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United States Department of Agriculture

Agricultural Research Service

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2002 Annual Performance Report & 2003, 2004, 2005 Annual Performance Plans
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1 - Introduction
2 - Table of Contents
3 - Goal I
4 - Goal II
5 - Goal III
6 - Goal IV
7 - Goal V
8 - Goal VI
9 - Summary of Agency Resources for FY 2003
10 - Summary of Agency Resources for FY 2004
Goal II

Goal II:  To Promote a Safe and Secure Food and Fiber System.

 Funding by Program Activity ($000's)

      FY 2002

      FY 2003

      FY 2004

     Soil, Water & Air Sciences

            7,232

7,084

          7,153

     Plant Sciences

        202,560

       218,928 

      229,221

     Animal Sciences

        129,629

       125,702   

      117,869

     Commodity Conversion & Delivery

          60,190

         64,296   

        64,313

    Human Nutrition

                  0

                 0

                0

     Integration of Agricultural Systems

            6,051

           6,217

          6,232

                Total

      $405,662

      $422,227

     $424,788

     FTEs

            3,481

           3,624 

          3,698  

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 is the focus of much of ARS’ research related to food safety and the security of the U.S. agricultural production system.  Under Goal II, 88 Indicators are aligned under 10 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 87 Indicators was completed or substantially completed during FY 2002.  One indicator was not accomplished because the Office of Scientific Quality Review gave it a relatively low priority, thus the work has not yet been addressed.  One hundred and thirty-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 described in the budget estimates for fiscal years 2003 and 2004.

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

OBJECTIVE 2.1:  Secure food and fiber system:  “Maintain a safe and secure food and fiber system that meets the Nation’s needs now and in the future.”

STRATEGY 2.1.1:  Plant and animal production systems:  Improve efficiency of agricultural production systems to ensure the security of the Nation's food, fiber, and energy supply.

PERFORMANCE GOAL 2.1.1.1:  Demonstrate increases in productivity above current levels, using sustainable technologies.

Indicators:

During FY 2002, ARS will evaluate new vaccine technologies for protection from disease and continue to develop complimentary strategies for disease protection.

ACCOMPLISHMENTS:  Vaccines or immunomodulators have been developed by scientists at various laboratories against Foot and Mouth Disease in swine, Brucellosis in bison, Newcastle disease and coccidiosis in chickens, and mastitis in dairy cows.

IMPACT/OUTCOME:  These new vaccines or immunomodulators will help producers combat losses from diseases where it exists and increase preparedness for controlling foreign diseases should incursion occur (e.g. Foot and Mouth Disease, Newcastle disease).

During FY 2003, ARS will

provide recommendations for alternative crops in traditional wheat fallow areas to increase overall productivity.

conduct large vaccination studies to determine the efficacy of new vaccines and determine the strengths and weaknesses of new products.

During FY 2004, ARS will further refine the vaccine technique by modifying delivery, dosage, adjuvant, etc., to address any deficiencies noted from previous trials.  Engage industry partners in the further development and potential licensing of the products.

During FY 2005, ARS will utilize microbial genetic information in the creation of genetically engineered vaccines which utilize specific microbial sequences that specifically confer protective immunity.

PERFORMANCE GOAL 2.1.1.2:  Demonstrate a more efficient and cost-effective use of resource inputs, while increasing productivity above current levels.

Indicators:

During FY 2002, ARS will develop biological and engineering strategies to manage animals during extreme weather events to improve survival, health, and well being, and transfer the information to producers.

ACCOMPLISHMENTS:  Temperature thresholds were demonstrated based upon animal response and incorporated into decision support tools for livestock producers to manage thermal changes.

IMPACT/OUTCOME:  The research was published in a number of scientific journals.  An electron devise was developed to give a warning based on weather data automatically picked up by local broadcasts.  This device provides advanced warnings to producers to take steps to protect animals in severe weather events.

During FY 2003, ARS will

develop practical information for ventilating broiler houses at high air velocity without additional fans or electrical energy.

identify optimum temperatures for minimizing the detrimental effects of disease exposure for use by producers to better manage and house piglets.

provide recommendations on the substitution of renewable resources such as green and animal manures for nonrenewable resources that increase productivity above current levels.

