently for the three irrigation methods.  Researchers from Phoenix, Arizona, found that improved fertilizer mixing and injection procedures can be used to improve the uniformity of the fertilizer applications to within 10 to 15 percent variation for surface irrigation practice.  Scientists at Lincoln, Nebraska, working with industry cooperators, developed a new electronic sensor that can be placed at different spacing atop a center-pivot irrigation system to apply variable rate fertilizer and water applications for precision farming.  This same sensor can be used on a high-clearance sprayer or other types of farm implements to precisely and accurately apply variable rate fertilizer applications on both irrigated and non-irrigated (rain fed) croplands.  Also, researchers at Parlier, California, have demonstrated that applying both fertilizers and water on nearly a continuous basis through drip irrigations, which are buried underground, can prevent seepage of excess nutrients into ground waters.


IMPACT/OUTCOME:  Current estimates are that various fertigation techniques will be used on 50 percent of the irrigated lands in the United States by 2010 for an additional increase in farm profits of at least $600 million dollars per year based on conservative estimates for fertilizer savings and increased yields alone with consideration given to environmental benefits.


ACCOMPLISHMENTS:  Phosphorus (P) transport with surface runoff can cause eutrophication (an increase in algae and other plants) in receiving water bodies.  Phosphorus losses from furrow and simulated sprinkler irrigation were measured in field and laboratory tests at Kimberly, Idaho.  Total phosphorus loss is directly related to sediment loss. Soluble phosphorus loss is more complicated, involving soil phosphorus concentration, suspended sediment concentration, and contact time with soil and sediment.  Soluble phosphorus concentration in filtered runoff was linearly related to soil phosphorus concentration.  Management practices that reduce sediment loss from fields also reduce total phosphorus loss.  Using sediment ponds to catch runoff from fields treated with anionic polyacrylamide (PAM) reduced total P loss by 86 to 98 percent compared to not using either treatment.  PAM and sediment ponds, however, did not affect soluble P concentrations.  Recent research has shown that applying 20 mg L-1 alum (about 15 gal per acre-ft) to irrigation return flow reduced soluble phosphorus concentration about 50 percent, but this practice may cost too much for routine use by irrigation districts (at least $8 per acre-ft).


IMPACT/OUTCOME:  Controlling soil erosion is essential for reducing phosphorus losses from irrigated land, but additional economically viable practices are needed to reduce soluble phosphorus losses from irrigated land.


ACCOMPLISHMENTS:  Although drip irrigation systems have been used to effectively and practically apply nutrients and a few pesticides, volatile soil fumigants have not been applied with irrigation water.  With the phase-out of methyl bromide, there is a need to develop alternative soil fumigants.  Registration of fumigants requires application methods that minimize worker and neighborhood exposure from these toxic substances.  ARS developed and refined methods to apply volatile fumigants through drip irrigation systems.  The closed application systems minimize worker exposure; and application in water through subsurface drip to plastic covered beds reduces air emissions and neighborhood exposure.  ARS developed application equipment and procedures; tested chemicals, formulations and mixing techniques; verified fumigant distribution in the soil profile; quantified efficacy of the treatments; and demonstrated the technique in over 25 grower field trials.  In addition, ARS researchers evaluated 39 strawberry drip irrigation systems, found that about half of the systems needed improvement, and presented six workshops on methods to improve strawberry irrigation uniformity.  Three drip-applied fumigants have been registered for use in the United States and several other countries.


IMPACT/OUTCOME:  Based on ARS’ research, the current estimate is that 25 percent of the Nation's commercial strawberries, with a value of $300 million, were drip fumigated in 2004.  Over the next few years, the strawberry acreage that is fumigated through drip irrigation systems could easily double and provide a savings to the grower of over $15 million dollars compared to more expensive alternatives.  The drip technique is also being used to fumigate melons, peppers, and tomatoes, and is being tested for orchards, vineyards, and nursery crops.


ACCOMPLISHMENTS:  Water treatment facility residues help reduce water pollution.  ARS scientists in Florence, South Carolina, and University Park, Pennsylvania, have found that residue from water treatment processes, often discarded as waste and placed in landfills, may make a great soil amendment for preventing loss of phosphorus (P) in runoff from agricultural fields.  ARS scientists have found an alum-based water treatment residual that can increase the soil's capacity to bond phosphorus, a vital plant nutrient.  The results should benefit States along the Nation's mid-to-southern-Atlantic seaboard, where sandy soils generally take up and hold less P than finer-textured soils.  In laboratory tests with sandy soil, the treatment increased P-binding potential four- to five-fold over that of untreated soil.


IMPACT/OUTCOME:  If successful, the use for waste from water-treatment processing not only could get rid of the waste, but would also hold P on the land until a crop uses it.  Economic benefits to the United States of reducing P in runoff are estimated to exceed at $200 million in addition to improving the quality of drinking water.


develop models and decision support systems that quantify the economic and environmental impact of conservation practices at field, farm, and watershed scale.


ACCOMPLISHMENTS:  There is increasing concern regarding the impact of water-borne pathogens on human health.  Enterohemorrhagic E. coli O157:H7 is a serious health threat, particularly in children.  At present, the risk from water-borne transmission of E. coli O157:H7 cannot be estimated because there are no reliable methods for the detection and enumeration of small numbers of these organisms in water samples.  ARS scientists at Beltsville, Maryland, have developed a novel method for the quantitative detection of E. coli O157:H7 in water samples using commercial antibodies coupled to magnetic beads (IM) and a light producing catalyst (ECL).  The method is relatively fast (less than 24 hours) and inexpensive, allowing for the analysis of multiple water samples daily for the detection of as few as one viable bacterium per 100 mL of water.  This assay is currently being used to screen samples from watersheds with different land uses (animal agriculture, urban/suburban, forested) for the prevalence of E. coli O157:H7.


IMPACT/OUTCOME:  A Cooperative Research and Development Agreement (CRADA), entitled “Development of Integrated Waveguide Biosensor for Pathogen and Toxin Detection in Water,” was initiated with Creatv MicroTech.  Hopefully it will be available soon to the public as a fast and economical means of testing for pathogens in public drinking water supplies.


ACCOMPLISHMENTS:  ARS scientists in Oxford, Mississippi, have developed a low-cost means of reducing gully and streambank erosion, one of the major causes of soil loss and sedimentation within our Nation’s streams.  Traditional measures for controlling this type of erosion require costly stone or concrete structures. ARS scientists developed large woody debris structures consisting of uprooted trees stacked in crossing layers anchored to the streambed with steel cables.  These structures provide shelter for fish and insects, restores riparian habitats, and costs less than traditional methods.


IMPACT/OUTCOME:  The structures reduce sediment transport, triggering natural deposition to heal channels enlarged by years of erosion.  Also, the structures cost about $25 per foot of treated bank, or 20 to 50 percent of the cost of recent stone bank stabilization projects in the region. 


