AGRICULTURAL RESEARCH SERVICE

FY 2002 ANNUAL PERFORMANCE REPORT and
FY 2003, FY 2004, and FY 2005 ANNUAL PERFORMANCE PLANS  

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 1,100 research projects, which are organized into 22 National Programs, undergoes a thorough external peer review conducted by the Office of Scientific Quality Review 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 scientific workforce.

The National Programs focus the work of the Agency on achieving the goals defined in the ARS Strategic Plan.  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, www.ars.usda.gov, open “Research.” 

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 take these developments into consideration. 

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—can 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 20^th 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.  Farms are larger, and production methods are more specialized.  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 technology, and global markets bring about continuing changes that affect farmers, processors, marketers, and consumers.

Congressional Support:  The ability of ARS to respond to the many and 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 bring the current number of scientists to over 2,100.

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, the ARS is able to use narrative descriptions of intermediate outcomes and indicators of progress instead of numerical metrics as specified in GPRA.  The FY 2002 accomplishments reflect actual achievements against the FY 2002 indicators previously identified.  The indicators shown will serve as measurable milestones during FY 2003, FY 2004, and FY 2005.  The research and technology transfer activities listed in this exhibit are not all inclusive of the Agency’s work.  The indicators reflect, but do not adequately capture, the broad range of basic research that underpins most of the Agency’s work.  The following qualitative indicators are specific accomplishments that the Agency anticipates achieving in the designated fiscal year, which constitute milestones or indicators of progress towards meeting the Agency’s goals, objectives, and initiatives.

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

GOAL I:  To Promote an Agricultural Food and Fiber System That Is Productive and Highly Competitive in the Global Economy.

Funding by Program Activity ($000's)	FY 2002	FY 2003	FY 2004
Soil, Water & Air Sciences	794	780	787
Plant Sciences	40,510	47,653	51,635
Animal Sciences	14,940	19,185	22,453
Commodity Conversion & Delivery	102,779	115,373	118,330
Human Nutrition	0	0	0
Integration of Agricultural Systems	1,097	1,126	1,128
Total	$160,120	$184,117	$194,333
FTEs	1,417	1,458	1,486

NOTE: Not included in the table are appropriations for repairs and maintenance of ARS facilities and for some of Homeland Security. 

Analysis of Results for FY 2002:  This goal is the focus of much of ARS’ research related to production agriculture.  Under Goal I, 29 Indicators are aligned under 12 Performance Goals.  Because of the unique and dynamic nature of research, several Indicators were added, deleted, or modified in this report that did not first appear in the Annual Performance Plan for FY 2002.  This was done to ensure that significant accomplishments that were not anticipated last year were reported.  While it is not possible to report research accomplishments numerically, the progress projected in all 29 Indicators was completed or substantially completed during FY 2002.  Sixty-seven significant accomplishments are reported below.

Means and Strategies:  To successfully accomplish the research activities under this goal, ARS will need the level of human, fiscal, physical, and information resources shown in the budget estimates for fiscal years 2003 and 2004.

Verification and Validation:  ARS currently 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.  A more detailed description of the evaluation plans can be found in the introduction of this plan.

OBJECTIVE 1.1:  Strengthen competitiveness:  “Enhance the competitiveness of the United States agriculture and food industry in an increasingly competitive world environment.”

STRATEGY 1.1.1:  Cost-effective agricultural production systems:  Develop new knowledge and integrated technologies for more efficient and economically sustainable agricultural production systems of all sizes.

PERFORMANCE GOAL 1.1.1.1:  Demonstrate integrated systems and transfer them to users.

Indicators:

During FY 2002, ARS will quantify stress responses of cattle, swine, and poultry to specific management practices and to the entire production system.

ACCOMPLISHMENTS:  Scientists of the Livestock Behavior Research Unit, West Lafayette, Indiana, published measures of well-being of animals kept in specific management systems.

IMPACT/OUTCOME:  This information was transferred to the industry and aided in making choices related to the tail-docking of dairy cattle.

During FY 2003, ARS will

develop technologies to enhance artificial insemination for the sheep industry.

develop selection methods to increase litter size in swine.

transfer to producers information for improving carcass quality in Brahman cattle.

have recommendations on weed control and fertility management for organic producers.

have information and recommendations on the performance of a number of management systems.

During FY 2004, ARS will

develop improved methods to estimate daily yields of herds using robotic milking or reduced sampling.

estimate direct and material breed efficiency effects of four types of cross-herd ewes using intensive and extensive production systems.

During FY 2005, ARS will

provide completed feed reference database for the Feed Information Technology System for corn silage and alfalfa.

transfer to beef cattle producers decision support software for evaluating composite breed formation and evaluation.

develop mathematical models to rate animal well-being for several production practices.

PERFORMANCE GOAL 1.1.1.2:  Demonstrate and transfer to users computer-based simulation models and decision support systems.

Indicators:

During FY 2003, ARS will

provide updates for the Crop Sequence Calculator and expand this decision aid’s capacity and capability.

develop four decision aids for peanut production and marketing, and a baseline for the optimal time path for resource allocation for small livestock/crop farms in Western Oregon.

STRATEGY 1.1.2:  Preharvest and postharvest control of pests:  Develop preharvest and postharvest technologies and processes to meet domestic needs and reduce or overcome non-tariff trade and quarantine barriers caused by pests (insects, weeds, pathogens, etc.).

PERFORMANCE GOAL 1.1.2.1:  Demonstrate techniques to control or eliminate preharvest and postharvest insects and diseases, and increase market quality and product longevity.

Indicators:

During FY 2002, ARS will

continue development of post-harvest insect control methods for stored grain and other commodities to replace insecticides and methyl bromide that are being phased out because of environmental and health concerns.

ACCOMPLISHMENTS:  New formulations of the insect growth regulator (IGR) methoprene helped control grain beetles, and data are now being used to support the reintroduction of methoprene into the stored grain market.  A volatile formulation of the IGR hydroprene (Pointsource) registered for cockroach control also was effective against the red flour beetle and the confused flour beetle, two common insect pests in food storage areas.  These species were added to the product label.  Thiamethoxam, a new neo‑nicotenoid compound used as a seed treatment for field crop pests, also controlled stored‑product beetles, and could protect stored seeds from economic damage.

IMPACT/OUTCOME:  Development of these biorational pesticides provides additional options for the protection of stored grain.

ACCOMPLISHMENTS:  Pheromone monitoring programs were developed and tested in a commercial warehouse and flour mill.  The data generated was used to determine the influence of trap type, location, and number of traps on insect capture and the interpretation of capture data.  Monitoring programs outside of commercial facilities were also conducted to determine the significance of insect immigration.  Some additional issues being addressed are the relationship between insect movement patterns and trap capture and the relationship between trap capture and product infestation.  Studies are also being conducted to measure the probability of a passing insect being captured by a pheromone trap.

IMPACT/OUTCOME:  Results of this research will help to make recommendations about the optimal trap types, attractants, locations, and trap numbers to maximize the quality of information generated by monitoring programs.

develop environmentally friendly biopesticides and natural product-based pesticides.

ACCOMPLISHMENTS:  Obtained a U.S. patent for a novel fungicidal saponin (CAY-1) that was purified from cayenne pepper.  Determined that CAY-1 is active at low levels against fungal pathogens affecting strawberries, blueberries, and grapes.

IMPACT/OUTCOME:  Successful field and greenhouse trials could lead to commercial use of crude or semipurified cayenne extracts as a new fungicide treatment on these crops.  This would provide a novel fungicide and enhance the economic value of cayenne pepper to farmers.

ACCOMPLISHMENTS:  Evaluated the compound sampangine and two analogs for activity against agriculturally important phytopathogens.  One compound (patent being written) had excellent antifungal activity against several economically important fungal pathogens.  Further evaluation of this compound and its active analogs was completed.

IMPACT/OUTCOME:  Transferred technology for miniaturized bioassays through collaborations and training of other scientists.

develop and demonstrate post-harvest insect control technology for use on stored commodities, storage facilities, and food processing plants.

ACCOMPLISHMENTS:  Scientists at Manhattan, Kansas, participated in a series of flour mill related studies that can be used to evaluate treatments, interpret trap catches, and determine impacts of insect movements outside the facilities on infestations within.

IMPACT/OUTCOME:  These studies will aid in development of methyl bromide alternatives for flourmills by providing information on when and why pest populations rebound after treatment.

During FY 2003, ARS will

elucidate and manipulate internal mechanisms of resistance to reduce postharvest decay.

reduce postharvest losses and improve quality through resistant cultivars.

continue development of post-harvest insect control methods for stored grain and other stored commodities to replace insecticides and methyl bromide being prohibited because of environmental and health concerns.

develop environmentally-friendly biopesticides and natural product-based pesticides.

During FY 2004, ARS will

continue development of postharvest insect control methods for stored grain and other commodities to replace insecticides and methyl bromide that are being phased out because of environmental and health concerns.

develop and demonstrate new fumigants and other insect control technology to control stored product pests of concern.

develop environmentally friendly biopesticides and natural product-based pesticides.

elucidate, manipulate, or induce existing internal mechanisms of resistance to reduce postharvest decay and improve the quality and longevity of commodities.

identify physical and biologically based approaches that enhance the performance of biocontrol agents against preharvest and postharvest pathogens.

During FY 2005, ARS will

develop practical, effective, economical alternatives to methyl bromide for soil fumigation.

develop practical, effective, economical alternatives to methyl bromide for postharvest treatment (including quarantine).

develop environmentally friendly biopesticides and natural product-based pesticides.

elucidate, manipulate, or induce existing internal mechanisms of resistance to reduce postharvest decay and improve the quality and longevity of commodities.

identify physical and biologically based approaches that enhance the performance of biocontrol agents against preharvest and postharvest pathogens.

PERFORMANCE GOAL 1.1.2.2:  Demonstrate technologies to control quarantine pests.

Indicators:

During FY 2002, ARS will

develop and demonstrate new fumigants and other insect control technology to control quarantine pests of  concern.

ACCOMPLISHMENTS:  Scientists at Parlier, California, have demonstrated that heat treatment, which is effective in controlling insects in fresh fruit commodities but generally causes unacceptable fruit damage, had no adverse effects on fruit when combined with low oxygen and high carbon dioxide.

IMPACT/OUTCOME:  This new type heat treatment shows promise as an alternative to methyl bromide fumigation for quarantine treatment of peaches and nectarines.  

continue to develop alternatives to methyl bromide for weed management.

ACCOMPLISHMENTS:  The invasive perennial vines, kudzu, redvine, and trumpetcreeper are difficult to control with conventional weed control methods and are becoming problematic in the southern United States.  ARS scientists at Stoneville, Mississippi, tested the bioherbicidal fungus, Myrothecium verrucaria, in combination with glyphosate for synergistic interactions. 

IMPACT/OUTCOME:  The weeds were controlled (94 percent, 86 percent, and 78 percent, respectively) in field sites that were infested by simultaneous application of glyphosate and corn oil emulsion formulations containing the fungus.  These results suggest that it may be impossible to greatly enhance the bioherbicidal potential of M. verrucaria using gylphosate as a disease synergist, thus saving land managers millions of dollars each year. 

ACCOMPLISHMENTS:  The search for methyl bromide alternatives in vegetable crop systems has led to the exploration of alternative technologies, including solarization.  Studies were initiated to evaluate the combined effect of heat treatments and durations of exposure on the viability of tubers of purple nutsedge and yellow nutsedge, the primary means of reproduction for these weeds.  Purple nutsedge tubers were shown to be more tolerant of elevated temperatures than were yellow nutsedge tubers. 

IMPACT/OUTCOME:  Solarization cannot be relied upon as a means of reducing nutsedge tuber viability due to the inability to raise soil temperatures for critical durations of exposure. 

continue to screen biological control agents for the mitigation of witches broom (Crinipellis perniciosa) and frosty pod (Moniliopthora roreri) under greenhouse conditions and in overseas test plots.

ACCOMPLISHMENTS:  Large-scale trials of Trichoderma as a candidate control agent (mycogenic) have been initiated in Brazil and Peru.  In both cases substantial reduction in brooms and new infection have been noted.  Innovative application technologies, which hasten colonization of control agents, have also been perfected and applied.

IMPACT/OUTCOME:  No commercial fungicides are effective in disease control for cocoa.  Copper sulfate is widely used, but has highly negative environmental impact.  Effective, low-cost, environmentally benign pesticides and biopesticides are urgently required.

initiate research to develop competitive endophytes for controlling black pod (Phytopthora spp.) in cocoa plantations in the Caribbean and West Africa.

ACCOMPLISHMENTS:  Cooperative agreements have been established with African, French, and private industry partners for trials at IITA in Abidan, Nigeria, and in Cameroon.  Work is ongoing.

IMPACT/OUTCOME:  Same as indicator (1), above.  Currently, trials with biopesticides are underway in collaboration with partners from industry, France and the Government of Cameroon in West Africa.

continue research to identify, assay, and field trial control agents for coffee berry borer (Hypothenemus hampei) with emphasis upon both parasitoids and insect pathogens.

ACCOMPLISHMENTS:  Artificial diets have been produced for Cepholomia, a parasitic wasp specific to the borer.  Releases have been made in Colombia and other countries in Central America.  An effective molecular map of Hypothenemus has been developed and published, which is a necessary tool in developing meaningful biological control strategies.

IMPACT/OUTCOME:  Endosulfans are widely used to control coffee berry borer.  These pesticides are dangerous to human and animal health, relatively expensive, and of decreasing effectiveness.  For economic reasons alone, cost-effective methods of integrated pest management are urgently required, especially in view of declining wholesale coffee prices.

continue coffee berry borer field trials, including limited scale releases of control agents in Costa Rica, Colombia, Peru, and Jamaica.

ACCOMPLISHMENTS:  These trials are continuing and Mexico (State of Chiapas) has been added to the field trials.

IMPACT/OUTCOME:  Most classical biological control strategies fail because large-scale field trials, under varying environments, are not carried out.

continue research to characterize and classify significant collections of cocoa (Theobroma cacao) in cooperation with European and South American collaborators using genetic mapping techniques, with a view to identifying important characteristics linked to disease resistance, quality, flavonoids, and postharvest stability.