During FY 2004, ARS will

identify the quantitative trait loci (QTL) for 3 generational families of the seven most prominent beef breeds in the United States to allow the effective use of single-nucleotide polymorphisms (SNP) to characterize genetic variation.

expand the number of reproductive traits analyzed from complex pedigrees using the single-nucleotide-polymorphisms (SNP) to characterize genetic variation.

verify growth models for medium and very lean growth swine.

During FY 2005, ARS will

determine the optimal level of sugars, grain and protein to feed with alfalfa-corn silage diets to lactating dairy cows.

identify genetic markers to improve swine litter size.

evaluate the effects of various forage types on chemical composition and consumer acceptance of pasture-finished beef.

evaluate impact of tropically adapted breeds of beef cattle on stocker productivity, feedlot gains and feed efficiency, and carcass quality.

validate a livestock safety monitor (LSM) and update empirical relationships.

STRATEGY 2.1.2:  Plant, animal, and ecosystems protection:  Improve integrated management systems that contribute to the protection of plants, animals, and ecosystems against pests (insects, weeds, pathogens, etc.). 
 

PERFORMANCE GOAL 2.1.2.1:  Demonstrate new integrated technologies to protect plants, animals, and ecosystems.

Indicators:

During FY 2002, ARS will

complete the demonstration of biologically based integrated pest management (IPM)strategies to control fire ants in South Carolina.

ACCOMPLISHMENTS:  A cooperative agreement was reached with Clemson University to oversee the expansion of the area-wide, Integrated Pest Management (IPM) fire ant control program in South Carolina.  Among other responsibilities, Clemson has taken on the production of extension materials to be used throughout the seven States participating in the areawide program.

IMPACT/OUTCOME:  South Carolina is on the northern border of the red fire ant territory so that successful establishment of self-sustaining biological control by microsporidian pathogens and parasitic phorid flies will provide a buffer against any further expansion of the affected area.

demonstrate the application of its ELISA test to distinguish screwworms from other blood-sucking flies.

ACCOMPLISHMENTS:  A method to rapidly differentiate the screwworm, Cochliomyia hominivorax, not only from similar fly species but among strains within the species, was developed using restriction fragment length polymorphisms (RFLP) on the DNA.

IMPACT/OUTCOME:  An outbreak of screwworm in livestock occurred in the eradication zone at Chiapas State, Mexico.  Because the outbreak was about 20 miles from the APHIS sterile fly production facility at Tuxtla, Mexico, initial suspicion was that the epidemic started from an undetected escape of fertile flies.  But DNA from specimens confirmed that the wild flies were a strain from Costa Rica and different than those used in the sterile fly release program.  This information not only aided in suppression of the outbreak but averted a possible diplomatic setback to the program.

develop and test improved traps and methods for the accurate and rapid survey of mosquitoes and other flies that transmit animal and human diseases.

ACCOMPLISHMENTS:  The Mosquito and Fly Research Unit, Gainesville, Florida, in collaboration with the Connecticut Agricultural Experiment Station, developed and began testing several new mosquito traps to be used in the surveillance of epidemic diseases, such as West Nile virus.  This work was funded in part by a special Congressional appropriation and by commercial partnerships.

IMPACT/OUTCOME:  The rapid spread of West Nile virus across the United States highlights the need for better tools to detect and combat vector-borne diseases.  ARS prototype traps being tested in Connecticut and elsewhere make use of specific attractants that eliminate much of the background data that slow the analysis of catches.  Innovations, such as solar panels and slow release CO2, increase the trap’s efficiency.

develop improved understanding of pathogenesis and control of diseases caused by species of the fungus Sclerotinia.

ACCOMPLISHMENTS:  Sclerotinia blight and head rot causes serious losses of peanuts, sunflower, canola, soybean, dry beans, and other crops each year.  ARS scientists at Fargo, North Dakota, evaluated sunflower breeding lines for Sclerotinia resistance using artificial inoculation.  Sources of resistance were derived from the study.  ARS scientists at Stillwater, Oklahoma, screened different lines of peanuts for resistance to Sclerotinia blight and found that one line with desirable oil and agronomic qualities had acceptable resistance.