ACCOMPLISHMENTS:  In response to mounting water quality concerns, many States have developed guidelines for land application of phosphorus (P) based on the potential for P loss in agricultural runoff.  These actions have been spurred, in part, by a Federal initiative in which the Environmental Protection Agency and USDA created a joint strategy to implement Comprehensive Nutrient Management Plans (CNMPs) on Animal Feeding Operations by 2008, which considers both agronomic and environmental impacts of applied P.  To address this need, ARS led the development and refinement of a P Index to rank the vulnerability of fields to P loss in runoff and identify those at greatest risk for loss.  The Natural Resource Conservation Service (NRCS) has adopted the use of the P index in 47 States as the basis for development of CMNPs, and over 2000 NRCS field agents and nutrient management consultants across the United States have received training.


IMPACT/OUTCOME:  Widespread adoption and use of the P Index is resulting in the first significant reduction in the threat to water quality from non-point sources of P.  Economic benefits of using this approach are estimated at $204 to $355 million and include increased recreational use of waters, better shellfish harvest, fewer fish kills, lower drinking water treatment costs, and reduced loss of livestock to disease.


ACCOMPLISHMENTS:  Soil salinization is a major problem, causing decreased crop production and water quality problems, in irrigated lands of arid and semiarid regions of the world including the Southwestern United States.  Over the past 15 years, ARS researchers at Riverside, California, have developed technology for using electrical resistivity and electromagnetic induction sensors (EM) to measure soil salinity.  Within the past four years, this technology was combined into a mobile platform (typically a modified spray tractor) with global positioning systems (GPS) and a computer to rapidly and remotely collect soil conductivity data.  In cooperation with the U.S. Bureau of Reclamation, a salinity assessment network has been recently deployed throughout the Lower Colorado Region.


IMPACT/OUTCOME:  The primary end users of this technology include technical specialists from the U.S. Bureau of Reclamation and the Natural Resource Conservation Service along with water district personnel throughout the Western United States, various university extension specialists, and research scientists in saline regions throughout the world, including Canada, Mexico, South America, Australia and the Middle East.


ACCOMPLISHMENTS:  Scientists from the Columbia Plateau Conservation Research Center participated in the multi-agency development of the Total Maximum Daily Load (TMDL) and Management Plan for the Umatilla River.  The Umatilla TMDL established limits for water quality and goals for its improvement.  The scientists served on the TMDL technical committee to design preliminary data collection methodologies for temperature, suspended sediment, riparian and stream morphology sampling and data analysis and interpretation; data collection; and review of the TMDL document.


IMPACT/OUTCOME:  The Umatilla River TMDL is one of the first Oregon TMDLs completed and approved by EPA for implementation.  The effort was a multi-agency effort involving private concerns, local municipalities, county, state, tribal, and Federal agencies and is now considered the standard for TMDL development within Oregon.  The broad participation in TMDL development bodes well for a coordinated effort to restore habitat in the Umatilla River and its tributaries to meet beneficial use requirements.


provide technical support to NRCS and the U.S. Forest Service as they deploy ARS soil erosion models throughout the Nation in support of the 2002 Farm Bill.

ACCOMPLISHMENTS:  ARS scientists in Boise, Idaho, working with the National Weather Service (NWS), developed new techniques to more accurately estimate rainfall using the NWS NAXRAD radar system.  The ARS scientists found that the original methods NWS was utilizing under-estimated rainfall by 25 to 60 percent compared to NWS' measurements of precipitation on six highly instrumented experimental agricultural watersheds.

IMPACT/OUTCOME:  The NWS has determined that the ARS-derived technique has greatly improved the accuracy and precision of rainfall estimation and has therefore reprogrammed its radar system in 2004.


ACCOMPLISHMENTS:  The U.S. Army was looking for a way to determine real-time accurate estimates of surface soil moisture to help it plan where and when they can drive vehicles without getting stuck in the mud.  The U.S. Army turned to ARS scientists in Tucson, Arizona, to develop a method for rapidly and accurately estimating these conditions.  The ARS scientists developed a new and simple remote sensing technique of image differencing in part by using data from the long-term highly instrumented Walnut Gulch watershed.


IMPACT/OUTCOME:  This new procedure was found to be superior to the more complex and expensive model currently used by the U.S. Army because it can account for the high rocks content commonly found in desert soils.


ACCOMPLISHMENTS:  SWAT, which stands for Soil and Water Assessment Tool, is being used worldwide to assess environmental benefits.  It was developed over the past 30 years by a team of ARS researchers at Temple, Texas, in cooperation with other ARS scientists in Bushland, Texas; El Reno, Oklahoma; Tucson, Arizona; Ft. Collins, Colorado; Miami, Florida; Ames, Iowa; and Tifton, Georgia.  Over the past four years, EPA and ARS have made SWAT available to State agencies and consultants throughout the Nation to evaluate and assess water quality impairments and to assist in developing watershed plans for addressing specific problems.  The Natural Resources Conservation Service used the SWAT model in its 1997 Resource Conservation Appraisal, in which the first national assessment of agricultural water use, tillage systems, and fertilizer management was made.  In 2004, NRCS and ARS are again using SWAT to work together to quantify the environmental benefits of conservation practices at the national scale and the watershed scale for the Conservation Effects Assessment Project (CEAP).


IMPACT/OUTCOME:  The newest version of SWAT has been distributed to hundreds of scientists and engineers at universities, government agencies, and consulting firms throughout the world.


ACCOMPLISHMENTS:  Scientists from the National Aeronautics and Space Administration (NASA), the National Oceanic and Atmospheric Administration, the Natural Resources Conservation, and Alabama A&M University joined ARS scientists from Beltsville, Maryland, in testing and designing satellites that one day will be able to monitor global soil moisture.  The techniques use sensors that require an antenna that looks like an umbrella or a satellite dish.  The technique functions like a mirror, constantly reflecting radiation emitted from Earth onto sensors that measure the strength of the radiation using microwave signals emitted from soil.  The ARS scientists are testing these methods for a new satellite called Hydros that NASA plans to launch by the end of the decade.


IMPACT/OUTCOME:  Once enhanced soil moisture predictions and measurements are part of daily weather forecasts, it should help predict when rainstorms will occur; provide better assessments of drought stricken areas; provide needed information for assisting in alerting the public to potential floods; and help farmers determine when to plant, fertilize, and harvest crops with more precision and accuracy than has every been available before.


Performance Measure 5.2.2:  Develop agricultural practices that maintain or enhance soil resources, thus ensuring sustainable food, feed, and fiber production while protecting environmental quality.




During FY 2004, ARS will


develop management practices and decision tools which make more efficient use of plant nutrients from fertilizers and other sources while protecting the environment.


ACCOMPLISHMENTS:  Elevated levels of nitrate nitrogen are found in ground water in areas where vegetables are grown in rotation with corn, alfalfa, soybeans, sorghum and wheat.  ARS scientists from Fort Collins, Colorado, found that nitrogen application rates on grain and silage crops could be greatly reduced when these crops followed vegetable crops that had received high nitrogen rates.  This practice significantly increased nitrogen use efficiency by the grain and corn silage crops and reduced nitrogen contamination of ground water.