ACCOMPLISHMENTS:  Collections in Trinidad and Puerto Rico have been mapped.  Mapping is ongoing in Ecuador, Costa Rica, and West Africa.

IMPACT/OUTCOME:  Cocoa has suffered as a crop due to a poorly developed genetic base.  Furthermore, modern breeding practices have not been implemented because existing international collections are incorrectly characterized in a large number of instances, making intelligent selections virtually impossible.

continue research to express genetic markers for resistance to Crinipellis, Phytopthora, and Moniliopthora.  Develop collaborative relationships with foreign collaborators to explore, breed, characterize, and introduce improved varietals in important genetic collections.

ACCOMPLISHMENTS:  Cooperative agreements have been signed with CIRAD, France for the development of BAC libraries, micro-satellites, INIAP, Ecuador, for Crinipellis resistance, CATIE-Costa Rica for genetic diversity studies, IITA-Nigeria for Phytopthora resistance.

Enriched micro-satellite maps have already been produced.  Some Quality Trait Loci have already been linked to resistance but will not be published until 2004.

IMPACT/OUTCOME:  Virtually all breeding to date has been for quality and productivity characteristics.  Establishing disease resistance in the coffee crop is urgent if it is to survive at any level as a commercial enterprise in the Western Hemisphere.  In Africa, the genetic base is dangerously narrow with little demonstrated Phytopthora tolerance.

continue to develop the Tropical Agricultural Research Station in Puerto Rico as a hemispheric source for disease-free tree crop genetic material for transfer to alternative crop programs in the Americas.

ACCOMPLISHMENTS:  A full time curator has been recruited in Mayaguez.  In Miami, the quarantine greenhouse has been rebuilt, allowing for the conservation and dissemination of clonal material, budwood, and grafts.

IMPACT/OUTCOME:  Sharing genetic material between countries in the Americas has been virtually impossible due to a lack of certified, disease free breeding material.

initiate soil and water conservation research with relevance to integrated pest management and sound agricultural husbandry applications to tropical tree crops in the Americas.

ACCOMPLISHMENTS:  In cooperation with industry, a micronutrient program has been initiated in Brazil.  In cooperation with the Government of Peru and the U.S. Embassy in Lima, an agro-forestry program has been initiated in the Amazonian region.

IMPACT/OUTCOME:  Little is known about the optimal cultural requirements for cocoa.  Micronutrients play a key role in the viability of other perennial tree crops and most likely will be significant in the case of cocoa, which is well suited to a mixed forestry environment.

continue a program of research and technology development and transfer to cooperating Federal and international organizations, to evaluate control methodologies involving integrated pest management directed to illicit cultivation of coca and opium in South America.

ACCOMPLISHMENTS:  ARS has supported the Department of State since 1987, by interagency agreement, in developing herbicidal applications, which are effective and environmentally safe for illicit crop eradication in South America.  A large number of granular and foliar agents have been evaluated both under simulated and field conditions.  The Government of Colombia has agreed to use glyphosate, a low toxicity herbicide, for the eradication of both crops.  Glyphosate is essentially harmless to human beings and vertebrates and quickly biodegrades in soil and water.  Technology transfer, through both the United Nations and the Department of State, has also been accomplished, which has included the development of appropriate application technologies and herbicidal adjuvants.

IMPACT/OUTCOME:  Results of the research and development program have been widely reported in interagency memoranda, to the Government of Colombia and the United Nations and in peer reviewed journals.

continue research and technology development in cooperation with U.S. land management and Federal enforcement agencies to identify, characterize, and control illicit cannabis grown in the U.S.

ACCOMPLISHMENTS:  Most illicit cannabis grown in the United States is grown under canopy or in buildings as a concealment strategy.  Currently, no technology exists to adequately perform remote sensing under these conditions.  Barring technological breakthrough, the program will not be renewed after calendar year 2004.

IMPACT/OUTCOME:  Aerial sensory techniques, applicable to public lands for the detection of cannabis in open terrain, have already been developed and have been provided to the Air National Guard, various state agencies and the Office of National Drug Control Policy.  Technology transfer for this portion of the research program is essentially complete.

During FY 2003, ARS will

identify at least two candidate organisms available for field trial release and evaluation for the control of witches broom (Crinipellis perniciosa) and frosty pod (Monilopthora roreri), the major diseases of cocoa in Central and South America.

establish one scientist at the International Institute of Tropical Agriculture in Nigeria, in cooperation with U.S. cocoa trade associations and counterpart European research institutions, to evaluate and field trial candidate organisms for the control of black pod rot (Phytopthora megakarya), the principal disease problem for cocoa producers in West Africa.

conduct field trials on at least one pathogen with control potential for coffee berry borer (Hypothenemus hampei), the most serious worldwide coffee pest in terms of total coffee crop, in cooperation with the Colombian Coffee Federation and its research arm, Centro de Investigation de Café (CENICAFE).

establish field trials of selected clonal cocoa materials to screen for resistance to Crinipellis and Monilopthora in Latin American countries, leading to a directed breeding program for cocoa with the goal of establishing disease tolerance.

establish spray technology suitable for delivering both chemical and biological control agents for cocoa and coffee pests, and complete technology transfer to recipient foreign institutions.

continue to develop alternatives to methyl bromide for weed management.

develop and demonstrate new fumigants and other insect control technology to control pests of quarantine concern.

During FY 2004, ARS will

develop and demonstrate new fumigants and other insect control technology to control quarantine pests of concern.

develop alternatives to methyl bromide for weed management. 

in collaboration with counterparts in Brazil and Peru, demonstrate that the use of competitive mycogens, along with improved cultural practice which can reduce the incidence of Witches Broom (Crinipellis Perniciosa).

in collaboration with its counterparts in the United Kingdom, France, and Brazil, produce an integrated cocoa genetic database, Web-accessible, linking phenotypic and molecular data.  The data will be in public domain and widely available to breeders, worldwide.

identify at least four quality trait loci (QTLs) associated with disease resistance.

During FY 2005, ARS will

develop a complete functional map of the cocoa genome.

publish a complete characterization of all commercially significant accessions in each major cocoa collection worldwide.  The development of this taxonomic guide will be based upon accepted molecular techniques utilizing internationally agreed markers.

PERFORMANCE GOAL 1.1.2.3:  New and improved diagnostic tests are developed and available.

Indicators:

During FY 2002, ARS will

commercialize a detection kit for detection 3 methylisoborneol.

ACCOMPLISHMENTS:  Research is continuing with the CRADA partner, Abraxis, in Warmister, Pennsylvania, using monoclonal antibodies.

IMPACT/OUTCOME:  Problems related to the level of sensitivity of the test has delayed field testing for about six months.

further expand diagnostic abilities by applying new technologies when appropriate to detect disease agents of high consequence to animal health.

ACCOMPLISHMENTS:  ARS scientists at Plum Island, New York; Athens, Georgia; Laramie, Wyoming; Beltsville and Frederick, Maryland; and Ames, Iowa, working in collaboration with the various universities, have developed and now validating rapid onsite tests that detect and identify important animal, plant and foodborne pathogens

IMPACT/OUTCOME:  Development of these new diagnostic rapid detection technologies will provide animal health officials in regulatory capacities (APHIS and State agencies) with greater ability to determine if a disease agent is present, where it is located, and when it is eradicated (if eradication is possible).  This will aid in ensuring that trading partners will have confidence in our ability to detect and control disease agents.

During FY 2003, ARS will

continue to document progress in surveys of both horn fly and tick populations for pesticide resistance-associated mutations in both the sodium channel and acetylcholinesterase (ACHE), and conduct analysis of the fitness of resistant ticks and horn flies.

continue to transfer technology potentially leading to development of an easy-to-use, field-ready identification kit using monoclonal antibodies in an enzyme-linked immunosorbent assay to distinguish screwworms from other wound inhabiting flies.

develop improved detection and identification tests for plant pathogens in commodities, seeds, and other plant products.

develop/transfer technology for detecting the presence of pathogen spores and inoculums.

develop Geographic Information Systems (GIS) technology to map the association between larval habitats of biting midges and the animal viruses they transmit, such as vesicular stomatitis and West Nile Virus.

test decision-making algorithms using a GIS-based system based upon Formosan subterranean termite field studies and environmental factors.

test and transfer GIS and surveillance and detection technology to the Binational USDA-APHIS Screwworm Eradication Program.

develop rapid molecular-based tests to survey fly, mosquito and tick populations for pesticide resistant mutations and the presence of animal or human pathogens.

develop rapid molecular or biochemical surveillance kits for identifying by species, screwworm and other potential invading flesh flies.

determine the ability of different diagnostic procedures to detect agents by performing full scale evaluations of the technology, either under experimental situations or by field evaluation in countries where the disease exists.

During FY 2004, ARS will

design and test improved decision-making algorithms using Geographic Information Systems (GIS) technology to rapidly detect and respond to outbreaks of insects that transmit diseases to, or damage, livestock or people.

develop and evaluate molecular and biochemical tests for rapidly and accurately detecting animal  pathogens and pesticide resistance in arthropods affecting the health of animals or humans.

transfer the validated technologies to various university and state laboratories for implementation into their existing diagnostic procedures for animal health surveillance.

develop improved detection and identification tests for plant pathogens in commodities, seeds, and other plant products.

develop/transfer technology for detecting the presence of pathogen spores and inoculums.

During FY 2005, ARS will

evaluate the use of dogs for detecting off-flavors from catfish ponds.

develop the above validated tests into field tests that can be put into the hands of first responder and border patrol officials to use in routine inspection of products. Make recommendations on diagnostic procedures and ensure that the technologies are transferred to the appropriate agencies.

design and test improved decision-making algorithms using Geographic Information Systems (GIS) technology to rapidly detect and respond to outbreaks of insects that transmit diseases to, or damage, livestock or people.

develop and evaluate molecular and biochemical tests for rapidly and accurately detecting animal  pathogens and pesticide resistance in arthropods affecting the health of animals or humans.

develop improved detection and identification tests for plant pathogens in commodities, seeds, and other plant products.

develop/transfer technology for detecting the presence of pathogen spores and inoculums.

STRATEGY 1.1.3:  Measurement of product quality and marketability:  Improve quality, uniformity, value, and marketability of commodities and other agricultural products.

PERFORMANCE GOAL 1.1.3.1:  Demonstrate postharvest technologies that add value and improve quality.

Indicators:

During FY 2002, ARS will demonstrate postharvest technologies that add value and improve quality.

ACCOMPLISHMENTS:  Researchers in Beltsville, Maryland, found that combining hydrodynamic pressure processing (HDP) with aging yielded optimal tenderization of beef and pork cuts 1 to 2 weeks sooner than aging alone.  HDP treatment was more effective in improving tenderness than extended aging alone.

IMPACT/OUTCOME:  Significant reductions in aging time could translate into tremendous refrigeration energy savings because of the shorter time required to deliver acceptably tender meat to the retail markets.  

ACCOMPLISHMENTS:  At the request of the Almond Board of California, researchers at Raleigh, North Carolina, conducted experiments and documented the percent reduction that various processing methods have on reducing aflatoxin in processed almonds.  Aflatoxin reductions in processed almonds were consistently in excess of 90 percent when the basic industry sorting methods were used. 

IMPACT/OUTCOME:  The European Union indicated that it would consider increasing the maximum aflatoxin limit for imported almonds to the current standards allowed for peanuts if documented evidence can be produced showing that processing methods reduce aflatoxin in almonds.  Results were incorporated into a document developed by the Almond Board of California and sent to the European Commission for review.

During FY 2003, ARS will

develop innovative intervention strategies for improving the microbial safety of animal products, including ready-to-eat foods, while reducing the impact on quality and consumer acceptance.

develop intervention strategies for improving the microbial safety of dairy products, particularly cheese and develop strategies that can be used by small processors.

demonstrate postharvest technologies that add value and improve quality.

During FY 2004, ARS will

develop innovative intervention strategies for improving the microbial safety of animal products, including ready-to-eat foods, while reducing the impact on quality and consumer acceptance.

develop intervention strategies for improving the microbial safety of dairy products, particularly cheese and develop strategies that can be used by small processors.

demonstrate postharvest technologies that add value and improve quality.

During FY 2005, ARS will

develop innovative intervention strategies for improving the microbial safety of animal products, including ready-to-eat foods, while reducing the impact on quality and consumer acceptance.

develop intervention strategies for improving the microbial safety of dairy products, particularly cheese, and develop strategies that can be used by small processors.

demonstrate postharvest technologies that add value and improve quality.

PERFORMANCE GOAL 1.1.3.2:  Provide knowledge and technology to expand and improve the grading systems for agricultural commodities and products.

Indicators:

During FY 2002, ARS will provide knowledge and technology to expand and improve grading systems.

ACCOMPLISHMENTS:  Concern about the accuracy and precision associated with results from grade samples taken from farmers’ stock peanut lots led the Federal State Inspection Service (FSIS) and the American Shellers Association to request assistance from researchers in Raleigh, North Carolina, who designed experiments, analyzed data, and documented results to determine the optimum number of pneumatic probe samples needed to obtain a representative grade sample. 

IMPACT/OUTCOME:  Shellers and FSIS are now considering an increase in the number of probe samples needed from the current 5 to 10 to improve the accuracy of estimating grade factors and determining the loan value of a farmer’s lot.

ACCOMPLISHMENTS:  An ARS engineer at East Lansing, Michigan, in collaboration with engineers and horticulturists from Michigan State University, developed a new near-infrared (NIR) sensing method and technique for predicting the firmness and sugar content of apples and cherries.  The technique allows measurements at multiple locations on fruit at a fast rate, and gives improved predictions of apple quality. 

IMPACT/OUTCOME:  Sorting for quality, especially firmness and sugar content, is considered a top priority by the apple industry.  This accomplishment is an important milestone in research to develop a real time sensing system that will allow commercialization of systems to sort apples for firmness and sugar content and allow marketing of apples based upon these quality attributes.

During FY 2003, ARS will provide knowledge and technology to expand and improve grading systems.