IMPACT/OUTCOME:  These studies improve the understanding of pathogenesis and control of this serious fungal disease.

describe the genetic variability, epidemiology, and ecology of diseases caused by Xylella species, including Pierce’s disease of grapes and citrus, variegated chlorosis, almond leaf scorch, and others.

ACCOMPLISHMENTS:  ARS’ multi-disciplinary research program determined the basis for host specificity of Xylella strains, the nature and scope of Xylella diversity, and the epidemiology of Xylella-induced diseases.  ARS scientists at Beltsville and Frederick, Maryland, developed a same-day, onsite portable molecular assay for the Pierce’s disease strain that allows grape stock to be diagnosed within 1-2 hours.  ARS researchers at Parlier, California, have determined the epidemiology and are developing control measures for the disease and its sharpshooter vector.  Researchers at Davis, California, tested substances that boost the grapevine’s defenses against the bacterium.  The largest collection of citrus variegated chlorosis (CVC) isolates is maintained at the ARS Fruit Laboratory in Beltsville, where diagnostic assays are being developed.

IMPACT/OUTCOME:  Xylella fastidiosa (Xf) species, including those causing Pierce’s disease of grapes and CVC, are responsible for millions of dollars in management costs and crop losses each year.  Other Xf diseases in the United States include alfalfa dwarf and leaf scorch in almond, pecan, elm, maple, and plum leaf scald.  ARS research on the genetic variability of Xf strains and development of rapid diagnostics will protect California’s grape and citrus industries.       

improve genetic resistance in soybean to the soybean cyst nematode.  Transfer improved germplasm to seed producers.

ACCOMPLISHMENTS:  ARS scientists at Urbana, Illinois, are identifying lines in USDA Soybean Germplasm Collection to improve yield, modify seed composition, and enhance resistance to the soybean cyst nematode.  Studies of population dynamics and improvement of management schemes for soybean cyst nematode are also being conducted at Urbana.  ARS scientists at Beltsville, Maryland, have discovered two cell-wall hydrolase genes that are expressed during infection.  The promoter for these genes may be used to express genes that produce proteins that are toxic to the nematode. 

IMPACT/OUTCOME:  Expression of these genes in the host plant during the early infection process may stop nematode damage before it occurs.  Improved germplasm will be transferred to seed producers.

develop improved detection and identification methods for viruses, bacteria, and fungi causing plant diseases. Emphasis will be on citrus canker, plum pox, bronze wilt of cotton, and soybean rust.

ACCOMPLISHMENTS:  Improved detection and identification methods for viruses, bacteria, and fungi causing plant diseases have been developed at several ARS laboratories.  ARS scientists have identified “signature” DNA sequences in viral, bacterial, and fungal genomes of crop pathogens and developed oligonucleotide primers and fluorescent probes for real-time Polymerase Chain Reaction (PCR) diagnostic assays to distinguish strains and isolates of the organism(s). 

IMPACT/OUTCOME:  PCR assays have been developed for emerging diseases, such as plum pox virus, citrus canker, soybean rust, bronze wilt of cotton, citrus tristeza virus, and other critical pathogens.  These techniques allow for rapid and accurate detection of these emerging diseases.   

develop improved methods for control and management of disease losses in plants using improved cultural, chemical, and biological control systems and increased host plant resistance.

ACCOMPLISHMENTS:  ARS strategies for the control of plant diseases include planting resistant crop varieties, changing crop cultural practices or storage conditions to those less favorable for disease development, employing biological controls, and using integrated management.  The ARS program is conducted in cooperation with related research in other public and private institutions. 

IMPACT/OUTCOME:  Effective management strategies have been developed for several emerging viral, bacterial, fungal, and nematode-caused diseases utilizing one or a combination of techniques listed above preserving millions of dollars of losses due to disease. 

develop basic knowledge about the ecology, epidemiology, and genetic variability of plant pathogens to identify potential points of control.

ACCOMPLISHMENTS:  ARS research on the processes that take place during disease development has uncovered vulnerable steps in the life cycles of pathogens where control measures can be used successfully.  ARS research has shown how pathogens move from plant to plant in the field or within harvested commodities in storage. 