IMPACT/OUTCOME:  This information can be used by crop consultants, extension agents, and Natural Resources Conservation Service personnel as they make fertilizer recommendations to producers.  Lower nitrogen fertilizer application rates will result in improved water quality and greater profits for producers.


ACCOMPLISHMENTS:  Excessive application of ammonia fertilizer can be attributed in part to farmers compensating for poor application uniformity of current equipment.  ARS scientists from Ames, Iowa, and their cooperators developed a new manifold that produces much more even distribution of anhydrous ammonia across the tool bar.  Benefits of this new technology will be reduced fertilizer application rates, reduced fertilizer cost, and improved water quality.


IMPACT/OUTCOME:  Efficiency of anhydrous application to agricultural lands has been advanced.  This innovative product received an award from the American Society of Agricultural Engineers.


develop management practices and decision tools which improve soil conditions and crop growth.


ACCOMPLISHMENTS:   Compacted soil layers limit yield and reduce overall productivity of soils.  ARS scientists from Auburn, Alabama, have developed real-time instrumentation to measure the depth to the compacted layer thus allowing farmers to till at the appropriate depth to disrupt the restrictive layer. 


IMPACT/OUTCOME:  Continuous measurement of soil compaction will allow tillage to be adjusted to target depths of soil compaction rather than setting a uniform depth of tillage that may be either too deep, wasting energy, or too shallow, ineffectively tilling the soil.  A patent has been received and a partnership with industry developed to produce equipment that will enable farmers to make continuous tillage depth adjustment-based on depth to the compacted layer.


ACCOMPLISHMENTS:  Rangeland assessments and monitoring based solely on vegetation indicators often fail to detect degradation until it is too late for management intervention.  ARS scientists from Las Cruces, New Mexico, have developed three new tools to indicate soil quality:  a soil stability kit, impact penetrometer, and infiltrometer.  These tools, which generate more sensitive and more cost-effective data than previously existing tools, are now available commercially.


IMPACT/OUTCOME:  These soil quality indicators enable rangeland managers to generate more useful information on the status and changes of both private and public rangeland.  The soil stability kit is the only quantitative soil quality protocol used in the Natural Resources Conservation Service-Natural Resources Inventory.  It has been adapted as a standard monitoring tool by groups within Bureau of Land Management, Department of Defense, and the Nature Conservancy.


Performance Measure 5.2.3:  Develop approaches that mitigate the impact of poor air quality on crop production and provide scientific information and technology to maintain or enhance crop and animal production while controlling emissions that reduce air quality or destroy the ozone layer.




During FY 2004, ARS will develop methods to reduce emissions of harmful gases from crop production systems and postharvest/quarantine treatments.


ACCOMPLISHMENTS:  ARS scientists in Gainesville, Florida, in collaboration with University of Florida scientists, studied the dispersion patterns and emissions of the methyl bromide alternative pre-plant soil fumigants: 1,3-dichloropropene (1,3-D), chloropicrin, and methyl isothiocyanate (MITC), the active breakdown product of metam sodium.  These were applied to a Florida sandy soil either as drip-tube placement, shank injection, or rototiller incorporation with three types of raised-bed row cover conditions. For all materials, beds covered with virtually impermeable film (VIF) gave higher concentrations for a longer period of time and better distributions of fumigants in the target rooting zones, possibly because VIF decreased the volatilization losses to the atmosphere.


IMPACT/OUTCOME:  These findings indicate that the use of VIF film row covers could increase the efficacy of fumigants and might decrease the required amount of material to be applied, while decreasing the volatilization to the atmosphere.  This would decrease the hazard to adjacent human habitations and perhaps decrease the set-back requirements of the treated field borders.  Shank injection appeared to be better than either rototilled incorporation or drip-tube application in Florida soil conditions.


ACCOMPLISHMENTS:  Scientists in Fort Pierce, Florida, have addressed the need to enhance the effectiveness of existing chemical fumigants while minimizing the impacts to the environment, thus providing a possible solution to commercial vegetable producers currently relying on soil fumigation with methyl bromide.  Trials were conducted using broadcast applications of Telone C-35 in combination with the herbicides Devrinol and Treflan and an additional application of chloropicrin.


IMPACT/OUTCOME:  In a 50-acre trial that was conducted four consecutive years in the same field, yields in the fourth year under the alternative were higher than in adjacent fields fumigated with methyl bromide.  The incidence of soilborne diseases was lower than in adjacent fields fumigated with methyl bromide.  


ACCOMPLISHMENTS:  Apple replant disease is a significant factor limiting production and profitability of orchards rejuvenated with new trees.  Studies were conducted by ARS scientists in Wenatchee, Washington, to assess the ability of soybean meal and a low glucosinolate rapeseed seed meal to provide control of Rhizoctonia solani AG-5, which causes root rot of apple and contributes to the development of apple replant disease. 


IMPACT/OUTCOME:  Rapeseed, but not soybean, seed meal amendment suppressed infection of apple roots by this fungal pathogen, and disease control was associated with an increase in populations of Streptomyces spp. bacteria naturally resident to orchard soils, and specifically those Streptomyces spp. that possess the capacity to produce nitric oxide, a chemical known to induce plant defense responses.  These studies provide further evidence that sustainable, environmentally friendly systems can reduce apple replant disease.


ACCOMPLISHMENTS:  ARS scientists in Parlier, California, in collaboration with the University of California tested several methyl bromide alternatives in replanted peach and plum orchards and vineyards in a series of field trials located at the SJVASC research station and in growers' fields in Dinuba, California.


IMPACT/OUTCOME:  Emulsified formulations of alternative fumigants 1,3 dichloropropene (1,3-D) and chloropicrin applied through subsurface drip irrigation systems produced tree growth and yields equal to that treated with methyl bromide.  Control of plant parasitic nematodes in vineyard replant plots treated with drip-applied 1,3-D or shank-injected iodomethane was comparable to control achieved by methyl bromide after six growing seasons.


ACCOMPLISHMENTS:  Strategies to replace methyl bromide use for suppression of nematodes and other soilborne plant pathogens are needed for vegetable growers.  In a three year field study scientists in Beltsville, Maryland, have shown that biologically-based treatments incorporating nematode-resistant cover crops for nematode population suppression in tomato cropping systems provided tomato yields similar to, or greater than, treatments using methyl bromide.  In addition, the biologically-based system had significantly lower production costs.  The net return per hectare over two years was $20,084 for methyl bromide and $20,490 for velvetbean cover crop treatments.


IMPACT/OUTCOME:  Biologically-based production systems are an economically feasible alternative to production systems reliant on methyl bromide fumigation, are friendlier to the environment, and contribute significantly to soil fertility.


develop methods and control technologies which reduce particulate matter emissions from crop and animal production systems.


ACCOMPLISHMENTS:  A number of factors control ammonia emissions from wasteful lagoons.  ARS scientists from Watkinsville, Georgia, and their cooperators found that over the short-term (2 to 3 weeks) turbulence of the air is the strongest factor effecting emissions, while over the longer term (6 to 12 months) temperature of the lagoon water is the next most dominant factor.