During FY 2004, ARS will provide knowledge and technology to expand and improve grading systems.

During FY 2005, ARS will provide knowledge and technology to expand and improve grading systems.

PERFORMANCE GOAL 1.1.3.3:  Demonstrate methods to measure the critical processing and end-use properties of agricultural commodities important to the agricultural marketing system and the processing industry.

Indicators:

During FY 2002, ARS will demonstrate methods to measure critical processing and end-use properties of agricultural commodities important to the agricultural marketing and processing systems.

ACCOMPLISHMENTS:  Research engineers at Manhattan, Kansas, cooperated with scientists at Kansas State University to develop the system.  A commercial prototype of the new system is being built by a CRADA partner. 

IMPACT/OUTCOME:  This system will allow measurement and sorting based on quality factors such as bunted kernels, protein, moisture, scab damage, and color class at grain elevators, thus allowing segregation at the first point of sale.  It will also provide breeders with a means to sort kernels with desirable traits from samples when developing new cultivars.

ACCOMPLISHMENTS:  Researchers at Raleigh, North Carolina, examined peanuts that had been shipped to Europe from the United States, China, and Argentina.  Data on oil quality and both descriptive sensory and consumer analysis of flavor clearly demonstrated the superior quality of U.S. peanuts.

IMPACT/OUTCOME:  The data demonstrate superior quality of U.S. peanuts in export markets.  The information has been presented in international forums and used in developing marketing information on U.S. peanuts.

ACCOMPLISHMENTS:  Researchers at Raleigh, North Carolina, developed methods to design and evaluate the performance of Tilletia controversy Kuhn (TCK) sampling plans to minimize both the exporter’s risk (good lots rejected) and importer’s risk (bad lots accepted) associated with testing export shipments.  Data from the study provided adequate information on which to base USDA sampling plans that would satisfy U.S. exporters and Chinese importers.

IMPACT/OUTCOME:  China and the United States signed an Agricultural Cooperation Agreement whereby China will import U.S. wheat produced in the Pacific Northwest with 30,000 or less TCK spores per 50 grams of wheat.  Results of the study will result in millions of dollars of export wheat sales to China.  

ACCOMPLISHMENTS:  Researchers at Fargo, North Dakota, determined that the falling number value of the stirring number value is very effective in determining the extent of sprout damage in oats and that increased groat breakage is the most significant quality characteristic affected by sprout damage.

IMPACT/OUTCOME:  Oats serve as an important food and feed source.  They contain high levels of protein and soluble fiber, the latter of which has been shown to lower blood cholesterol in humans.  Improvement of American oat quality is important in light of eroding U.S. oat production, which is being replaced by imports from Canada during a time when American demand for oats is increasing.  Sprout damage has only recently been recognized as a problem in oats.  As a result of this research, milling companies in the United States, Canada, and Finland are now requiring the oats that they buy pass a sprout damage test before purchase.

ACCOMPLISHMENTS:  Scientists at Albany, California, identified a method using x-rays to identify afflicted fruits and developed an algorithm for automatic detection.

IMPACT/OUTCOME:  The pineapple industry needs a method to non-destructively identify pineapples that suffer from “translucency,” a disorder similar to watercore in apples.  The results of the research were submitted to a major pineapple producer for possible cooperation in the development of a real-time sorting device to improve the quality of pineapples going to market and aid in breeding research.

ACCOMPLISHMENTS:  In response to the unilateral and sudden imposition of new quality standards for cotton imported into the People’s Republic of China, the U.S. cotton industry asked ARS for help in determining the difficulty and the value of the required measurements.  ARS responded immediately with an analysis of the required devices and procedures, followed by the formation of task forces to generate data evaluating the efficacy of these new procedures.  The task forces were structured to produce answers within weeks of being organized. 

IMPACT/OUTCOME:  The early analyses by ARS allowed the U.S. industry to protest the new required measurements as inappropriate and uninformative.  At stake is the importation of almost 4 million bales of cotton by China, which is part of the agreement for it to enter the World Trade Organization. 

During FY 2003, ARS will demonstrate methods to measure critical processing and end-use properties of agricultural commodities important to the agricultural marketing and processing system.

During FY 2004, ARS will demonstrate methods to measure critical processing and end use properties of agricultural commodities important to the agricultural marketing and processing system.

During FY 2005, ARS will demonstrate methods to measure critical processing and end use properties of agricultural commodities important to the agricultural marketing and processing system.

STRATEGY 1.1.4:  International technology interchange:  Develop a strategy for selective international research interchange to supplement ARS technology developments and strengthen competitiveness of U.S. agriculture.

PERFORMANCE GOAL 1.1.4.1:  Strategic alliances formed with specific foreign institutions, leading to the joint development of germplasm and value-added technologies, mutually protected through intellectual property agreements.

Indicators:

During FY 2002, ARS will

coordinate research results from scientists at ARS locations and selected international agricultural research centers of the Consultative Group on International Agricultural Research (CGIAR).

ACCOMPLISHMENTS:  Initiated a cooperative project with the International Institute for Tropical Agriculture (IITA) pertaining to disease resistance in cacao.  This is a new 3-year effort co-funded by the American Cocoa Research Institute and USAID.

Continued collaborative research with the International Center for Improvement of Maize and Wheat (CIMMYT) in mirroring the Maize DB at CIMMYT and entering its information into the system.

Completed a cooperative study with IITA pertaining to inbred maize lines for higher bioavailable iron content.  Varieties containing significantly higher bioavailable iron were identified.

Completed a 5-year project with the International Center for Tropical Agriculture (CIAT) on integrated pest management of whitefly, a major pest of several food crops. 

Facilitated a cooperative project, funded by USAID, between IITA and Purdue University to study the impact of gene flow in cowpea.

Established a project on herbal and medicinal plants in Tunisia, in cooperation with the Institut des Regions Arides in Medenine and the International Center for Agricultural Research in the Dry Areas (ICARDA).

IMPACT/OUTCOME:  The cacao project with IITA will utilize genetic approaches to identify germplasm that is resistant to phytopthera, a fungal disease that can devastate the crop in both Latin America and West Africa.  This project is significant to both consumers in developed nations and producers in developing nations.

The joint effort CIMMYT has resulted in the new CIMMYT MaizeDB data repository.  This repository is a valuable tool for researchers attempting to enhance both the production and quality of maize.

As malnutrition and under-nutrition continues to plague Africa, crop varieties that are productive in Africa with higher available iron content developed in conjunction with IITA can reduce illnesses associated with micro- and macro-nutrient malnutrition.

Integrated pest management strategies for the suppression of whitefly, developed at CIAT under the auspices of ARS, have received global acclaim.  The documented approaches provide tools to protect a number of crops from damage caused by the insect and associated disease.

Cowpea, a major staple pulse in Africa, is being genetically manipulated at IITA to improve insect resistance, which would greatly improve production in Africa.  As West Africa is a known Center of Origin for cowpea, it is important to understand the impact of introducing a transgenic cowpea prior to its release.

The equivalent of $250,000 has been granted from the USDA-Foreign Agriculture Service (PL480 funds) to fund the herbal and medicinal plant project with ICARDA.  An extensive socio-economic survey was completed.

participate in long-term cooperative research and development projects involving the World Bank, the Global Environmental Facility (GEF) and client countries.

ACCOMPLISHMENTS:  ARS developed three projects that are approved and/or awaiting implementation.  They are the Marsa Matrouh Resource Management Project in Egypt, the Aquaculture Improvement Project in China, and the Gansu-Xinjiang Pastoral Development Project also in China.

IMPACT/OUTCOME:  ARS scientists located in Mandan, North Dakota, and Lincoln, Nebraska, participate in the Marsa Matrouh Resource Management Project.  The Egyptian government and the World Bank are expected to further discuss Phase II when non-disbursed funding from Phase I is spent in Fall 2003.

The Aquaculture Improvement Project was slowed due to a restructuring of the effort, making it difficult to predict whether the project will be terminated or continued.

The World Bank approved the Gansu-Xinjiang Pastoral Development Project.  Implementation starts in Spring 2003.  ARS scientists from El Reno, Oklahoma, will participate.

participate in World Bank/GEF identification missions to Kazakhstan and Jordan.

ACCOMPLISHMENTS:  ARS developed two projects that were approved and/or awaiting implementation.  They are the Kazakhstan Drylands Management Project and the Conservation of Medicinal and Herbal Plants Project in Jordan.

IMPACT/OUTCOME:  The Global Environment Facility approved the Kazakhstan Drylands Management Project.  The Project Appraisal Document is in preparation for the appraisal mission to be conducted in Spring 2003.  Negotiations and implementation are expected to follow shortly thereafter.

The World Bank internal review of the Conservation of Medicinal and Herbal Plants Project Appraisal Document was accepted and negotiations between Jordan’s Ministry of Planning and the World Bank Board of Directors is expected in March 2003.  Implementation is likely shortly thereafter.

develop formal agreements with international research institutions of excellence to address agricultural problems of mutual interest.

ACCOMPLISHMENTS:  ARS signed Memoranda of Understanding with the Mexican National Institute of Agricultural and Forestry Research, the Post Graduates College, and the Center for Research in Food and Development.

IMPACT/OUTCOME:  The Memoranda of Understanding with the Mexican National Institute of Agricultural and Forestry Research, the Post Graduates College, and the Center for Research in Food and Development, are part of an overall effort to strategically refocus research cooperation with Mexico in high priority areas of the U.S.-Mexican Binational Commission, which includes trade and environmental impact.

ACCOMPLISHMENTS:  Broad cooperation was established between the United States and the Peoples’ Republic of China that focuses on natural resource management.

IMPACT/OUTCOME:  On May 20, 2002, the Joint Centers for Soil and Water Conservation and Environmental Protection were opened. One is hosted by the Chinese Academy of Sciences, Institute for Soil and Water Conservation, on the campus of the Northwest Sci-tech University for Agriculture and Forestry at Yangling, Shaanxi Province, China.  The other center is located in the Institute for the Study of Planet Earth on the campus of the University of Arizona in Tucson in cooperation with three ARS laboratories (National Soil Erosion Lab, West Lafayette, Indiana; National Sedimentation Lab, Oxford, Mississippi; and the Southwest Watershed Research Lab in Tucson, Arizona).

ACCOMPLISHMENTS:  The U.S.-Israel Binational Agricultural Research and Development Fund (BARD) program reviewed approximately 90 proposals for joint research.  The U.S.-BARD addresses many agricultural problems of common interest to Israel and the United States, such as water quotas for agriculture, labor issues, production and environmental issues, etc.

IMPACT/OUTCOME:  The U.S.-Israel Binational Agricultural Research and Development Fund Board of Directors approved 25 project proposals in 11 disciplines for funding at about $300,000 each.  The U.S.-Israel Binational Agricultural Research and Development Fund remains a cornerstone of mutual U.S.-Israel efforts to overcome agricultural problems through sound science.

ACCOMPLISHMENTS:  The Labex Program, in which scientists from Embrapa (Agricultural Research Corporation) of Brazil are housed in ARS laboratories, was enhanced by two formal agreements.  Mutually beneficial research was conducted in the areas of integrated pest management, animal health, precision farming, global change and industrial utilization of commodities.

IMPACT/OUTCOME:  Labex fostered considerable high-impact, large-scale U.S.-Brazil cooperative projects, including those concerned with the complete genome sequence of X. fastiosa (causative agent of Pierce’s Disease), genomic identification of disease resistance in bovines, porcine, and avian manure management, and sensory tools for the economic and efficient use of agricultural inputs.

ACCOMPLISHMENTS:  ARS utilizes three specific cooperative agreements with the Tropical Agricultural Research and Higher Education Center (CATIE) in Costa Rica, facilitating research and capacity building activities in that country in agriculture, and the management, conservation and sustainable use of natural resources.

IMPACT/OUTCOME:  ARS collaborates with the CATIE on research that is vital to the Central American region, in particular the maintenance of a sustainable tropical tree crop program.  The program includes field trials of biological control agents for cocoa and sustainable production of coffee and banana, emphasizing adequate soil and water conservation.  Capacity building activities at CATIE offer direct benefits to the region, develop greater scientific linkages, and strengthen the ability to transfer technology to the people of the region. This ultimately builds relationships and capacity to foster long-term partnerships in other countries in areas of strategic importance to the agency’s mission.

with funding from the Department of State Freedom Support Act, engage former Soviet biological weapons (BW) scientists to redirect their efforts to peaceful, agricultural research and help reduce the risk of proliferation of weapons of mass destruction.

ACCOMPLISHMENTS:  ARS teams traveled to Russia and Kazakhstan to assess research institutes and identify collaborations of mutual benefit.  The teams focused on research institutes that are primarily dedicated to agriculturally important animal and plant diseases.

Since inception (1998), 46 projects have been approved under the ARS-Former Soviet Union (FSU) scientific cooperation program.  The projects focus on plant research, animal health, and natural resources, which involve over 900 FSU scientists, half of whom are former bio-weapons scientists.  Twenty new projects were approved, and 11 funded for a total of approximately 3.6 million dollars.

Fifty-five Russian, Kazakhstani, and Uzbek scientists traveled to the United States to meet with ARS counterparts to develop project proposals or work on existing projects.  In addition, 22 ARS scientists and representatives traveled to Russia and Kazakhstan under on-going projects or as part of ARS team visits. 

IMPACT/OUTCOME:  All funded projects are enhancements to the ARS National Research Programs.

The program advances basic and applied research in agriculture and supports the transition of the Newly Independent States (NIS) to a market economy by strengthening scientific communities and integrating NIS scientists into the international community.

The program also supports U.S. foreign policy:  The proliferation risk for weapons of mass destruction is reduced; transparency at former Soviet bio-weapons research sites is increased; and activities of former Soviet weapons scientists in Russia, Kazakhstan, and Uzbekistan are redirected to peaceful, agriculturally beneficial research.