IMPACT/OUTCOME:  Possible control strategies are being developed based on how pathogens survive in the absence of host materials and how they are affected by their environment.       

continue to develop Integrated Pest Management (IPM) components and systems as alternatives to pesticides that endanger human health and the environment.

ACCOMPLISHMENTS:  Eliminating pink bollworm – a pest that eats cotton bolls and has caused billions of dollars of damage to the cotton industry – has been the focus of ARS scientists in Phoenix, Arizona, for a number of years.  Many of the research findings have now become management strategies used by the National Cotton Council Pink Bollworm Action Committee in its pink bollworm eradication program.  A combination of four of the most successful technologies is being used in the program.  First is a “host-free” period making it harder for the pest to survive from one year to the next, and second is to plant transgenic pest-resistant cotton.  A third strategy involves methods for using the female’s pheromone that, when released in cotton fields, makes it difficult for males to find the females.  The final part of the program involves the release of sterile pink bollworm male moths in cotton fields to interfere with normal matings.

IMPACT/OUTCOME:  The pink bollworm eradication program has already started and is proposed for three phases in different locations in the southwestern United States and northern Mexico.  The strategies for the program were adopted from effective control technologies developed and demonstrated by ARS.  The last phase of the eradication program will start in 2004 or 2005, and is estimated to prevent millions of dollars in losses to the cotton industry. 

ACCOMPLISHMENTS:  ARS scientists at Sidney, Montana, in a collaborative effort with USDA’s Animal and Plant Health Inspection Service, and the University of Wyoming, developed a CD-ROM and a Web site to provide land managers with the best pest management resources to help them deal with grasshopper pests.  The Web site and CD-ROM are comprehensive sources for the most recent research in grasshopper management, identification, biology, ecology, and control tactics for Federal, State and local land managers, weed and pest districts, extension agents, and ranchers.  Decision-making software, which is part of the package, will help land managers decide if and when pesticide spraying will make economic and environmental sense.

IMPACT/OUTCOME:  The grasshopper management CD-ROM has been widely distributed for use by grasshopper managers, growers, and researchers in all affected parts of the United States.  About 2,000 CD-ROMs also have been requested by individuals from more than 70 countries – from Peru to Tunisia, and from Thailand to Ethiopia.  While the information and software are specific to U.S. conditions, many countries are interested in it as a model for developing their own program to facilitate management of grasshopper populations.

continue development and expansion of areawide pest management programs demonstrating alternatives to at-risk and other environmentally hazardous pesticides.

ACCOMPLISHMENTS:  ARS initiated three new areawide pest management projects.  These projects target the: (1) Russian wheat aphid and greenbug on wheat in the U.S. Great Plains, using customized cultural practices, pest-resistant cultivars, biological control agents, and other biologically based pest control technologies.  This project is managed out of Stillwater, Oklahoma;  (2) Melaleuca (from Australia), which is the first project that targets an invasive tree.  This project is based in Fort Lauderdale, Florida, and uses natural enemies (insects and microbial organisms), judicious use of herbicides, mechanical control (mowing), physical control (fire), and combinations of these tactics; and (3) Tarnished plant bug on cotton in the Delta area of Mississippi and Louisiana using host destruction, host-plant resistance, new insecticidal chemicals, and remote-sensing technology.  This is an extension of an ongoing, in-house program at Stoneville, Mississippi.

Two other projects, initiated in 2000 and 2001, respectively, have been expanded.  These include research of: (1) Fruit flies in the Hawaiian Islands using sanitation, male annihilation, baits, biological control, and sterile male fruit flies.  The target species include Mediterranean, melon, oriental, and Malaysian fruit flies.  The overall goal is to suppress these pests below economic thresholds; and (2) fire ants, which is managed out of Gainesville, Florida, and is operational in Florida, Texas, Oklahoma, Mississippi, and South Carolina on pastures, using natural enemies, microbial pesticides, attracticides, and Geographic Information System/Global Positioning System (GIS/GPS).