IMPACT/OUTCOME:  The results suggest that ammonia emissions from lagoons can be managed by reducing turbulence and controlling water temperature.  Two statistical ammonia emissions models have been developed that are limited in scope, but accurate in the geographic area where they were developed.


ACCOMPLISHMENTS:  Elevated ammonia levels in high rise laying hen houses can threaten bird and worker health, and reduce egg production.  ARS scientists from Fayetteville, Arkansas, developed an automated liquid alum delivery system to reduce ammonia levels in the hen house from 90 parts per million to 10 parts per million.


IMPACT/OUTCOME:  The system improved worker safety and bird health.  Egg production was increased 3.3 percent and feed conversion was improved, resulting in a net return of $426 per house per week.


Performance Measure 5.2.4:  Develop agricultural practices and decision support strategies that allow producers to take advantage of beneficial effects and mitigate adverse impacts of global change.




During FY 2004, ARS will


assess the potential risks and benefits to agricultural systems that may arise from global change, and develop agricultural management practices and decision support strategies that enable producers to take advantage of beneficial effects and mitigate adverse impacts.


ACCOMPLISHMENTS:  ARS scientists at several locations have found increased risks to rangeland systems arising from increases in the concentration of carbon dioxide in the atmosphere.  At Beltsville, Maryland, scientists found that the increase of carbon dioxide that already occurred during the 20th century stimulates cheatgrass growth and alters the balance of carbon and nitrogen in its tissues. Combined, these changes result in an increased fuel load that favors more frequent fires than would be expected with native vegetation and promotes cheatgrass invasions.  Similarly, scientists at Temple, Texas, found that increases in carbon dioxide from pre-industrial levels to current day concentrations changed the species composition of intact grassland communities over four years.  Such changes in plant communities may affect the value of rangelands for livestock grazing.  Researchers at Cheyenne, Wyoming, found that exposing shortgrass prairie communities to increased carbon dioxide led to changes in species composition and reduced the nitrogen content of the plants.  These combined effects reduced the digestibility of the native forage.


IMPACT/OUTCOME:  Results of many studies have shown that increasing carbon dioxide concentrations in the atmosphere can stimulate plant growth, which may be beneficial for crop production in some cases.  However, results of recent ARS studies show that there are some risks as well.  Changes in plant communities and the composition of plant tissues may have economic impacts via frequency and intensity of fires or by reducing the value of forage in grazing lands.  Such impacts could require modifying current range management practices, such as fire management and animal stocking rates.


ACCOMPLISHMENTS:  ARS scientists have demonstrated that continued global warming can be detrimental to the production of a variety of crops.  At Gainesville, Florida, scientists found that grain sorghum yields failed completely when the plants were grown at temperatures that may occur in the late 21st century; seed head emergence was inhibited, dwarfism was induced, and benefits of increased carbon dioxide concentration did not reduce temperature sensitivity.  Researchers at Beltsville, Maryland, found that higher than normal temperatures and ultraviolet-B radiation alone or in combination with increased carbon dioxide reduced pollen production and fruit set in soybean; increased temperature during flowering also reduced boll retention by cotton plants.  Such impacts suppress yields, but effects vary among crop varieties.


IMPACT/OUTCOME:  Although studies have shown that increasing carbon dioxide in the atmosphere can benefit some crop plants because they capture more carbon from the air, recent experiments by ARS scientists show that environmental changes accompanying carbon dioxide increases have detrimental effects that offset the benefits.  Increasing carbon dioxide causes global warming, and the increased temperatures adversely impact yields.  Further increases in both carbon dioxide concentration and temperature are expected during the 21st century, so management options such as choosing stress-tolerant crop varieties must be considered, along with other techniques, to sustain yields.


identify the processes that control the rate at which agricultural systems release and absorb greenhouse gases, and develop agricultural management practices that contribute to reductions in the Nation’s net greenhouse gas emissions.


ACCOMPLISHMENTS:  ARS scientists at Watkinsville, Georgia, determined that soil carbon sequestration during the first five years of bermudagrass pasture management was two to three times greater under grazed pastures than under hayed or unharvested management pastures.  ARS scientists at Cheyenne, Wyoming, found that managing the mixture of plant species in rangelands also can increase sequestration. Legumes are a minor component of Great Plains native rangeland ecosystems, and interseeding the native plants with yellow flowering alfalfa increased soil organic carbon by 17 percent after 36 years.  Furthermore, emission of nitrous oxide, a very potent greenhouse gas, was not increased by introducing the nitrogen-fixing alfalfa into the native system. 


IMPACT/OUTCOME:  Sequestering carbon from the atmosphere into soil offsets emissions of greenhouse gases implicated in global climate change.  Results of these studies show that certain management practices for forage and livestock can maintain a productive agricultural system even while enhancing the removal of greenhouse gases from the atmosphere, contributing to improvements in environmental quality and potentially developing carbon credits that may be traded to enhance farm income.


ACCOMPLISHMENTS:  The goal for carbon sequestration in dryland agricultural soils is to return the soils to pre-management levels of organic matter.  In contrast, carbon sequestration may exceed native amounts in properly managed arid zone soils.  ARS researchers in Kimberley, Idaho, and Ft. Collins, Colorado, demonstrated that the carbon in arid soils can be increased above native amounts by a combination of irrigation and conservation tillage practices in soils supporting pastures or crops.


IMPACT/OUTCOME:  Results show that choosing the right combination of management options can benefit not just yield and soil productivity in arid production areas, but also raise carbon sequestration to new levels, which removes carbon dioxide from the atmosphere and slows global climate change.  Enhanced soil carbon may become an increasingly tradable commodity.


Performance Measure 5.2.5:  Develop management practices, treatment technologies, and decision tools for effective use of animal manure and selected industrial and municipal byproducts to improve soil properties and enhance crop production while protecting the environment.




During FY 2004, ARS will


develop management practices and treatment technologies which reduce nutrient losses from animal manure to the environment.


ACCOMPLISHMENTS:  Beef cattle in feedlots are typically fed diets that contain a constant concentration of protein.  ARS scientists from Bushland, Texas, found oscillating dietary crude protein concentrations between moderately deficient (10 percent of dry water) and adequate (14 percent of dry water) at 48 hour intervals resulted in nitrogen retention by the animal and a 5 percent improvement in the average daily gain by finishing cattle


IMPACT/OUTCOME:  This feeding system has the potential to decrease the quantity of nitrogen fed by 5 to 15 percent, resulting in decreased feedlot nitrogen losses through runoff and volatilization.


ACCOMPLISHMENTS:  Soluble phosphorus in manure can impact water quality through runoff and leaching.  ARS scientists from Beltsville, Maryland, found they could reduce the solubility of phosphorus in manure by treating the manure with synthetic zeolites.  The zeolites bind phosphorus in the manure and prevent its movement to water, thus protecting water quality. 