During FY 2003, ARS will

provide mutual exchange and cooperative development of Lotus spp. germplasms by INIA (Uruguay) and ARS for the co-development of rhizomatous lines with suitable winter-hardiness for adaptation in both countries.

engage former Soviet biological weapons scientists to redirect their efforts to peaceful, agricultural research and help reduce the risk of proliferation of weapons of mass destruction with funding from the Department of State Freedom Support Act.

coordinate research results from scientists at ARS locations and selected international agricultural research centers of the CGIAR.

participate in long-term cooperative research and development projects involving the World Bank or USAID.

develop formal agreements with international research institutions of excellence to address agricultural problems of mutual interest.

During FY 2004, ARS will

engage former Soviet biological weapons scientists to redirect their efforts to peaceful, agricultural research and help reduce the risk of proliferation of weapons of mass destruction with funding from the Department of State Freedom Support Act.

coordinate research results from scientists at ARS locations and selected international agricultural research centers of the CGIAR.

participate in long-term cooperative research and development projects involving the World Bank or USAID.

develop formal agreements with international research institutions of excellence to address agricultural problems of mutual interest.

During FY 2005, ARS will

engage former Soviet biological weapons scientists to redirect their efforts to peaceful, agricultural research and help reduce the risk of proliferation of weapons of mass destruction with funding from the Department of State Freedom Support Act.

coordinate research results from scientists at ARS locations and selected international agricultural research centers of the CGIAR.

participate in long-term cooperative research and development projects involving the World Bank or USAID.

develop formal agreements with international research institutions of excellence to address agricultural problems of mutual interest.

OBJECTIVE 1.2:  Develop new uses and products:  “Develop new uses and new products for agricultural commodities, such as alternative fuels, and develop new crops.”

STRATEGY 1.2.1:  New and alternative crops:  Develop new and alternative crops with economic and social value.

PERFORMANCE GOAL 1.2.1.1:  Experimentally develop and demonstrate production of new, improved, and alternative farm animals, crops, and horticultural products.

Indicators:

During FY 2003, ARS will develop new fruit, vegetable, nut, and ornamental germplasm with competitive enhancements (yield, pest resistance, quality) for producers, while providing exciting new market choices for consumers.

During FY 2004, ARS will

develop new and improved horticultural crops targeted at specific production-limiting challenges.

develop new and improved horticultural crops targeted specifically at enhancing consumption patterns and marketability.

During FY 2005, ARS will

develop new and improved horticultural crops targeted at specific production-limiting challenges.

develop new and improved horticultural crops targeted specifically at enhancing consumption patterns and marketability.

PERFORMANCE GOAL 1.2.1.2:  Experimentally demonstrate new and improved management practices for production, harvesting, and postharvest handling procedures of these commodities.

Indicators:

During FY 2002, ARS will

continue to develop strategies for protecting and using insect pollinators to increase crop production.

ACCOMPLISHMENTS:  Scientists at the Honey Bee Research Unit in Tucson, Arizona, have developed an artificial diet for honey bees that can be used as the bee’s sole food source. 

IMPACT/OUTCOME:  This provides beekeepers with an inexpensive and easy to use artificial diet that can help insure strong, populous colonies for pollination, particularly for use in spring build-up, e.g., for almond pollination in California.

ACCOMPLISHMENTS:  Scientists at the Pollinating Insect-Biology, Management, Systematics Research Unit in Logan, Utah, conducted research on a nesting block design for the blue orchard bee that was inexpensive, durable and easily sanitized. 

IMPACT/OUTCOME:  This research, done in collaboration with a cherry producer in Utah, has resulted in a patent (U.S. Patent 6,364.738 Solitary Bee Nesting Block) for a nesting block that will make it easier for growers to manage non-honey bee pollinators for apples, pears, cherries, and other orchard crops.

ACCOMPLISHMENTS:  Scientists at the Pollinating Insect-Biology, Management, Systematics Research Unit in Logan, have completed the second year of a research and demonstration project that uses meadowfoam, an oil-seed crop, to increase populations of the blue orchard bee. 

IMPACT/OUTCOME:  This discovery could ultimately lead to zero pollination costs per acre as well as increased profitability from the sale of surplus bees.

ACCOMPLISHMENTS:  Scientists at the Beneficial Insects Research Unit at Weslaco, Texas, completed research that compared methods for applying the antibiotic tylosin -- in a dust with powdered sugar or in a grease patty -- to bee hives for control of American foulbrood disease.  The grease patty method was as effective as the dust method, but hives treated with the grease patty experienced significant increases of the damaging small hive beetle.

IMPACT/OUTCOME:  This information provides a warning to beekeepers that use of grease patties in areas with the small hive beetle may result in increased damage due to this invasive pest.

ACCOMPLISHMENTS:  Scientists at the Beneficial Insects Research Unit at Weslaco, Texas, determined that use of the pesticide coumaphos did not significantly affect bee mortality or adversely affect reproducing queens.

IMPACT/OUTCOME: This provides additional evidence that coumaphos can be used safely for control of the varroa mite.

ACCOMPLISHMENTS:  Scientists at the Honey Bee Breeding, Genetics, and Physiology Research Unit in Baton Rouge, Louisiana, have shown that honey bees imported from far eastern Russia have strong genetically-based resistance to the varroa mite.  Russian bees also exhibited strong resistance to the tracheal mite.  In addition, Russian bee honey production was as good or better than that of commercial U.S. stocks of honey bees and the Russian bees exhibited excellent winter hardiness.  Also, a different strategy, one that employs domesticated bee stocks, is showing promise for increasing the frequency of mite-resistant genes.  Honey bees were found to express a high level of resistance to varroa mites when bees were selected for only one resistant trait [suppression of mite reproduction (SMR)].  A significant level of mite resistance was retained when commercially reared queens with the SMR trait were allowed to mate freely with unselected drones. 

IMPACT/OUTCOME:  This research suggests that commercial queen producers can produce mite resistant queens by using their traditional methods of queen production using new bee stock from Russia. 

ACCOMPLISHMENTS:  Scientists at the Beneficial Insects Research Unit in Weslaco, Texas, have found a fungal pathogen of varroa mites to be as effective as pesticides currently in use, and with no adverse effects on honey bees.

IMPACT/OUTCOME:  The commercialization and widespread use of this pathogen could lead to the elimination of pesticides in beehives.

During FY 2003, ARS will

continue to develop strategies for protecting and using insect pollinators to increase crop production.

improve technology to reduce spray drift, while providing effective spray distribution in tree canopies.

develop integrated cropping, harvesting, and postharvest handling systems.

During FY 2004, ARS will

continue to develop strategies for protecting and using insect pollinators to increase crop production.

improve technology to reduce spray drift, while providing effective spray distribution in tree canopies.

develop integrated cropping, harvesting, and post-harvest handling systems.

During FY 2005, ARS will

continue to develop strategies for protecting and using insect pollinators to increase crop production.

improve technology to reduce spray drift, while providing effective spray distribution in tree canopies.

develop integrated cropping, harvesting, and post-harvest handling systems.

STRATEGY 1.2.2:  New uses and products:  Develop new food and non-food uses and products from plants and animals, and new processes and other technologies that add value.

PERFORMANCE GOAL 1.2.2.1:  Experimentally demonstrate improvements in processing technologies and develop new bioproducts and uses that have potential to increase demand for agricultural commodities.

Indicators:

During FY 2002, ARS will

experimentally demonstrate improvements in processing technologies and develop new bioproducts and uses that have potential to increase demand for agricultural commodities.

ACCOMPLISHMENTS:  Scientists at Wyndmoor, Pennsylvania, developed a method for the rapid extraction of pectin from orange peels that is less expensive than microwave heating and which produced pectin with properties superior to commercial pectin extracted from lime/lemon peel.  Other scientists within the unit, in collaboration with researchers in the United Kingdom, demonstrated that Florida orange peels could enhance the growth of health-promoting gut bacteria at the expense of disease-causing gut bacteria. 

IMPACT/OUTCOME:  U.S. citrus processing generates 106 tons of orange peel/pulp per year, most of which is used in low-value animal feed.  These results offer potential for new value-added uses for Florida orange peels.

ACCOMPLISHMENTS:  Researchers at Wyndmoor, Pennsylvania, demonstrated that leather treated with low molecular weight polyethylene glycol solutions significantly reduces the stiffness of leather.

IMPACT/OUTCOME:  Hides are the most important byproduct of the meat packing industry, providing the raw material for the domestic leather industry and generating over a billion dollars in foreign trade.  Fatliquors are routinely applied to leather to lubricate the fibrous structure and to increase the compliance of leather, but they do not promote the retention of essential moisture and therefore, over drying can be a consequence.  This research may provide a possible alternative or supplement to traditional fatliquors and thereby, help prevent aged leather products from becoming brittle and fragile. 

ACCOMPLISHMENTS:  Researchers at Wyndmoor, Pennsylvania, in cooperation with the American Sheep Industry Association and an enzyme company, demonstrated that the structure of the wool scales that surround the fiber and contribute to prickle could be altered by an enzyme treatment.

IMPACT/OUTCOME:  Consumer acceptance of domestic wool in garments and upholstery is limited, in part, because of skin irritation and prickle.  The enzymatic treatment is an alternative to conventional scale alteration by chlorination and may facilitate the establishment of wool’s competitive market share and increase the demand for natural fiber blends of wool.

ACCOMPLISHMENTS:  Scientists in New Orleans, Louisiana, invented a dry instantization process for reducing the cooking time of brown and dry rice from 45-50 minutes to that of white rice (20 minutes).  A patent application has been filed, five companies are pursuing licensing of the technology, and a prototype continuous system for production of the products has been built.

IMPACT/OUTCOME:  Existing methods of instantizing rice require significant input of water and energy that, in turn, creates considerable expense.  The new process reduces the cost of processing to make instant rice, reduces environmental pollution, and will make nutritious brown rice more appealing to the consumer.   

ACCOMPLISHMENTS:  Researchers at New Orleans, Louisiana, cooperated with engineers at Wyndmoor, Pennsylvania, to chemically modify soybean hulls to develop an efficient, cost-effective cation exchange resin that could compete with commercial resins in the marketplace. 

IMPACT/OUTCOME:  Hulls from soybeans are low value, high volume processing by-products that amount to about 13 billion pounds annually.  ARS transferred the technology to a private sector partner and is cooperating in product scale-up.  The private sector partner has had numerous requests from companies to use the modified hulls as a replacement cation exchange resin in place of more expensive synthetic commercial resins.

ACCOMPLISHMENTS:  Researchers at Raleigh, North Carolina, in collaboration with scientists at North Carolina State University, designed, constructed, and tested pilot plant equipment for evaluating bag-in-box technology for producing “process ready” brined/fermented vegetables.

IMPACT/OUTCOME:  Brining is an inexpensive means for temporary preservation of cucumbers and certain other produce, but current technology creates a negative environmental impact due to waste generation (salt and organics) and variable product quality and uniformity.  The new technology can benefit farmers by providing value enhancement and a market hedge.  Processors will reduce waste and produce more uniform and higher quality products.

ACCOMPLISHMENTS:  Scientists at Albany, California, developed a novel ethanol-based method to displace starch from well-developed dough, thus improving the vitality of gluten significantly relative to that from the conventional water displacement method.  The gluten derived from ethanol cold-processing exhibited mixing properties and comparable or improved baking properties.  Most importantly, the ethanol-separated gluten was much more resistant to high temperature extremes of drying.

IMPACT/OUTCOME:  In the traditional water-based separation of gluten from wheat, the gluten loses much of its vitality.  Improved gluten quality via the ethanol process will reduce energy costs and improve the competitiveness of U.S.-produced gluten.

ACCOMPLISHMENTS:  ARS agricultural engineers at Dawson, Georgia, in collaboration with dryer manufacturers, determined that a continuous flow dryer with alternating heating and tempering sections increased drying capacity to approximately twice that of conventional wagon drying systems, while having minimal detrimental effects on quality.

IMPACT/OUTCOME:  Increased peanut harvest capacity has caused a severe shortage of capacity at commercial curing facilities.  If the peanut marketing system is modified to allow the use of continuous flow dryers, these findings can eliminate the shortage of curing capacity faced by the peanut industry.

ACCOMPLISHMENTS:  Researchers at Albany, California, developed casting technologies to create 100 percent fruit and vegetable wraps and entered into a CRADA with an industrial partner to scale up the production process for these films.  The research generated an extraordinary amount of national and international press interest and won a Best of What’s New Award from Popular Science magazine.  In related research, the researchers also developed and licensed a technology for forming 100 percent fruit health bars from pears to add value and create new markets for pears. 

IMPACT/OUTCOME:  The wraps should be commercially available in the near future and will increase utilization and consumption of fruits and vegetables, improving not only the American diet, but also the environment by reducing large amounts of disposable packaging materials.  The industrial partner who licensed the fruit health bars technology is scaling up the process at a plant in a rural area of Oregon, which presently has high unemployment, to begin to manufacture the fruit bars.  This grass-root effort on behalf of pear growers has recently expanded beyond pears into other fruits and vegetables from the Western States and is expected to increase growers’ profits, while assisting Americans in meeting their daily dietary requirements for fruits and vegetables. 

ACCOMPLISHMENTS:  Researchers at Peoria, Illinois, prepared soybean oil-based composites by cross-linking epoxidized soybean oil with a resin and five different gelling agents and using a solid free-forming fabrication method (SFF), which doesn’t require the use of molds. 

IMPACT/OUTCOME:  The preparation of structurally strong composites from renewable resources is attractive due to the environmental sustainability of the raw materials used and the new markets created for farm products.  The combination of natural fibers with soybean oil will also produce composites that will be cheaper than the available alternatives.  Using SFF will also open the door to a broad range of new applications such as in the automotive, construction, aircraft, and military industries.  The U.S. patent on the process is pending and a CRADA with an industry partner is in progress.      

ACCOMPLISHMENTS:  Cooperative work with the University of Illinois and a private company has established that gin trash – the material left behind after the cotton fiber and the seeds have been separated and cleaned – makes an effective mulch that suppresses weeds and promotes grass establishment more effectively than some commercial mulches.  Other work with Texas Tech University, Cotton Incorporated, and private companies showed that this material provides excellent roughage in a typical feedlot diet that promotes weight gain and efficiency of cattle. Extruded gin trash also can be pelletized for use as a high-quality fuel in pellet stoves. 