IMPACT/OUTCOME:  All of the areawide pest management (AWPM) projects – Russian wheat aphid/greenbug, melaleuca, tarnished plant bug, fruit flies, and fire ants – have been demonstrating the positive impacts and advantages to farmers and ranchers of integrated pest management (IPM), resulting in increased grower profits, reduced worker risks from chemical pesticides, an enhanced environment, and a proven strategy that incorporates biologically based pest control technologies.  These projects are resulting in adoption of environmentally sound IPM technologies by farmers and ranchers.  The ARS AWPM Program is focused on management of pests where existing technologies (including pheromones, biological control agents, and alternatives to chemical pesticides) are most effective when used over a multi-State or multi-regional area.  The success of the program thus far has resulted from full partnering and participation among Federal and State agencies, farmers and ranchers, and other private sector (the environmental community, consultants, industry, etc.) entities.  These projects have already resulted in a 75 to 100 percent reduction in chemical insecticide and herbicide applications at the project demonstration sites using the environmentally benign technologies provided by the projects.

continue to provide critical identifications of newly found pest species, provide needed taxonomic revisions of critical groups of insects, identify new natural control agents, and produce updated keys to agriculturally important insect groups.

ACCOMPLISHMENTS:  Systematics directly impacts food security, animal and plant health, the recognition and management of invasive pest species, and global trade.  Last year, ARS scientists in Beltsville, Maryland, provided over 12,000 identifications of port specimens, including 5,134 of urgent priority, and discovered 14 species to be new immigrants into the continental United States, Hawaii, or Puerto Rico.  Major systematics works include: 1) a large study of the parasitic wasps of caterpillars in Costa Rica; 2) a review of ornamental pestiferous woodwasps and seed-feeding wasps, such as those attacking pistachio; 3) demonstration that leaf-mining flies often are a complex of pest and non-pest species, information that was used by the Animal and Plant Health Inspection Service (APHIS) in modifying its quarantine programs to prevent entry of the pest species; 4) a comprehensive revision of the armyworms (including production of an expert identification system), the Anastrepha serpentina species group of fruit flies, and description of a new fruit fly closely related to the pepper maggot; 5) fieldwork in Nepal and China leading to the systematics of flea beetles; and 6) clarification of relationships among the aphid-feeding (Cycloneda) lady beetles.  Data entry for the diaspidine armored scale insects has been completed and placed in ScaleNet at:  www.sel.barc.usda.gov/scalenet/scalenet.htm.

IMPACT/OUTCOME:  These varied systematics accomplishments, together with a Systematics Summit, held at Beltsville, Maryland, on November 1, 2002, facilitate the strategic tailoring of programs to address newly introduced pests.

ACCOMPLISHMENTS:  Genomics tools were developed for identification of organisms and cells.  DNA probes provide a new tool for studies of insect parasitism in the field, particularly for detecting and identifying minute insects such as whitefly parasitoids.  ARS scientists in Fargo, North Dakota, have developed DNA probes specific for the insect parasitoids Encarsis and Eretmocerus.  Similarly, ARS scientists in Columbia, Missouri, can now identify insect cells, clones, and cell lines derived from specific tissues and species needed for cultivation of insect pathogenic viruses by using DNA markers.

IMPACT/OUTCOME:  These new methods will make possible the identification of parasitoids without having to hold the parasitized whitefly nymphs in the laboratory until the adult parasitoids emerge.  They will facilitate the identification of cell lines for virus production.

use classical and augmentative biological control approaches, along with the conservation of natural enemies, to suppress invasive insect pests and weeds with parasites, predators, and pathogens.  This includes using ARS overseas laboratories to collect, evaluate, and ship new exotic biological control agents to ARS quarantine laboratories and to develop methods to conserve, mass produce, and deliver those control agents that are beneficial.

ACCOMPLISHMENTS:  In the Mid-South Area, researchers demonstrated that the soy isoflavones and optimized quantities of antioxidants such as the preservatives BHT and BHA reduced dietary quality for reared insects.

IMPACT/OUTCOME:  This information will be used to improve diets for the mass rearing of insects. Identification of gut enzymes will allow a better match with diet components. 

ACCOMPLISHMENTS:  Scientists at the Crop Protection and Management Research Unit in Tifton, Georgia, initiated on-farm studies to assess the benefits of various winter cover crop schemes.  The results demonstrate that winter covers, including legume blends, crimson clover, and legume/rye mixes, fostered increased beneficial numbers and reduced the need for pesticide interventions with reduction in yield.  Also, these studies show that significant natural enemy species are coming from edge vegetation, that the type of edge vegetation is important for particular species, and that natural enemies are not reaching the center of large fields during the growing season. 