IMPACT/OUTCOME:  The results have been transferred to the Zero Waste Alliance and are being recommended as a phosphorus recovery strategy for dairies in the Northwestern United States.


develop management practices and treatment technologies which reduce gaseous and particulate matter emissions from animal production operations.


ACCOMPLISHMENTS:  Ammonia and hydrogen sulfide emissions from manure storage systems are considered environmental and potential health problems.  ARS scientists from Ames, Iowa, found that a polymer lagoon biocover reduced ammonia emissions by 54 percent and hydrogen sulfide emissions by 58 percent over a three month period.  The longer the biocover was on the lagoon the more effective it became due to the development of a stable anaerobic layer.


IMPACT/OUTCOME:  Lagoon covers can provide a cost-effective method for reducing emissions from lagoon systems and benefit producers who need to reduce emission while operating their current manure storage systems.  


ACCOMPLISHMENTS:  There is insufficient paucity of U.S. data on ammonia losses following field application of manure. ARS researches at Beltsville, Maryland, found that surface applied dairy manure slurries lost 40 to 80 percent of ammonium nitrogen within 24 to 48 hours of application, while solid manure, such as poultry litter had losses of 10 to 30 percent over one week.  They found that compared to surface application, incorporation of manure into the soil by chisel plowing, tandem disk plowing, or moldboard plowing reduced ammonia losses by 80 percent, 90 percent, and 99 percent, respectively.


IMPACT/OUTCOME:  These results will be useful to the Natural Resources Conservation Service and private consultants as they develop nutrient management plans.  Results from these studies have contributed to the development of an ammonia volatilization decision support system that is being used to update ammonia loss estimates in Maryland’s Nutrient Management Program. 


Performance Measure 5.2.6:  Develop agricultural and decision support systems that assist in increasing the efficiency of agricultural enterprises and achieve economic and environmental sustainability.




During FY 2004, ARS will develop new production practices and decision support tools that increase profitability and improve environmental quality.


ACCOMPLISHMENTS:  Due to excessive cultivation and wind erosion in the Lower Rio Grande Valley of south Texas, soil organic matter has decreased from 4 percent at the time of settlement to as low as 0.3 percent today. To improve soil productivity, ARS Scientists at the Kika de la Garza Subtropical Agricultural Research Center, Weslaco, Texas, developed an integrated conservation tillage system that trades most tillage trips over cotton and sorghum fields for a blanket of stems, leaves, and stalks.  Their research showed that when using this system, organic matter doubled in a nine year period, and soil loss to wind erosion was prevented.  In fact, soils with 60 percent crop residue cover accumulated soil blown from nearby fields.  The researchers also developed ways to effectively control weeds without extensive tillage which was critical for success.


IMPACT/OUTCOME:  These conservation practices protected the soil from wind erosion.  Farmers have accepted these practices because production costs have been reduced, giving them greater profits.  An added benefit of this research was the conservation tillage systems were more productive during drought periods. Because of these multiple benefits, this integrated system has been adopted on more than 100,000 acres in the Lower Rio Grande Valley of south Texas. 


ACCOMPLISHMENTS:  Research by scientists at the U.S. Dairy Forage Research Center, Madison, Wisconsin, has shown that modifying diets of confined dairy cattle can increase milk productivity while reducing environmental impacts.  When birdsfoot trefoil with optimal tannin levels was fed in place of tannin-free alfalfa, dairy cattle produced 15 percent more milk and excreted 20 percent less urinary nitrogen - a form of nitrogen readily lost to the atmosphere.  The increased milk production and reduced adverse environmental consequences of dietary condensed tannins are due to improved protein utilization by dairy cattle.


IMPACT/OUTCOME:  Using the ARS Integrated Farm System Model, researchers predicted Wisconsin dairy farms would experience long-term profit increases of up to 12 percent and reduced nitrogen losses of up to 25 percent if dairy farms produced and fed an alfalfa with moderate tannin levels.  This work demonstrates how integrated crop and animal research using computer decision support can provide a road map to develop agricultural systems that are both economic and environmental friendly.

ACCOMPLISHMENTS:  ARS scientists at the Forage Seed and Cereal Research Unit, Corvallis, Oregon, are not only determining the benefits of direct seeding and vegetative buffers to reduce agricultural nutrient and sediment movement from fields to waterways, but also how agricultural drainages and nearby trees can benefit wildlife.  Working with partners from Oregon State University Department of Fisheries and Wildlife, it was shown that native fish use seasonal streams near grass seed fields during the winter.  Nutrient and sediment concentrations in these south Willamette River basin drainages were generally less than those reported to adversely affect fish health, and some fish species even used these drainages to reproduce.  Also, trees naturally growing in fields along drainages were shown to provide habitat for winter songbirds.  University of Massachusetts and ARS scientists in Corvallis, Oregon, showed 17 times more birds were found along forested than non-forested drainages, but only 15 percent of the total land cover was needed to be in trees to maximize songbird diversity.

IMPACT/OUTCOME:  This research shows in addition to providing farmers income from their crops, the seasonal drainages and vegetation near these grass seed fields are providing valuable habitats supporting native fish and bird populations in a landscape that is significantly impacted by cities and towns.  Because aquatic wildlife protected under the Endangered Species Act can be sensitive to high concentrations of sediments and nutrients found in field runoff, these findings will support landowner applications for conservation program payments under the USDA Farm Bill, and help demonstrate compliance with provisions of the Clean Water Act.

Goal 6



OBJECTIVE 6.0:  Provide Mechanisms To Ensure the Relevance, Quality, and Performance of the ARS Research Program.


Performance Measure 6.0.1:  Relevance—ARS’ basic, applied, and developmental research programs are well conceived, have specific programmatic goals, and address high priority national needs.




During FY 2004, ARS will track and report for the number of National Program Workshops, meetings, other workshops, and conferences that were designed, in whole or in part, to review the research focus of each National Program or to establish the research focus for the next 5-year program cycle.


ACCOMPLISHMENTS:  ARS conducted or participated in eleven National Program Workshops or other major meetings, workshops, or conferences that helped to confirm, refine, or direct the research focus of a specific National Program or Programs.


IMPACT/OUTCOME:  ARS’ continuing interaction with its customers, stakeholders, and partners ensures the relevancy of the Agency’s research in meeting the needs of American agriculture.  Meetings during the 5-year program cycle either confirm the direction of the research or allow the Agency to refine the direction.  National Program Workshops with customers, stakeholders, and partners, at the beginning of the 5-year cycle, help ARS establish that National Program’s research agenda.  These processes help enable ARS to fulfill its mission statement to:  “conduct research to develop and transfer solutions to agricultural problems of high national priority and provide information access and dissemination to ensure high quality, safe food, and other agricultural products, assess the nutritional needs of Americans, sustain a competitive agricultural economy, enhance the natural resource base and the environment, and provide economic opportunities for rural citizens, communities, and society as a whole.”


Performance Measure 6.0.2:  Quality—ARS research projects are reviewed by National Program external peer review panels at the beginning of the 5-year program cycle.