IMPACT/OUTCOME:  Disposal of gin trash is an economic burden.  All of these uses could turn the economic losses from handling gin trash into profits for the ginner.

increase ethanol yield by partial saccharification of corn fiber by use of new organisms which ferment pentoses, or do not produce succinate, or ferment xylose without glucose repression.

ACCOMPLISHMENTS:  Metabolic engineering was used to manipulate the biosynthetic pathways of microorganisms to develop a series of biocatalysts that improve conversion of biomass sugars to fuel ethanol.  Strains of bacteria were developed that increase ethanol production by co-utilization during fermentation of the multiple sugars present in agricultural biomass.

IMPACT/OUTCOME:  The microorganisms developed bring the commercial production of fuel ethanol from agricultural biomass closer to reality.

During FY 2003, ARS will

experimentally demonstrate improvements in processing technologies, and develop new bioproducts and uses that have potential to increase demand for agricultural commodities.

develop new enzymes, by use of molecular evolution, to reduce the costs and energy use for producing bioethanol.

scale up enzymatic production of sugars from corn fiber for fermentation to ethanol and higher-value co-products by recombinant organisms.

identify specific enzymes that can best serve to replace sulfites for steeping corn.

complete a comparative cost analysis of a plant producing ethanol from both corn starch and corn stover.

During FY 2004, ARS will

experimentally demonstrate improvements in processing technologies and develop new bioproducts and uses that have potential to increase demand for agricultural commodities.

develop processes to increase the efficiency and reduce the cost of ethanol production and increase the value of ethanol coproducts.

develop enzymes, organisms, and processes for lower cost and more efficient conversion of cellulosic biomass into ethanol, and technology to integrate stover-to-ethanol with grain-to-ethanol production.

improve understanding of relationships among biodiesel feedstocks, conversion processes, chemical structure, physical properties, fuel quality, storage stability, emissions, and economics that will remove technological barriers to biodiesel use.

During FY 2005, ARS will

experimentally demonstrate improvements in processing technologies and develop new bioproducts and uses that have potential to increase demand for agricultural commodities.

develop processes to increase the efficiency and reduce the cost of ethanol production and to increase the value of ethanol coproducts.

develop enzymes, organisms, and processes for lower cost and more efficient conversion of cellulosic biomass into ethanol, and technology to integrate stover-to-ethanol with grain-to-ethanol production.

improve understanding of relationships among biodiesel feedstocks, conversion processes, chemical structure, physical properties, fuel quality, storage stability, emissions, and economics that will remove technological barriers to biodiesel use.

During FY 2005, ARS will

identify and characterize genes for resistance in crop plants to develop host plant resistance.

improve methods of evaluating host resistance, e.g., identifying molecular markers for resistance.

identify new sources for resistance genes through the integration of the genes by conventional breeding and bioengineered methods.

identify and exchange new sources of plant, microbial, and insect genetic variability, especially those threatened in natural habitats, so as to conserve them and augment the diversity of genes available for research or genetic improvement.

improve methods for conserving plants, beneficial microbes, and insects in genebanks. 
 

PERFORMANCE GOAL 2.1.3.2:  Documented DNA base sequences of agricultural importance.

Indicators:          

During FY 2002, ARS will

evaluate and report the results of transgenic modification of two alfalfa genes to improve growth, protein content, nitrogen fixation, and nitrogen utilization.

ACCOMPLISHMENTS:  Genes affecting aluminum tolerance, disease resistance, and fiber digestibility have been characterized by scientists at St. Paul, Minnesota, who introduced them into alfalfa plants.  Crosses have been made with these enhanced plants and their offspring are being evaluated.  The enhanced plants are now being evaluated under a variety of field environmental conditions to identify those that are the most promising, which will provide the germplasm for developing new commercial varieties.

IMPACT/OUTCOME:  Alfalfa is the third largest crop after corn and soybeans.  Improving aluminum tolerance will allow production in areas that are now too acid.  Improving disease resistance will increase crop persistence and reduce production costs by reducing the frequency of reseeding.  Improved fiber digestibility enables livestock to gain more energy from alfalfa at a lower production cost.

identify molecular genetic markers for cold temperature growth in Leymus wild ryes, salt tolerance in alfalfa, and apomictic behavior in sandberg bluestem, so that populations can be screened to identify germplasm having these desired characteristics to improve seedling vigor, productivity, and ground cover.

ACCOMPLISHMENTS:  Scientists at Logan, Utah, have identified markers for several characteristics of Leymus wild ryes, including cool temperature growth, digestible carbohydrate content, and nutrient composition.  Scientists at Prosser, Washington, have developed an improved method for determining alfalfa genotypes using a novel method based on PCR techniques.  This method can identify markers rapidly and accurately (>98 percent) to determine the number of copies of important genes.  Scientists at El Reno, Oklahoma, have evaluated hybrids of native bluestem grasses for desired forage characteristics.  In crossing Sandberg bluestem (produces seed sexually) and Texas bluestems (produces viable seeds without fertilization, i.e., "apomictic"), the scientists found that some of the hybrids were apomictic.  This mix of hybrid bluestems made it possible to find genetic markers for the presence of apomixis.

IMPACT/OUTCOME:  Identifying markers for important characteristics in rye and other grasses will make it possible for plant breeders to improve forage crops more rapidly and economically.  The great majority of molecular markers in alfalfa and other plants are for dominant characteristics.  These markers cannot be used to identify plants with a copy of a recessive gene when one or more copies of the dominant gene are present.  Expensive and time‑consuming greenhouse tests are required to identify plants with a recessive gene that has desired qualities, such as salt tolerance in alfalfa.  This method will accelerate plant-breeding programs and can be broadly applied for genotyping all diploid plant species.  The advantage of apomictic seed production in bluestem and certain other grasses is that all the seeds have exactly the same genetic makeup, and will always produce plants with identical characteristics.  Having such markers allows plant breeders to select plants with desirable forage qualities that will always breed true.  This reduces the cost of seed production and provides farmers and ranchers with the certainty the forages they are planting will have the improved characteristics.

perfect and implement highly efficient methods for determining DNA sequence variability in genomes.

ACCOMPLISHMENTS:  ARS researchers and scientists at the University of Nebraska and Cornell University developed an innovative reporter transposon-tagging method for rapidly and efficiently identifying functional Hrp gene promoters by analyzing the entire genome of the important bacterial plant pathogen P. syringae.  The Hrp genes are important because they control a variety of functions essential for virulence.

IMPACT/OUTCOME:  This combined experimental/computational approach identified variation in bacterial genomic structure potentially important in pathogenesis.  These findings may accelerate efforts to develop control strategies for bacterial diseases of plants.

arrange in order expressed sequence-tagged sites (ESTs) in crop genomes, and discover their associated biological functions.

ACCOMPLISHMENTS:  The wheat chromosomal regions containing genes (as revealed by mapping of expressed sequences) have been poorly characterized, despite the crop’s worldwide importance.  ARS researchers are completing the first detailed analyses of a single segment of the wheat genome that contains the high-molecular-weight (HMW) glutenin genes encoding the proteins most responsible for wheat’s food quality, and the unique range of products that can be produced from wheat flour.  The DNA sequence of the HMW-glutenin region was determined for all three regions within wheat, plus the similar region for barley.

IMPACT/OUTCOME:  This first complete description of this critical region of the wheat genome identified for the first time several adjacent genes not previously associated with the HMW-glutenin genes, which has important implications for understanding evolution of wheat and its relatives.

maintain genetic and genomic data on well conceived databases constructed with powerful, up-to-date information management software, and implemented on high speed, high capacity computer networks accessible via standard software from the Internet.

ACCOMPLISHMENTS:  ARS and Cornell University researchers at Ithaca, New York, designed and constructed a relational database to house P. syringae genomic information.                         

IMPACT/OUTCOME:  This database stores and makes readily accessible the results of DNA sequence analyses performed by a large suite of sequence-based tools (e.g., BLAST, glimmer, etc.).  The data generated and the analytical tools developed will help elucidate biologically significant features of bacterial genomes.

ACCOMPLISHMENTS:  ARS researchers from Ithaca, New York, in cooperation with scientists at Cold Spring Harbor Laboratory, completed and released a portable and highly configurable Web-based genome browser now used by some genome databases and about a dozen commercial and academic Web sites.  They also completed and released a portable and highly configurable Web-based comparative map viewer, and completed and documented, but not yet released, a “portable” database for managing insertional mutagenesis projects. 

IMPACT/OUTCOME:  These extensive computer programming efforts furnished additional bioinformatic tools that may accelerate the pace of gene discovery from, and functional analyses of, DNA sequences.

ACCOMPLISHMENTS:  USDA/ARS researchers at Albany, California, and Ithaca, New York, have enhanced existing genome database resources for wheat and barley in collaboration with researchers at National Library of Medicine and at the International Triticeae Initiative (Dundee, Scotland).

IMPACT/OUTCOME:  The developments will facilitate access to the increasing amounts of wheat and barley genomic data.  Such access is critical if U.S. cereal researchers are to make maximum progress in improving these important crops. 

construct and maintain more precise physical, genetic, and transcript genomic maps to estimate the number of genes that constitute crop genomes, the genomic location of these genes, and to elucidate comparative gene function, structure, and organization.

ACCOMPLISHMENTS:  USDA/ARS and University of California scientists at Davis, California, developed a molecular linkage map for walnut consisting of AFLP and SSR markers.  The SSR markers will yield data for a cultivar fingerprint database that is of interest to the walnut nursery industry.  To date, more than 30 of these markers have been extensively tested on 46 walnut cultivars.

IMPACT/OUTCOME:  The genetic map of walnut will facilitate genetic improvement efforts in that crop. The database, to be published on the Internet, will be used by the molecular marker service industry as a tool for maintaining genetic purity in walnut nursery stock.

distribute genomic probes and DNA primers as tools for more effectively mapping and identifying genes.

During FY 2002, ARS will

develop more effective statistical genetic approaches for analyzing genetic marker data.

ACCOMPLISHMENTS:  ARS researchers at Madison, Wisconsin, developed new statistical genetic approaches for analyzing randomly amplified polymorphic DNA (RAPD) genetic marker variation in duplicate potato germplasm samples maintained by the U.S. national potato gene bank, Russia’s Vavilov Research Institute (VIR) potato gene bank, and in original and regenerated seed lots of the same potato samples.

IMPACT/OUTCOME:  These statistical analyses demonstrated that samples thought to be duplicates were actually genetically different, and suggested that little or no genetic variability was lost from potato samples as a result of seed increase.

conduct germplasm evaluations to identify and develop novel “high-value” industrial or ornamental traits, increased adaptation, vigor, and nutritional value, enhanced productive potential, capacity, and efficiency, and improved resistance to environmental extremes, pests, and diseases.

ACCOMPLISHMENTS:  Introduction of new diseases, and genetic changes in pathogen and insect populations represent a major threat to crop production.  Host plant resistance provides the most economical means of controlling such pests.  ARS scientists evaluated thousands of sorghum samples for host-plant resistance to sorghum ergot in Puerto Rico. 

IMPACT/OUTCOME:  Potential sources of resistance were identified.  It appeared that sorghum from specific countries might possess greater genetic diversity for types of host-plant resistance than in others.  These sources of resistance may furnish multiple pathways for effectively controlling diseases, thereby reducing crop loss and production costs.

ACCOMPLISHMENTS:  The incorporation of new genetic variability is vital for continued small grains genetic improvement.  ARS scientists at Aberdeen, Idaho, and Raleigh, North Carolina, evaluated more than 1,200 wheat accessions for host-plant resistance to powdery mildew in field trials in North Carolina and found that more than 180 samples were highly resistant. 

IMPACT/OUTCOME:  This information was made available to researchers via the Germplasm Resources Information Network (GRIN) database.  Seeds of the resistant lines were distributed to breeders for research purposes and germplasm enhancement, which may help accelerate development of new, improved cultivars.

ACCOMPLISHMENTS:  ARS and university scientists evaluated thousands of wheat germplasm samples for host-plant resistance to Fusarium head blight, growth habit, spike and seed descriptors, and agronomic traits.  Thousands of barley germplasm samples were evaluated for beta-glucan, protein, and lipid content; and host plant resistance to stripe rust, crown rust, and barley stripe mosaic hordeivirus (BSMV).  The data from these evaluations were entered into the GRIN database. 

IMPACT/OUTCOME:  Incorporating the evaluation data into GRIN facilitates its use by researchers worldwide. Seeds of valuable lines were distributed for research purposes and germplasm enhancement, including the development of new, improved cultivars.

ACCOMPLISHMENTS:  Pungency in pepper is an economically important trait; however, information on pungency characteristics of pepper germplasm is not available, partially because of the relatively high cost of standard analytical procedures. An enzyme immunoassay (EIA) method was evaluated for its ability to estimate pungency in pepper fruit.

IMPACT/OUTCOME:  Results suggested that EIA is an effective alternative to HPLC, a relatively expensive analytical procedure, for analysis of pungency, which may encourage the use of this and similar techniques for analyzing pungency and other fruit quality characteristics.

ACCOMPLISHMENTS:  Disease resistance in wild apple from Turkey was evaluated and horticultural evaluation of these and Central Asian, Chinese, and Russian Caucasus samples are underway.  Preliminary results indicate that the samples include resistant types.

IMPACT/OUTCOME:  If these sources of resistance remain effective over time, they may furnish important new disease resistance genes for use in apple breeding programs.

perfect more efficient and effective germplasm evaluation methods which exploit genetic associations between useful traits and molecular (DNA) markets to facilitate crop improvement.

ACCOMPLISHMENTS:  ARS researchers at Stoneville, Mississippi, used variability of RFLP genetic markers to map quantitative trait loci (QTLs) in cotton that are statistically associated with important agronomic, physiological, and fiber quality traits.

IMPACT/OUTCOME:  The tangible statistical association of variability in the genetic markers with variation in important agronomic, physiological, and fiber quality traits may enable cotton breeders to forego expensive phenotypic evaluations and, instead, evaluate and select cotton breeding lines based on genetic marker genotypes.