During FY 2004, ARS will report summary information on the number and percentage of projects reviewed for prospective quality, and the number in each Office of Scientific Quality Review (OSQR) category; summary data from the Research Position Evaluation System (RPES) peer reviews of Agency scientists; and the number of on-site expert reviews (location reviews) conducted to ensure the ongoing quality and performance of the research program. 


ACCOMPLISHMENTS:  OSQR conducted prospective peer reviews on 240 Project Plans with the follow results:


No Revision                     25       10.42%

Minor Revision                 98       40.83%

Moderate Revision            61       25.42% 

Subtotal             184       76.67%


Major Revision                 44       18.33%

Not Feasible                    12         5.00%

Subtotal               56       23.33%


IMPACT/OUTCOME:  ARS’ OSQR external independent peer review process has strengthened the overall ARS research program.  ARS, as part of its PART analysis, has set a goal of gradually increasing the number of projects that receive a rating of No Revision, Minor Revision, or Moderate Revision to 80 percent by 2010.


Performance Measure 6.0.3:  Performance—ARS will monitor and measure the performance of each research unit and National Program.




During FY 2004, ARS will report summary information that measures specific activities that indicate, to some extent, how well the overall ARS research program is performing.  These activities include the number of papers published, number of CRADAs executed, number of patents issued, number of licenses granted, and the number of new plant varieties and breeding lines released.  Beginning in FY 2004, ARS asked each research leader to assess his/her project’s progress against the milestones in their Project Plan, and indicate whether the each milestone was fully met, substantially met, or not met.  An explanation of why a milestone was not met was also requested.


ACCOMPLISHMENTS:  ARS scientists published 3,587 peer reviewed journal articles and book chapters.


IMPACT/OUTCOME:  Scientific publications are one of the principal mechanisms for transferring research products/findings to potential users of the information.  This is especially true of research knowledge generated by basic or fundamental research where the principal customers are other scientists who carry the work forward through applied and developmental research.


ACCOMPLISHMENTS:  ARS established 44 new CRADAs, received 50 new patents, and granted 29 new licenses.


IMPACT/OUTCOME:  These formal mechanisms enable ARS to more promptly and more effectively transfer new or improved research derived technologies to entities that can use the information to produce new or improved goods and services that benefit American agriculture and the economy.


ACCOMPLISHMENTS:  ARS released 57 new plant varieties and breeding lines.


IMPACT/OUTCOME:  ARS develops and releases new and improved plant varieties and breeding lines that have a wide range of desirable characteristics, such as greater productivity, resistance to diseases and/or pests, or greater tolerance to stresses, such as drought, salinity, etc.  These releases enable public and private sector scientists and breeders to develop new plants and market them to producers.


ACCOMPLISHMENTS:  ARS identified a total of 5,407 milestones across its 1,000+ research projects.  Of these, 3,169 milestones were fully met (59 percent) and 1,419 were substantially met (26 percent) for a total of 4,588 (85 percent) being fully or substantially met.  Eight hundred and nineteen milestones were not met (15 percent). The principle reasons why a milestone was not met were: a vacancy in the lead scientist position (through retirement, death, or delays in recruitment), redirection of the work into areas of higher national priority, failure of a collaborator to provide material in a timely manner, a research methodology did not perform as expected, aberrant weather conditions prevented the research from moving forward (e.g., continuing drought on Western rangeland), and changes in experimental design.  It should be noted that first year data is often open to question.  The Agency expects to refine the guidance governing this data before collecting FY 2005 data.




Analysis of Results:  Under Goal 6, Management Initiative 1, 3 Indicators are aligned under 3 Performance Measures.  While it is not possible to report all accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2004.  Twenty-six significant accomplishments are reported below.


OBJECTIVE 6.1:  Provide Rapid, Comprehensive, and Long-Term Access to the Full Range of Agricultural Information Resources Through a Variety of National Agricultural Library (NAL) Delivery Systems, with Particular Emphasis on Digital Technologies.


Performance Measure 6.1.1:  Develop and deliver content for the NAL National Digital Library for Agriculture (NDLA).




During FY 2004, NAL will continue to expand and improve services based on customer usage and satisfaction data.


ACCOMPLISHMENTS:  NAL built a database to capture statistics about the management and delivery of digital information services, including electronic journals, reference materials, books, web sites, reference responses, and digitized collections.  The work was performed in conjunction with the Association of Research Libraries’ E-Metrics project.


IMPACT/OUTCOME:  NAL used the database to collect FY 2004 data and anticipates that the system will enable NAL to collect and compare cost and usage data consistently over time.  NAL plans to share the database with other research libraries.


ACCOMPLISHMENTS:  NAL increased the total volume of direct customer services by more than 30 percent, to nearly 67 million transactions.


IMPACT/OUTCOME:  More NAL customers were supplied with more services and more information on a 24/7 basis than ever before.


ACCOMPLISHMENTS:  NAL established a pilot small grants program for the Agriculture Network Information Center (AgNIC) members.  Grants were provided to members for digitization projects that would add important agriculture-related content to the web and the AgNIC portal.  An example of a project funding by a grant was the digitization of Farm Bill texts not previously publicly available on the web.


IMPACT/OUTCOME:  More important agriculture information has been available on the web by collaborations between NAL and AgNIC partners.


ACCOMPLISHMENTS:  The AgNIC - - portal architecture was completed in early 2004.  The distributed database interface has allowed one Spanish language partner in Mexico to enter records into the shared AgNIC database.  Most of these will be entered during 2005.


IMPACT/OUTCOME:  These new technologies will support far greater participation in AgNIC by HBCUs and Tribal institutions, as well as the Hispanic Serving Institutions and those institutions located in Spanish speaking countries.  The underlying architecture will also allow distributed web site development, easy content management, and other-than-English language interfaces (i.e., Spanish).


ACCOMPLISHMENTS:  The AgNIC Alliance began working with twelve potential partners ranging from tribal colleges to HBCUs to international organizations and U.S. Federal agencies.


IMPACT/OUTCOME:  The new USDA AgNIC membership encourages broader participation by USDA agencies and programs and establishes a model for partnering between USDA and an academic institution for AgNIC membership.   A small grant for travel expenses will further engage three additional HBCU institutions in a partnership to prepare a subject site on “goals” during 2005.  The distributed system will allow fuller participation by Spanish language communities throughout Latin America.


ACCOMPLISHMENTS:  Penn State University joined the AgNIC partnership to offer information on the History of 4-H.  The site will feature two new electronic finding aids jointly produced by Penn State and NAL -- one describes the earliest 4-H projects and the other provides citations and abstracts to 4-H intern reports.


IMPACT/OUTCOME:  For Penn State, the benefits of becoming an AgNIC partner stem from working with NAL and the 4-H materials.  The information regarding these historical materials is not presently available electronically.


ACCOMPLISHMENTS:  Maintaining the lowest possible turnaround time remained the highest priority for improving services to NAL document delivery customers.  Throughout FY 2004, NAL consistently maintained its goal of completing 98 percent of filled requests in two days.


IMPACT/OUTCOME:  Fast turnaround times and expanded electronic delivery options have been positively received by NAL customers.


ACCOMPLISHMENTS:  The Relais Enterprise document delivery system was installed and preparations were made for a spring 2005 launch.


IMPACT/OUTCOME:  The system will bring significant improvements in services by allowing USDA staff to submit requests for documents electronically from the AGRICOLA database without having to re-key or enter redundant information.  Documents will be delivered to users via the web.


ACCOMPLISHMENTS:  NAL completed the conversion of data from its legacy electronic library management system to the new library management system, Voyager.  The system was fully implemented.


IMPACT/OUTCOME:  Voyager’s search interface and better searching capabilities improves access to the Library’s online catalog, AGRICOLA.  The new system improves customer access to print and electronic materials in the Library’s collection.  The system will support a faster more efficient process for requesting copies of printed materials ensuring speedier delivery of content to NAL customers.


ACCOMPLISHMENTS:  The second year of the NAL-led Digital Desktop Library for USDA (DigiTop) showed continued success.  In addition to the establishment of ongoing funding from ARS, substantial funding was received from other USDA agencies, including the Forest Service.  In addition to providing continuous online access for USDA staff to the full text of electronic journals and newspapers, and to research databases, DigiTop added the provision of an end-user searchable Table of Contents service and an automated Selective Dissemination of Information or article citation alert service.


IMPACT/OUTCOME:  DigiTop provides 24-hour-a-day access to high demand databases, journals, newspapers, and other important digital information resources to USDA’s more than 100,000 staff members, who can search current citations and abstracts for more than 8,000 scholarly academic journals and the tables of contents for over 23,000 journals.  For periodic alerts of new publications of interest, DigiTop customers can have individualized search strategies developed, where appropriate databases are selected to meet specific needs, and duplicate records from overlapping databases are removed.  DigiTop services enable direct access to much needed information immediately, thereby providing a much stronger support to policymaking, research, and operations than was possible before DigiTop.


ACCOMPLISHMENTS:  The Food Safety Information Center (, which has two major emphases, saw significant increases in web site usage; more than 25 percent on the Food Safety Research Information Office web site and 111 percent on the Foodborne Illness Education Information Center (FSRIO) web site.  The center also began work on a trust fund agreement with the National Food Service Management Institute to provide information management and technical assistance on food service projects related to HACCP.  FSRIO hosted an ARS researcher for eight weeks who learned how to develop information products and provided a researcher’s perspective to the FSRIO products.  Significant progress in the migration to a database-driven web site was made in the FSRIO program as well as the ability to share the same database to display links, such as the Foodborne Illness program.


IMPACT/OUTCOME:  The FSRIO web sites’ growing usage has increased the ability to support information sharing for researchers and educators in food safety.  Sharing technology reduces duplication of work effort and saves time and cost of producing online resources.


ACCOMPLISHMENTS:  In collaboration with the ARS National Program Leader for Animal Health, NAL produced a major publication in support of the 2003 ARS Immunology Research Workshop, held in December 2003.  An electronic version of the publication will be available in 2005 on the web via the NAL Animal Welfare Information Center (AWIC) web site -


IMPACT/OUTCOME:  The workshop proceedings publication showcases the depth and breadth of the USDA immunology research and details results of four working groups tasked with identifying future research needs.  It also serves as an example of how NAL information centers can provide important support to the operational programs of USDA agencies.


ACCOMPLISHMENTS:  The Water Quality Information Center produced a comprehensive four volume bibliography covering environmental effects of USDA conservation programs, reviews of state-of-the-art conservation practices, environmental credit trading, and barriers and incentives to implementing conservation practices.  The volumes are available in print and online.


IMPACT/OUTCOME:  The four volume bibliography was produced to support the goals of USDA's multi-agency Conservation Effects Assessment Project (CEAP).  The bibliography was the first major accomplishment of the project and was distributed at the 12th National Non-point Source Monitoring Conference and to various stakeholders with interests in agricultural and environmental issues, including authors of a USDA-led literature synthesis of conservation practices used in cropping systems.


ACCOMPLISHMENTS:  NAL began working with the Economic Research Service (ERS) on a new Food Stamp Nutrition Connection recipe database scheduled to premier in June 2005 that will integrate data from the Infoscan database containing food price information from over 11,000 vendors in the United States.


IMPACT/OUTCOME:  The database will be used by Food Stamp educators nationwide to help program beneficiaries better manage family food dollars while preparing nutritious meals.


ACCOMPLISHMENTS:  Other publications and web-based information services developed by NAL covered various topic areas and emerging issues including:  Soybean Rust; Alternative Farming - Organic Marketing; Technology Transfer - Bioenergy and Biofuels; Water Quality - Conservation Programs and Practices; Food Safety - Risk Assessment, Biosensors, Predictive Microbiology; and Animal Welfare - Care and Use of Insects, Beef Housing and Welfare, Spaying and Neutering, Care of Selected Birds, Giant Panda Care, Traveling with Animals, BSE, and Other Animal Related Transmissible Spongiform Encephalopathies.


IMPACT/OUTCOME:  The development of these publications, often published quite rapidly, is one example of NAL’s response to customer information needs.  NAL’s web sites are linked to tens of thousands of institutions around the world and Web-site evaluation organizations continuously direct customers to NAL and make awards to NAL sites.


ACCOMPLISHMENTS:  Working under a formal agreement with the Technology Transfer Information Center, Artifex Equipment, Inc., was awarded a $75,875 SBIR grant from USDA to test the feasibility of using a corn-based, ARS-developed super absorbent polymer to dry wet materials.  A potential product called Dri-Gel emerged.  Nineteen additional agreements were signed to allow other libraries and organizations to test the product, and a provisional patent application was filed.  Additional testing by USDA chemists confirmed that the product does not harm paper.  Artifex received orders for the early stage product and is beginning to move into manufacturing. 


IMPACT/OUTCOME:  The funding received from SBIR/USDA allowed the testing, design, and early development of a new biobased product, Dri-Gel, for drying wet books and other materials, and the product is moving toward commercialization.  Artifex signed an agreement with another SBIR company and will begin marketing two products, Dri-Gel and an environmentally friendly de-acidification product.  This could result in the adoption of two new technologies by NAL and the archive community, and the prosperity of two very small companies.  This work illustrates how the Technology Transfer Information Center and other information centers use NAL’s electronic information sources to serve as an information support system to connect customers to research, market and manufacturing information, and to promote economic development.


ACCOMPLISHMENTS:  Content enhancements to the web site in FY 2004 include: Western Rangelands Invasive Plants; seventeen new species profiles; images added to nearly all species profile pages; a species of the month feature; enhanced coverage for legislation; international meetings; educational resources, etc.  The program continues to plan for change; input was gathered at a stakeholder workshop and through the ForeSee Customer Satisfaction Survey.