ACCOMPLISHMENTS:  ARS researchers at Stoneville, Mississippi, identified RFLP markers with significant statistical association with host-plant resistance and susceptibility to reniform nematode.

IMPACT/OUTCOME:  The standard approaches for evaluating plants for host-plant resistance to nematodes involve tedious, labor-intensive, and expensive maintenance of nematode populations, followed by inoculation, and individual plant assessment.  Genetic markers may provide a far more rapid, accurate, and inexpensive means of evaluating cotton lines for host-plant resistance to this pest.

develop new fundamental knowledge about gene function, interactions, and mechanisms of gene regulation.

ACCOMPLISHMENTS:  Discovered two cell wall hydrolase genes that are expressed during infection of soybean cyst nematode susceptible soybeans.

IMPACT/OUTCOME:  Soybean cyst nematode is the major pest that limits U.S. soybean production causing about $1 billion in losses to farm income annually.  The discovery of genes that have high activity when soybeans are infected with soybean cyst nematode provides a new strategy for control of this pathogen.  The DNA that triggers the expression of these genes may be used to construct functional genes that produce proteins that are toxic to the nematode.  This approach may help prevent the infection process to avoid nematode-caused damage before it occurs.    

develop new knowledge about methods for gene transfer across wide genetic barriers and the mechanisms by which the process can be precisely controlled.

ACCOMPLISHMENTS:  Determined that outcrossing between herbicide-resistant rice and the weed, red rice, occurs at very low levels and is reduced even more by decreasing synchronization of flowering under field conditions.

IMPACT/OUTCOME:  Rice producers will have new information about the biosafety of herbicide-resistant rice to help them in making management decisions.

describe the structure, function, and regulation of agriculturally important genes in model plants and crop plants.

ACCOMPLISHMENTS:  Discovered a gene that targets transgenes to non-grain tissue of barley

IMPACT/OUTCOME:  This gene promoter can be used to target transgenes to the outer covering (chaff) of barley grains.  This will enable plant scientists to better protect grain from pests that can harm cereal grains without inserting the transgene into the grain that is consumed as food or feed.

During FY 2003, ARS will

establish key reference populations for major livestock species for use in genomic and germplasm evaluation research.

evaluate market assisted selection of cattle for carcass traits and calving ease.

test for the presence of genetic markers of selected strains of rainbow trout that correlate with growth and digestibility of cereal grain-based feeds.

develop more effective statistical genetic approaches for analyzing genetic-related market data.

conduct germplasm evaluations to identify and develop novel “high value” industrial or ornamental traits, increased adaptation, vigor, and nutritional value; enhanced productive potential, capacity, and efficiency; and improved resistance to environmental extremes, pests, and diseases.

perfect more efficient and effective germplasm evaluation methods which exploit genetic associations between useful traits and molecular (DNA) markers to facilitate crop improvement.

characterize plant genetic systems to expand knowledge about control of metabolic functions of plant cells, and use that knowledge to genetically modify plant composition or improve economically important traits.

improve plant genetic transformation systems to expand their usefulness and improve efficiency.

describe the structure, function, and regulation of agriculturally important genes in model plants and crop plants.

develop effective strategies to replace or augment antibiotics.

During FY 2004, ARS will

develop the tools and protocols needed for screening cattle, swine, and poultry for the presence of genes associated with both the progression of hyper-responsiveness to disease and genes that must be induced to assist in restoring homeostasis.

develop marker assisted selection strategies to improve economically important traits such as disease resistance and dress-out percentage.

develop and enhance marker assisted breeding strategies for crops of horticultural importance

characterize plant genetic systems to expand knowledge about control of metabolic functions of plant cells and use the knowledge to genetically modify plant composition or improve economically important traits.

describe the structure, function, and regulation of agriculturally important genes in model plants and crop plants.

improve plant genetic transformation systems to expand their usefulness and improve efficiency.

develop effective strategies to replace or augment antibiotics.

develop more effective statistical genetic approaches for analyzing genetic marker data.

conduct germplasm evaluations to identify and develop novel "high‑value" industrial or ornamental traits, increased adaptation, vigor, and nutritional value, enhanced productive potential, capacity, and efficiency, or improved resistance to environmental extremes, pests, and diseases.

perfect more efficient and effective germplasm evaluation methods which exploit genetic associations between useful traits and DNA markers to facilitate crop improvement.

During FY 2005, ARS will

test the efficiency of on-surgical embryo transfer techniques in swine.

use improved models for QTL detection and marker assisted selection in complex pedigrees.

use genomic and proteomic information to identify critical regulatory steps controlling reproduction in beef cattle.

identify candidate genes for QTL in cattle and swine.

develop new marker systems in swine which will permit more rapid and economical genotyping.

develop trout lines with good stress responses and innate immunity.

develop and enhance marker assisted breeding strategies for crops of horticultural importance.

characterize plant genetic systems to expand knowledge about control of metabolic functions of plant cells and use the knowledge to genetically modify plant composition or improve economically important traits.

describe the structure, function, and regulation of agriculturally important genes in model plants and crop plants.

improve plant genetic transformation systems to expand their usefulness and improve efficiency.

develop effective strategies to replace or augment antibiotics.

develop more effective statistical genetic approaches for analyzing genetic marker data.

conduct germplasm evaluations to identify and develop novel "high‑value" industrial or ornamental traits, increased adaptation, vigor, and nutritional value, enhanced productive potential, capacity, and efficiency, or improved resistance to environmental extremes, pests, and diseases.

perfect more efficient and effective germplasm evaluation methods which exploit genetic associations between useful traits and DNA markers to facilitate crop improvement.

STRATEGY 2.1.4:  Plant and animal biological processes:  Develop biologically-based technologies to improve productivity, safety, nutrient content, and quality of plants, animals, microbial organisms, and their products.

PERFORMANCE GOAL 2.1.4.1:  Make technologies available for improving productivity, safety, and quality.

Indicators:

During FY 2002, ARS will

develop life cycle husbandry practices of arctic char adapted to Appalachia.

ACCOMPLISHMENTS:  Life cycle husbandry practices of arctic char was completed and published in scientific reports.

IMPACT/OUTCOME:  Two producers are using this technology in West Virginia and one producer is using it in Canada.  This technology allows producers to raise and market Artic Char, a high-value food fish.

develop and assure one-tenth commercial scale recirculation systems (50 metric tons annual) for arctic char.

ACCOMPLISHMENTS:  One-tenth commercial scale recirculation system for arctic char is producing market-sized fish.

IMPACT/OUTCOME:  This research has been published in scientific journals and is being used in commercial-scale char production in West Virginia and for Atlantic salmon smolt production in Maine, British Columbia, and New Brunswick, Canada.

develop a natural product treatment for safely controlling algae-related off flavors in catfish.

ACCOMPLISHMENTS:  ARS scientists at the National Product Laboratory in Oxford, Mississippi, in collaboration with Mississippi State University scientists, tested a natural product to control off-flavor under pond conditions with promising results.

IMPACT/OUTCOME:  A CRADA partner is being sought to commercialize this product.

work on developing detection, prevention, and control strategies for transmissible spongiform encephalopathies.

ACCOMPLISHMENTS:  A rapid diagnostic test has been developed for the detection of scrapie and chronic wasting disease.

IMPACT/OUTCOME:  Further understanding of the immunopathogenesis of diseases and detection and control measures to mitigate their effects will ultimately lead to greater productivity of livestock.  The transfer of the knowledge and technologies involved in the detection and control of scrapie, chronic wasting disease, and foot and mouth disease to industry and related government agencies, such as the Animal and Plant Health Inspection Service (APHIS), is necessary for the advances to be fully implemented.

work on developing sensitive diagnostic methods and effective vaccines to control foot and mouth disease.

ACCOMPLISHMENTS:  A new recombinant vaccine against foot and mouth disease has been developed and an agreement has been entered into with a commercial company to further develop and validate this vaccine.

IMPACT/OUTCOME:  Further understanding of the immunopathogenesis of diseases and detection and control measures to mitigate their effects will ultimately lead to greater productivity of livestock.  The transfer of the knowledge and technologies involved in the detection and control of scrapie, chronic wasting disease, and foot and mouth disease to industry and related government agencies, such as APHIS, is necessary for the advances to be fully implemented.

work on determining the immunopathogenesis of porcine respiratory disease complex.

ACCOMPLISHMENTS:  The immunopathogenesis of porcine respiratory disease complex has been further elucidated.

IMPACT/OUTCOME:  Further understanding of the immunopathogenesis of diseases and detection and control measures to mitigate their effects will ultimately lead to greater productivity of livestock.

develop new fundamental knowledge that will bring about regulation of the photosynthetic process for improved crop yields and production efficiency.

ACCOMPLISHMENTS:  Discovered the biochemical basis for heat tolerance in cotton.

IMPACT/OUTCOME:  Heat stress slows photosynthesis, thus reducing crop yields.  The photosynthetic enzyme that is most affected by heat stress can now be modified by plant scientists to maintain or even stimulate photosynthesis at high temperatures.             

develop new basic knowledge that will lead to improved efficiency in the use of inputs by plant production systems for food, feed, fiber, and bioenergy.

ACCOMPLISHMENTS:  Identified peanut varieties with high water-use efficiency.

IMPACT/OUTCOME:  Development of methods to identify crop varieties that efficiently use water as well as producing good yields will promote crop production efficiency.  Breeding methods that include selection for water-use efficiency will lead to the release of “water-saver” peanut varieties.  

develop new knowledge that will lead to elucidation of regulatory mechanisms of plant growth and development.

ACCOMPLISHMENTS:  Discovered a gene (Clv3) as a key process in cell-to-cell communication during plant development.

IMPACT/OUTCOME:  This new discovery yields new information about how plants form new shoots and blooms.  The results can be used to develop new and unusual plants and flowers for growers and florists.

develop new basic knowledge about mechanisms of organismal interactions that will make possible  enhanced symbiotic or mutual associations of crop plants with other beneficial organisms.

ACCOMPLISHMENTS:  Identified genes expressed in the root hairs of sorghum.

IMPACT/OUTCOME:  Determination of all the genes expressed in sorghum roots enables plant scientists to better understand the mutual association of crop plants with soil microorganisms.   New knowledge of natural products produced by crop plants can be used to incorporate use of beneficial microbes into crop management systems.

develop new fundamental knowledge that will improve the management of pests using environmentally safe methods by enhancing the plant’s natural processes of defense or by introducing new resistance mechanisms.

ACCOMPLISHMENTS:  Biotechnology was used to protect peanuts from attack by viral diseases.

IMPACT/OUTCOME:  Transgenic peanut plants with an introduced coat protein will have enhanced protection from viral diseases.  These biotech plants will be resistant to tomato-spotted wilt virus, a virus causing significant losses to peanut production in the Southeast and becoming a threat in the Southwest.

develop new basic knowledge that will be the basis for improved productivity when crops are subjected to environmental stress.

ACCOMPLISHMENTS:  Discovered a wheat protein that helps protect winter wheat from freezing damage. 

IMPACT/OUTCOME:  Severe freezing temperatures can kill winter and spring wheat resulting in major economic losses to producers and damage to the environment through soil erosion.  Discovery of a protein that accumulates in winter, but not spring wheat, subjected to freezing temperatures can accelerate the development of other, more cold-hardy crops and ornamental species.

develop new fundamental knowledge of plant processes that will lead to greater product quality, uniformity, and value, and to improved marketability of agricultural products.

ACCOMPLISHMENTS:  Discovered how to control the gene that is the key to making ripening tomatoes develop full flavor.

IMPACT/OUTCOME:  Current tomato production and shipping practices require that tomatoes be harvested before ripening.  While this makes possible long-term storage and shipping, the tomatoes do not always achieve full flavor.  Learning how to control the gene that regulates multiple ripening processes, including full flavor, will enable plant scientists to develop tomatoes with improved flavor and marketability.

develop new fundamental knowledge of plant processes that generate important nutritional and healthful properties of plants grown for human or animal consumption.

ACCOMPLISHMENTS:  Genetic engineering was used to increased levels of antioxidants in tomato.

IMPACT/OUTCOME:  Transgenic strategies are just beginning to be used to improve phytonutrient content.  Development of tomatoes with enhanced antioxidants may be one of the first examples of the benefit of this new technology to improve healthfulness of foods.

ACCOMPLISHMENTS:  By 2002, a soybean strain was genetically engineered to remove a major human allergen.

IMPACT/OUTCOME:  Food allergies are an increasing concern for oilseed crops. A biotechnological approach called “gene silencing” was used to prevent the synthesis of an allergenic protein in soybean seed. The new allergen-minus soybean germplasm can be used to develop soy-based foods that have a lower allergenic risk to consumers.            

develop new underlying knowledge as the basis for predicting global change effects on crop productivity and to take advantage of any benefits of global change to enhance crop yields, competitiveness with weeds, and adaptation to changes in atmosphere and the environment.

ACCOMPLISHMENTS:  Discovered biological mechanisms that confer thermotolerance in plants.

IMPACT/OUTCOME:  Identification of an inducible, multi-component heat protection system in plants will provide the basis for identifying genes that can protect crops from warmer temperatures.  Plant breeders can exploit these genes to select plants that can thrive at warmer temperatures.

develop new knowledge that will enable production, storage, and processing of safe plant products to decrease incidences of mycotoxins and other contaminants of food and feed, and reduce levels of naturally-occurring toxicants.

ACCOMPLISHMENTS:  Determined the action mechanism of a Fusarium toxin that causes plant cell death.

IMPACT/OUTCOME:  New information shows that this toxin is a structural analogue of the simple sugar, fructose, and that the toxin is activated by phosphorylation.  This new information can be used to design strategies to inactivate this potent plant cell toxin.             

develop new knowledge of the occurrence and activities of biologically active natural products to enhance the ability to utilize this abundant natural resource.

ACCOMPLISHMENTS:  Determined that kenaf has the ability to absorb larger molecular weight, odor-causing molecules such as benzaldehyde and P-cresol.

 IMPACT/OUTCOME:  Kenaf can be an effective alternative to activated carbon for odor control systems.  In the future, kenaf may be used to remove pungent odors generated by industries such as wood pulp processing plants.  Kenaf may also make a useful contribution to improving air quality.

address the issues raised by the Food Quality Protection Act (FQPA) of 1996 regarding the loss of many broad spectrum pest control products.  The ARS IR-4 program, a National agricultural program designed to clear pest management agents for minor uses, will cooperate with CSREES State partners to provide growers of minor crops with effective pest management agents that have a minimal impact on the environment and meet the more stringent safety requirements of FQPA.

ACCOMPLISHMENTS:  New tools are available for minor crop producers to reduce pest losses, improve yields, and maintain product quality.  The success of minor crop producers is tied closely to the IR‑4 (Minor Use Pesticide) Program, since the agrochemical industry, for economic reasons, does not pursue registration of chemicals for many small acreage crops.  At the request of minor crop growers, ARS scientists conducted high-priority field tests and residue analyses at Beltsville, Maryland; Charleston, South Carolina; Tifton, Georgia; Wooster, Ohio; Urbana, Illinois; Weslaco, Texas; Prosser, Washington; Wapato, Washington; Corvallis, Oregon; and Salinas, California; that contributed to new use registrations, as well as emergency use exemptions for many fruits, vegetables, and ornamentals.  These uses included asparagus, cantaloupe, watermelon, basil, snap beans, floral, and nursery/greenhouse plants. 

IMPACT/OUTCOME:  This research focused on pest control materials having reduced risk chemistries to coincide with the goals of the Food Quality Protection Act of 1996, thus not only serving to promote the economic viability of minor crop growers, but also to provide safer pest management options.

During FY 2003, ARS will

develop and evaluate a mobile, pond-side testing kit to enable field testing of therapeutic chemicals used for treating fish to satisfy FDA efficacy requirements.

develop a modified live and killed vaccine against Edwardsiella tarda for the prevention of E. tarda septicemia in a number of species of food fish.

work on developing sensitive diagnostic methods and effective vaccines to control foot and mouth disease.

develop new prevention and control strategies for Marek’s disease, Newcastle disease, and cattle fever.

work on developing detection, prevention, and control strategies for transmittable spongiform encephalopathies.

address emerging animal diseases offshore.

use fundamental knowledge about plant development, production efficiency, responses to environment, and interactions with other organisms to identify potential genetic sources of improvement for introduction into crops (including introduction by genetic engineering).

address the issues raised by the Food Quality Protection Act (FQPA) of 1996 regarding the loss of many broad spectrum pest control products.  The ARS IR-4 program, a national agricultural program designed to clear pest management agents for minor uses, will cooperate with CSREES-State partners to provide growers of minor crops with more effective pest management agents that have a minimal impact on the environment and meet the more stringent safety requirements of FQPA.

During FY 2004, ARS will

quantify yield and economics of three loading rates for channel catfish reared for market using an intensively managed, microbial-based production system.

determine stage-of-life differences for pigs microbial shedding response to transport.

continue to improve diagnostic and control methodologies for infectious diseases of animals and transfer the technology to commercial companies or government partners.

produce research data for clearances of pest control products on minor food and ornamental crops.  The ARS Minor Use Pesticide Program will cooperate in these efforts with the CSREES IR-4 program and their State partners, providing growers of minor crops with more effective pest management agents that have a minimal impact on the environment and meet the more stringent safety requirements of the Food Quality Protection Act of 1996.  ARS will concentrate its efforts on the newer reduced risk chemistries that lessen impacts on the environment.

use fundamental knowledge about plant development, production efficiency, responses to environment, and interactions with other organisms to identify potential genetic sources of improvement for introduction into crops (including introduction by genetic engineering).

During FY 2005, ARS will

partner with appropriate companies to ensure diagnostic and control methodologies are provided to agriculture commodity groups which would benefit from that technology.

produce research data for clearances of pest control products on minor food and ornamental crops.  The ARS Minor Use Pesticide Program will cooperate in these efforts with the CSREES IR-4 program and their State partners, providing growers of minor crops with more effective pest management agents that have a minimal impact on the environment and meet the more stringent safety requirements of the Food Quality Protection Act of 1996.  ARS will concentrate its efforts on the newer reduced risk chemistries that lessen impacts on the environment.

use fundamental knowledge about plant development, production efficiency, responses to environment, and interactions with other organisms to identify potential genetic sources of improvement for introduction into crops (including introduction by genetic engineering).

OBJECTIVE 2.2:  Safe food:  “Maintain an adequate, nutritious, and safe supply of food to meet human nutritional needs and requirements.”

STRATEGY 2.2.1:  Plant and animal product safety:  Provide knowledge and means for production, storage, and processing of safe plant and animal products.

PERFORMANCE GOAL 2.2.1.1:  Transfer knowledge developed by ARS to industry and regulatory agencies.

Indicators:

During FY 2002, ARS will

elucidate the ecology and epidemiology of pathogens on food producing animals, animal products, seafood, fruits and vegetables, and within the processing environment.  The necessary data to carry out risk assessment will be provided.  Critical control points will be identified and parameters of existing critical control points that lead to the design of control or intervention strategies will be validated to lower the presence of pathogens.  Predictive models will also be developed and validated.

ACCOMPLISHMENTS:  No information concerning prevalence of non-O157 Shiga toxin-producing E. coli (STEC) contamination of beef carcasses had been reported in the United States.  ARS scientists at the Meat Animal Research Center, Clay Center, Nebraska, sampled carcasses from beef processing plants in the United States, and the prevalence and virulence characteristics of non-O157 STEC strains contaminating beef carcasses were determined. 

IMPACT/OUTCOME:  This is the first comprehensive study of non-O157 STEC carcass contamination in the United States and will provide the Food Safety and Inspection Service (FSIS) and producers with information to be used in establishing baseline prevalence levels.

ACCOMPLISHMENTS:  Chickens from campylobacter-free flocks were tested for the presence of the organism after being transported in crates that had previously been used for campylobacter positive birds.  It was discovered that the presence of campylobacter in a transport dump coop from the feces of a campylobacter positive flock can contaminate the outer surfaces of the next flock.  The resulting contamination can remain on previously negative broiler carcasses through the killing, scalding, and defeathering processes, thus bringing campylobacter into the processing facility.

IMPACT/OUTCOME:  Inadequately cleaned and/or sanitized transportation coops can be considered as a critical control point for reduction of pathogens on poultry and a means of introduction into processing plants. Different coop design, or better cleaning methods for existing transportation coops need to be considered.

ACCOMPLISHMENTS:  Through participation in the National Animal Health Monitoring System (NAHMS) Swine Study in collaboration with the Animal and Plant Health Inspection Service, ARS scientists at the Eastern Regional Research Center (ERRC), Wyndmoor, Pennsylvania, determined the prevalence of pathogenic Y. enterocolitica and of STEC in swine in the United States.  To accomplish the study, methods for processing swine feces and detection, isolation, and characterization of Y. enterocolitica and STEC were developed.  Results indicated that swine can harbor pathogenic Y. enterocolitica and are a potential reservoir for many serotypes of STEC strains that may cause human illness.

IMPACT/OUTCOME:  The results of the prevalence of Y. enterocolitica in U.S. market weight hogs were included in a report to the National Pork Board.  The information generated from the study is useful for identifying on-farm management and processing practices leading to carriage of the pathogens by swine, and ultimately leading to reduction in Y. enterocolitica and STEC transmission from pork to humans. 

ACCOMPLISHMENTS:  Contamination of ground beef by E. coli O157:H7 is a critical issue for regulatory-action agencies, industry, and consumers.  In order to more fully assess the risk for contamination, ARS scientists at ERRC developed mathematical models to estimate the effects of grinding processes on the distribution of E. coli O157:H7.  Beef trim contaminated with E. coli O157:H7 was processed similarly to that done by industry to produce a ground product.  The research showed that there were defined distribution patterns at different levels of contamination, and that the pathogen accumulates and resides in selected components of the grinder.

IMPACT/OUTCOME:  These results will greatly assist in reducing the uncertainty of how beef is contaminated in the grinding process.  Furthermore, the findings will aid processors and regulatory agencies in risk assessment, and in the design of HACCP system for both large and small processors.  Additionally, they will provide assistance in designing improved sanitation and microbiological sampling procedures. Ultimately, this will benefit consumers by providing a safer product.

ACCOMPLISHMENTS:  Broiler carcasses contaminated with feces must be detected with an imaging system capable of operating at processing-line speeds.  ARS scientists at the Richard Russell Research Center, Athens, Georgia, in association with industry developed a real-time, portable multispectral imaging system that can capture carcass images to detect contamination at a rate of 140 birds per minute.

IMPACT/OUTCOME:  FSIS has a zero-tolerance regulation for feces on poultry carcasses prior to the carcass entering the ice/water immersion chiller.  Development of this ARS system will aid inspectors to determine the absence or presence of fecal contamination on carcasses and it will aid industry to meet the zero tolerance standard for visible fecal material.  This will ultimately provide the consumer with a microbiologically safer product with longer shelf life.

identify the sites and mechanisms of pathogen colonization in animals, identify and characterize virulence attributes which play a role in the host-pathogen relationship, and develop intervention strategies which reduce colonization and shedding of pathogens by animals used for food.

ACCOMPLISHMENTS:  The pathogen of greatest concern to the safety of animal-based foods is E. coli O157:H7, which is primarily a problem of beef cattle.  ARS scientists in Clay Center, Nebraska, demonstrated that the hide surface and the oral cavity of finished beef feedlot cattle usually have a higher E. coli O157:H7 prevalence than do bovine feces. 

IMPACT/OUTCOME:  This finding can help explain several recent outbreaks of this pathogen in children following farm tours and visits to county fairs, and opens up additional sites for researchers to easily obtain samples for microbiological identification of the pathogen.

ACCOMPLISHMENTS:  An ARS laboratory in College Station, Texas, developed workable protocols for administration and evaluation of a new pathogen control compound for beef and dairy cattle prior to slaughter.  Specially formulated sodium chlorate preparations administered in feed and/or drinking water a few days prior to slaughter selectively killed pathogenic E. coli and salmonella in the animal’s gut, reduced hide and carcass contamination with these pathogens, and had no negative effects on final product quality.

IMPACT/OUTCOME:  This will provide a practical, efficacious, cost-effective and commercially viable product that significantly enhances the microbiological safety of beef food products.  Further study to receive Food and Drug Administration approval will be necessary.

ACCOMPLISHMENTS:  To assess the potential for cattle and aquatic mammals to serve as reservoirs of pathogenic microsporidia parasites, ARS scientists in Beltsville, Maryland, developed diagnostic assays and tested cattle fecal samples from Maryland, Pennsylvania, Virginia, and Florida, and aquatic wildlife fecal samples from around the Chesapeake Bay.  Several species of microsporidia were identified in cattle in three of the four States.  The same microsporidia was also identified in fecal samples collected from muskrat, beaver, otter, raccoon, and fox. 

IMPACT/OUTCOME:  This is the first finding of the organism in cattle of North America and in wildlife worldwide, and it identifies these animals as potential sources of an emerging human pathogen, thus providing direction for further research to protect the food supply.

ACCOMPLISHMENTS:  The acquisition of antibiotic resistance and/or enhanced virulence by bacterial pathogens is a threat to human health and methods are needed to mitigate this resistance.  Using a novel genetic system and high-throughput screening assays, an ARS laboratory in Ames, Iowa, identified six salmonella proteins that are essential for growth, virulence, or antibiotic resistance.

IMPACT/OUTCOME:  Identifying specific proteins and their functions will provide research directions to understand antibiotic resistance and prevent its spread and acquisition by other bacteria.

ACCOMPLISHMENTS:  Accurate classification of bacterial pathogens is necessary to trace their movement through natural and manmade environments.  The current classification and identification scheme for Enterococcus, based on phenotypic analysis, is both tedious and laborious, requiring at least 24 hours.  ARS scientists in Athens, Georgia, developed a DNA-based assay that will identify the genus and species for19 of 25 Enterococcus strains that have been isolated and classified.  The entire process is cost-effective, rapid, and accurate, and requires approximately three and one half hours.

IMPACT/OUTCOME:  This classification process will help establish a firm basis for antibiotic use recommendation to decrease pathogen resistance to drugs.

develop methods to assure that pathogens and chemical contaminants from animal manure do not pose a food safety hazard.

ACCOMPLISHMENTS:  In water-scarce areas the potential for bacterial regrowth in reclaimed water used for crop irrigation must be understood.  ARS scientists in Phoenix, Arizona, assessed the survival and regrowth potential of bacteria present in treated effluent used for crop irrigation and surface water discharge as it passed through a model laboratory distribution system.  Total bacteria increased three- to four-fold orders of magnitude, and that E. coli remained viable during the 11-day experiment.  

IMPACT/OUTCOME:  This research has established that although the reclaimed water met Environmental Protection Agency standards for irrigation at the treatment plant, there is great potential for bacterial regrowth during transport, making the water out of compliance at the point of intended use and capable of spreading pathogens.  This information will provide the basis for further study and help prevent future problems of food contamination via wastewater irrigation.

ACCOMPLISHMENTS:  The endogenous hormones, estradiol and testosterone, which are produced by all animals, are found in animal manure, particularly from concentrated animal feeding operations, and may pose a threat to human health through contamination of surface and ground waters.  ARS scientists in Fargo, North Dakota, determined the degradation rate of these hormones during composting of manure.  Initial concentrations of testosterone and estradiol in chicken manure averaged 212 and 92 parts per billion (ppb), respectively, but dropped gradually over 129 weeks to 13 ppb for testosterone and 16 ppb for estradiol.  The rate of degradation of testosterone was three times that of estradiol. 

IMPACT/OUTCOME:  This research demonstrates that composting may be an environmentally friendly technology suitable for reducing the amounts of endogenous hormones at concentrated animal operation facilities, thus preventing their transport into surface or groundwater systems that could be a source of drinking water.

develop sampling plans and methods that have regulatory, industry, and research use for the isolation, identification, and quantification of pathogens.