IMPACT/OUTCOME:  Impact of the web site continues to grow.  October 2004 saw nearly twice as many hits compared to the same month in 2003; altogether in the last year the web site was accessed more than two million times.  The stakeholder workshops and the ForeSee survey results are yielding information to guide development of the web site to better meet customer needs.


Performance Measure 6.1.2:  Integrate the NAL AGRICOLA database into the NDLA.




During FY 2004, NAL will continue to increase the amount and types of agricultural information covered by AGRICOLA, particularly online full text publications, reduce the time required for indexing top priority journal articles, and improve ways of finding information in AGRICOLA.


ACCOMPLISHMENTS:  NAL’s Technical Services Division continually monitors USDA and GPO web sites to identify new titles that should be added to NAL’s collection, including those available in electronic format.  In addition, numerous titles formerly received as gifts or on exchange are now available only via the web.  URLs for these types of publications are continually added to AGRICOLA, ensuring that access is continued and increasing the titles for which full text is available via AGRICOLA.


IMPACT/OUTCOME:  Materials that are shifting to e-only format are routinely identified, captured, and updated in the AGRICOLA catalog ensuring continued access to content and increasing the proportion of materials that are available electronically.  This will transition the NAL collection, as access becomes available, to electronic format and ultimately serve as the backbone for the National Digital Library for Agriculture.


ACCOMPLISHMENTS:  NAL catalogers and indexers added 9,533 links to online digital publications into the AGRICOLA database.  This represents a 19 percent increase over 2003 levels bringing the total to over 52,000 links.


IMPACT/OUTCOME:  AGRICOLA provides full text at the desktop for an additional 9,533 full text electronic publications.


ACCOMPLISHMENTS:  NAL implemented the use of the Voyager indexing module.  Enhancements to the indexing module remain to be implemented in order to maximize production, but the indexing of journal articles has recommenced and streamlined production was implemented.  This is part of an overall restructuring of the indexing workflow and the introduction of automated bibliographic systems that will speed up the creation of indexing records for AGRICOLA.  


IMPACT/OUTCOME:  NAL has established the environment and technology for new procedures and programs that will streamline the creation of citations for AGRICOLA in FY 2005 - 2006.


ACCOMPLISHMENTS:  In January, NAL published an updated 2004 version of the National Agricultural Library Thesaurus (NALT), which is used for indexing journal articles in AGRICOLA.  AGRICOLA bibliographic records were updated with the new terminology.


IMPACT/OUTCOME:  Updates in terminology which is alignment with agricultural trends and innovations simplifies finding relevant information in AGRICOLA.


ACCOMPLISHMENTS:  In August, a duplicate (mirror) web site for the NALT was established at the College of Agriculture and Natural Resources (CANR), Michigan State University.


IMPACT/OUTCOME:  A duplicate (mirror) web site ensures the availability of the thesaurus web pages and search functionality to customers in the case of unforeseen circumstances at either location and distributes system load among and between the two IT systems so that performance and reliability are optimal for customers.


Performance Measure 6.1.3:  Ensure long-term access to the resources of the NAL NDLA.




During FY 2004, NAL will continue to preserve, protect, and secure its national collection of agricultural information.


ACCOMPLISHMENTS:  NAL maintained currency with the latest versions of the software for Lots of Copies Keeps Stuff Safe (LOCKSS), a collaborative digital preservation demonstration project led by Stanford University.  NAL also began participation in the LOCKSS program as part of the LOCKSS/DOCS program working collaboratively with the Government Printing Office, Stanford University, and other universities in an effort to provide long-term access to government documents.  To that end, GPO visited NAL and did a system security scan of the LOCKSS hardware/software system.


IMPACT/OUTCOME:  NAL’s participation in the LOCKSS demonstration program is important in exploring options for providing citizens access to digital government information over time.  This effort marks pioneering efforts to address the issues of long-term storage, authenticity, and access for digital information.


ACCOMPLISHMENTS:  NAL’s digitizing efforts included completion of an effort to digitize the heavily used USDA Home and Garden series publications, improving access to the Journal of Agriculture and the Yearbook of Agriculture, increasing availability of digitized historical photographs, and other small collections which meet the needs of users.  The subject emphasis for digital conversion in 2004 was rural information.  Planning for links from the AGRICOLA database to NAL-digitized texts is underway.


IMPACT/OUTCOME:  Digitizing important library materials is key to meeting the needs of a varied customer base.  Digitization of the Home and Garden series publications was a model collaborative digital content building project among NAL, AgNIC, and Michigan State University.  This project not only provides customers with online access to a highly desirable and historic collection of USDA publications, but also provides a model for resource sharing to complete such a project.  Additional projects in 2005 will build on resource sharing and address the challenges encountered in digital projects.


ACCOMPLISHMENTS:  Cybersecurity activities included upgrading NAL’s firewall, instituting new user password change procedures in conjunction with migrating to Windows XP, responding to USDA security mandates, providing ARS online training in computer security, implementing a proxy server for USDA access to licensed databases through NAL, and launching a Virtual Private Network (VPN).


IMPACT/OUTCOME:  NAL’s improved security posture provides an even higher level of assurance for data integrity, mitigation of computer and network vulnerabilities, and at the same time, improved functionality for users.


ACCOMPLISHMENTS:  ARS designated the Abraham Lincoln Building as one of its mission critical sites due to NAL’s collection of materials that could be researched and utilized in the event of a national disaster.  As a result, approximately $1 million was provided to NAL for facility security upgrades in FY 2003.  Most of the upgrades were completed by the end of FY 2004.


IMPACT/OUTCOME:  Security upgrades are 95 percent complete and all of the systems are operational.  The contractor still has to complete minor corrections to the different security systems.  The security upgrades will provide better oversight of access to the building.  A state-of-the-art camera system provides a visual overview of activities at several critical locations at both internal and external areas around the building.  Guard service was also increased to ensure better coverage throughout the building, especially the entrances, loading dock, and the parking areas.




Analysis of Results:  Under Goal 6, Management Initiative 2, 1 Indicator is aligned under 1 Performance Measure.  While it is not possible to report all accomplishments numerically, the progress projected in this Indicator was completed or substantially completed during FY 2004.  The accomplishments are reported below.


Performance Measure 6.2.1:  Complete priority buildings and facilities projects on schedule and within budget.




During FY 2004, ARS will continue to modernize and construct new research facilities on a priority basis. 


ACCOMPLISHMENTS:  ARS completed design of research facilities at the following locations:  Albany, California; Hilo, Hawaii; Peoria, Illinois; Ames, Iowa; St. Paul, Minnesota; Oxford, Mississippi; Sidney, Montana; Wyndmoor, Pennsylvania; Charleston, South Carolina; Logan, Utah; and Leetown, West Virginia.  ARS completed construction of research facilities at the following locations:  Ames, Iowa; Miles City, Montana; Wyndmoor, Pennsylvania; and Albany, California.


IMPACT/OUTCOME:  New or modernized laboratory facilities have been provided to support the mission of the Agency in the areas of nutrition, food safety/quality, animal production and protection, natural resources and sustainable agricultural systems, and crop production and protection.

Last Modified: 8/17/2005