ACCOMPLISHMENTS:  A method to characterize and type the bacterial pathogen listeria from foods is critically important for regulatory-action agencies and industry.  ARS scientists at the Western Regional Research Center developed an accurate, rapid, reproducible, cost effective method for typing L. monocytogenes strains using commercially prepared components, with a sensitivity level 1,000-fold better than currently used.  The method was tested on over 100 reference and unknown strains, and proved highly accurate.

IMPACT/OUTCOME:  The new method will have a significant impact on the ability of industry and regulatory agencies’ ability to rapidly detect and characterize listeria monoctyogenes from food products.

ACCOMPLISHMENTS:  Shellfish are common sources of food-borne viral illnesses.  ARS scientists at the Center of Excellence in Aquaculture, Delaware State University, developed a new virus extraction procedure for isolation and detection of both hepatitis A and Norwalk-like viruses.  The methods were successfully used and validated by assisting the FDA to detect viruses in a food-implicated outbreak of illness that occurred. 

IMPACT/OUTCOME:  The new procedure has been readily accepted by regulatory agencies.  The FDA sponsored a number of VirusNet Workshops designed to discuss the implementation of virus testing among State health departments.  A training CD entitled “Method to Extract Enteric Virus RNA from Shellfish” was developed.

develop pathogen intervention strategies to assist regulatory agencies in establishing the basis for Hazard Analysis Critical Control Point (HACCP) system  programs, aid both the large and small processors in carrying out good practices, and decrease the potential for introduction of zoonotic pathogens into processing environments.  The effects of intervention strategies to reduce pathogens on food and antimicrobial resistance will be determined.

ACCOMPLISHMENTS:  A large number of viruses can cause sickness and/or death of consumers who eat raw or lightly cooked molluscan shellfish.  ARS scientists in the Center of Excellence in Aquaculture at Delaware State University showed that hepatitis A virus and Caliciviruses (Norwalk-like viruses) in oysters could be killed using high pressure processing techniques.

IMPACT/OUTCOME:  This technology could readily and easily be implemented by industry to provide consumers with a safe product that could be eaten raw.

ACCOMPLISHMENTS:  The number of recalled ready-to-eat foods, such as hot dogs, due to contamination by listeria has dramatically increased during the past few years.  ARS scientists at the Eastern Regional Research Center (ERRC), Wyndmoor, Pennsylvania, in association with industry, conducted a study to assess the prevalence of listeria monocytogenes in commercially produced, vacuum-sealed packages of hot dogs.  The study showed that 1.6 percent of the 33,000 sampled packages tested statistically positive for the pathogen.  There was no appreciable difference in recovery rate of the pathogen due to time or storage at either 4 or 10 degrees C, the latter being the temperature of most household refrigerators.  Seasonality of manufacture, for example, summer versus winter, also had no influence.

IMPACT/OUTCOME:  This baseline data on prevalence was critical for industry and regulatory-action agencies in developing guidelines for setting a safe shelf life for hot dogs relative to the risk of listeriosis, and/or for recommending conditions for heating hot dogs prior to consumption by consumers.

ACCOMPLISHMENTS:  Fresh produce has been implicated in an increasing number of major foodborne illness outbreaks during the past few years.  This has led FDA to recommend that customs officials halt the import of certain fruits and vegetables into the United States.  ARS scientists at the ERRC investigated why pathogen contamination persists on certain produce.  Studies of various pathogens demonstrated that some bacteria such as salmonella, due to their outer chemical structure, attached more firmly to the outside (rind) making them more resistant to treatment with sanitizers.

IMPACT/OUTCOME:  These findings assist in explaining why certain bacteria, for example salmonella, are often associated with foodborne illness due to the consumption of fresh produce.  The outcome is that more effective means of either detaching or killing the attached bacterial pathogens are required to help ensure the safety of some produce for the consumer. 

ACCOMPLISHMENTS:  Contaminated fruits, vegetables, and tree nuts present a high risk to public health because they are often consumed without further preparation.  ARS scientists at the Western Regional Research Center, Albany, California, in collaboration with industry developed a method using chlorine dioxide gas to reduce bacterial pathogens on produce, such as strawberries and almonds, without adversely affecting the desirable marketing properties, and to extend cold storage life by controlling mold growth.  Chlorine dioxide gas was also demonstrated to reduce pests in soil, such as nematodes, fungi and weeds that are detrimental to plants, and could be a potential alternative for methyl bromide, a widely used soil fumigant that is being phased out because it depletes the ozone layer. 

IMPACT/OUTCOME:  The studies have the potential to significantly impact the produce industry, and the environment.  Already, the Almond Board of California is evaluating the technology to disinfect almonds produced within that State, which have been implicated in several major outbreaks of salmonella associated food-borne illness.

ACCOMPLISHMENTS:  Development of successful intervention strategies are urgently needed in order to reduce the level of bacterial pathogens associated with poultry products.  ARS scientists at the Richard Russell Research Center, Athens, Georgia, in association with industry and commercial partners evaluated a new Generally Recognized As Safe (GRAS) compound that can significantly reduce salmonella, campylobacter, and E. coli pathogens on broiler carcasses.

IMPACT/OUTCOME:  Due in large part to the ARS research, the GRAS-compound has been approved by the Food Safety Inspection Service (FSIS).  FSIS has approved the products use as an in-plant, pre-chill treatment.  Ongoing commercial studies should confirm that this product would allow delivery of a microbiologically safer product with an increased shelf life and less environmental impact.

develop methods to control mycotoxins produced by Fusarium Aspergillus fungi in food crops.  Methods to detect, quantitate, sample and/or separate toxin containing commodities will be developed.  Methods to control insect vectors utilizing biocontrol fungi, and/or optimization of production practices will also be developed.

ACCOMPLISHMENTS:  Contamination of tree nuts by aflatoxins produced from infection by the fungus Aspergillus flavus and A. parasiticus is a serious problem because of the stringent regulatory levels imposed for these toxins, and the potential threat to human health.  ARS scientists in Albany, California, demonstrated that the sources of the high aflatoxin resistance of the seed coat pellicle of the Tulare variety of walnut is a series of complex, structurally related polar compounds of which gallic acid is a major component.  ARS scientists demonstrated that gallic acid is a potent inhibitor of aflatoxin synthesis when the fungus is exposed to these compounds. 

IMPACT/OUTCOME:  Measurement of gallic acid levels in various tree nuts will provide a means of assessing the aflatoxin resistance of individual varieties that will result in lesser amounts of aflatoxin in tree nuts and greater protection of the public health.

ACCOMPLISHMENTS:  The occurrence of aflatoxin severely limits the value of cottonseed, an economically important by-products of cotton production in Texas.  An ARS scientist in New Orleans, Louisiana, identified the importance of the second (post maturity) phase of aflatoxin contamination of cottonseed that occurs when exposure of mature bolls to high humidity, temperature, and rainfall stimulates crop invasion by aflatoxin producing fungi.

IMPACT/OUTCOME:  Recognition of these key features may make possible identification of predisposing environmental and agronomic factors and, as a result, improved management recommendations can be made to prevent the occurrence of aflatoxin.  This will increase the safety of cottonseed in human and animal food and increase the returns to growers.

ACCOMPLISHMENTS:  Aflatoxins produced by the fungus Aspergillus flavus can infect crops, such as corn, cotton, peanuts and tree nuts causing a potential food safety hazard and lowering their economic value.  ARS scientists in New Orleans prepared a cloned genetic library of the aflatoxigenic fungus.  The DNA of each these clones was sequenced in collaboration with The Institute for Genomics Research (TIGR) to identify unique genes that the fungus uses to accomplish all of its biological and physiological functions.  These scientists have also begun to profile all the genes that are functional and active during both fungal invasion of the crops and aflatoxin formation.

IMPACT/OUTCOME:  This information will provide the basis for understanding how aflatoxin is formed in crops and deciphering how environmental factors affect the fungus, and it will help to devise effective and lasting strategies to modulate or control aflatoxin formation.

determine the absorption, metabolism, distribution, excretion, and elimination properties of drugs and environmental contaminants in food producing animals.  Screening and confirmatory methods to detect and quantify drug and contaminant residues will be developed.  Strategies for reducing the occurrence of residues will be devised.

ACCOMPLISHMENTS:  ARS scientists at the Eastern Regional Research Center, Wyndmoor, Pennsylvania, developed a new quick, easy, cheap, effective, rugged, and safe method (acronym QuEChERS [pronounced “catchers”]) for the purification, detection and quantification of chemicals, especially pesticide residues.  The new method provides high quality results for a wide range of compounds.  Using the method, a single technician can prepare 12 samples in less than 30 minutes using a single piece of reusable glassware at a cost of $10.

IMPACT/OUTCOME:  Industry as well as regulatory-action agencies in the United States and worldwide, need improved and highly cost-effective methods to detect chemical compounds in agricultural commodities.  This new technology will have a significant national and international impact on monitoring the food supply for harmful and illegal contaminants.

ACCOMPLISHMENTS:  The supercritical laboratory in the National Center for Agricultural Utilization Research, Peoria, Illinois, has made a major contribution in the area of chemical and antibiotic residue, isolation, purification and quantitation.  Two natural chemicals, carbon dioxide and water, along with small quantities of organic solvents, are used to extract analytes (pesticides, nutrients, and veterinary drugs).  This method was the first instrumental method for the isolation and quantitation of the banned antibiotic avoparcin, and the pesticide triazine.

IMPACT/OUTCOME:  Reduction or total elimination of the use of objectionable organic solvents in the laboratory environment is currently desired by regulatory agencies and industry.  Aside from the environmental benefit and help in ensuring a safe food supply for consumers, eliminating the use of the solvents and chemicals would substantially reduce the costs and difficulties associated with the disposal of such substances.  Furthermore, laboratory personnel would be protected from exposure to the toxic, flammable chemicals.

develop knowledge and technology to prevent weight loss or decreased gains, reproductive performance, or other toxic effects in food producing livestock from grazing plants.

ACCOMPLISHMENTS:  Grazing of ponderosa pine needles causes abortion/premature parturition, retained placentas and endometritis in pregnant cattle, resulting in substantial economic losses to cattle producers in the Western United States.  ARS scientists at Logan, Utah, developed rapid tests (ELISAs) for isocupressic acid (ICA) and its metabolites using polyclonal antibodies.  Similarly, assays were developed to detect and measure two significant teratogenic steroidal alkaloids in veratrum plant species, as well as the photosensitivity agent, phylloerythrin.

IMPACT/OUTCOME:  These assays for rapidly screening biological samples for the presence of these toxins will help speed further research to find the ultimate cause of both reproductive failures and photosensitivity, and/or will ultimately aid ranchers in identifying areas to avoid grazing by susceptible animals.

determine whether there is an association of transport stress with shedding of microorganisms that are of food safety significance.

ACCOMPLISHMENTS:  The threat of a reservoir of pathogens is compounded when animals are shipped to slaughter because the stress of handling and transportation increases the shedding of the pathogens.  ARS scientists in West Lafayette, Indiana, developed a stress model of transportation and created the ability to induce swine to shed the pathogen, salmonella, under controlled laboratory conditions.

IMPACT/OUTCOME:  This information will aid in identifying characteristics of individual animals that shed pathogens in order to compare them with infected, but non-shedding herd mates.  Understanding these critical differences in individual animals will pave the way for interventions to be developed that will decrease pathogen shedding and thus help to ensure food safety.

develop sampling plans and methods that have both regulatory, industry, and research use for the isolation, identification, and quantification of pathogens.

ACCOMPLISHMENTS:  A method to characterize and type the bacterial pathogen listeria from foods is critically important for regulatory-action agencies and industry.  ARS scientists at the Western Regional Research Center developed an accurate, rapid, reproducible, cost-effective method for typing L. monocytogenes strains using commercially prepared components at a sensitivity level 1,000-fold better than currently used.  The method was tested on more than 100 reference and unknown strains and proved highly accurate.

IMPACT/OUTCOME:  The new method will have a significant impact on industry and regulatory agencies’ ability to rapidly detect and characterize listeria monoctyogenes in food products.

ACCOMPLISHMENTS:  Shellfish are common sources of foodborne viral illnesses.  ARS scientists at the Center of Excellence in Aquaculture, Delaware State University developed a new virus extraction procedure for the isolation and detection of both hepatitis A and Norwalk-like viruses.  The methods were successfully used and validated by assisting the Food and Drug Administration to detect viruses in a food implicated in an outbreak of illness. 

IMPACT/OUTCOME:  The new procedure has been readily accepted by regulatory agencies.  The FDA sponsored a number of VirusNet Workshops designed to discuss the implementation of virus testing methods by State Health Departments.  A training CD entitled, “Method to Extract Enteric Virus RNA from Shellfish,” was developed.

During FY 2003, ARS will

acquire cultures of important foodborne pathogens to further enhance the capabilities and resources of ARS’ microbial culture collection.

develop the national parasite collection as a primary genomics information resource.

determine the rates and extent of pathogen contamination in bivalve shellfish, and develop decontamination methods. 

determine which protozoa allow intracellular growth/survival of pathogens and whether they destroy environmental pathogens including those in biofilms.

determine the key risk factors of human pathogens in foods of animal origin.  Evaluate the impact of interventions and develop predictive user-friendly models to assist industry and regulatory agencies in making critical food safety decisions that impact public health.

develop advanced techniques for the analysis of drug residues in foods; imaging and related technologies for the identification of surface contamination; and practical, economical, reliable, automated, real time, machine visioning systems for the online detection of surface contamination of animal carcasses during slaughter that will assure food safety.

determine the microbial ecology and transmission of human pathogens during poultry processing, and identify the critical control points to reduce carcass contamination.

sequence genome regions of pathogens affecting animal health and food safety for subsequent development of diagnostic tests, intervention strategies, and therapeutic agents.  Develop bioinformatics tools to process, analyze, and interpret sequencing and mapping information.

identify and quantify sources of pathogens affecting food producing animals; determine any environmental influences, including seasonality and geography, and other animals and insects; and identify sites and mechanisms of colonization in animals/mechanisms of virulence.

develop intervention strategies which reduce colonization and shedding of pathogens in animals used for food including vaccines/competitive colonization/alleviation of stress/altered management practices.

determine how food safety is affected by manure handling practices and utilization.