IMPACT/OUTCOME:  Knowledge that winter cover crops foster increased numbers of beneficial insects and reduce the need for pesticides will enable scientists to design cropping systems to increase the densities and dispersion of natural enemies throughout crops.

ACCOMPLISHMENTS:  Scientists at the Beneficial Insects Research Unit at Weslaco, Texas, working with the ARS South American Biological Control Laboratory in Argentina, searched for parasites of relatives of the glassy-winged sharpshooter, a newly invasive vector of the Pierce’s disease microbe, in areas of South America pre-adapted to California’s climate. 

IMPACT/OUTCOME:  Three parasite species were found whose establishment could significantly reduce sharpshooter populations in California, thus reducing the impact of Pierce’s disease.

ACCOMPLISHMENTS:  Gypchek, the gypsy moth virus product currently being used by Federal and State action agencies, is not cost-effective and the dosage is too high to be economically practical.  Scientists at the Chemicals Affecting Insect Behavior Laboratory in Beltsville, Maryland, evaluated a cell culture produced virus that was comparable, and in some respects superior, to Gypchek in the field.

IMPACT/OUTCOME:  The cell-cultured virus could lead to a cost-effective, biologically based strategy for managing gypsy moths in areas where classical biological control efforts are not effective.

ACCOMPLISHMENTS:  Scientists at the Insect Biological Control Laboratory, Beltsville, Maryland, have discovered a strain of purple bacterium, Chromobacterium violaceum, which is toxic to major insect pests including the Southern corn rootworm, the diamondback moth, and the Colorado potato beetle.  Cell-free preparations were found to be lethal to these insects and to cause a weight reduction in gypsy moth larvae.

IMPACT/OUTCOME:  This discovery potentially adds another bacterium, and exploitable toxins, to the pest management tool kit.  

ACCOMPLISHMENTS:  Scientists at the Plant Protection Research Unit in Ithaca, New York, tested an insect microbial insecticide, the fungus Beauveria bassiana, against Colorado potato beetle (CPB) larvae.  They found that oil formulations might be more efficacious against CPB larvae under wet conditions, but that emulsifiable oil formulations do not substantially increase the virulence of the fungus against CPB under normal field conditions.  Three applications of B. bassiana made at 3-4 day intervals significantly reduced CPB larval populations, but applications at weekly intervals were ineffective.  Levels of control achieved in the tests were moderate at best, and the results do not justify the additional expense of such an approach.  Also, the standard label rate is nearly optimal, yet costly, which underscores the fundamental economic competitiveness problem associated with this microbial control agent.  

IMPACT/OUTCOME:  This research suggests that use of the fungus against CPB under some field conditions may not be cost-effective.  

ACCOMPLISHMENTS:  Researchers at the Crop Bioprotection Laboratory in Peoria, Illinois, showed that dried preparations of the insecticidal fungus Paecilomyces fumosoroseus infected and killed the Formosan termite and was transmitted among exposed nestmates without repellent effect.  Key formulation ingredients and physical conditions for spray drying encapsulated formulations of fungi such as these may yield preparations with improved characteristics, including enhanced solar stability for application to insects found in areas of high insulation.

IMPACT/OUTCOME:  Fungi shows promise in a comprehensive pest management program for control of the Formosan termite, a pest that causes $1 billion a year in damages to residential and commercial buildings, trees, docks, and railway ties in the southeastern United States and Hawaii.

determine pest and natural enemy (parasite, predator, and microbial) biologies (behavior, host range, interactions with plant signaling), persistence, and impact to improve use and establishment of natural enemies for biological control.  This includes methods that employ remote sensing or modeling.

ACCOMPLISHMENTS:  Whitefly nymph feeding was found to be undeterred by leaf shape.  In collaboration with North Dakota State University, ARS scientists in Fargo, North Dakota, demonstrated that the feeding styles of the smallest immature whiteflies could penetrate to the phloem bundle from any position on the leaf.

IMPACT/OUTCOME:  These findings reverse a long-held belief that the smallest nymphs were limited in their ability to reach the phloem food source and must use leaf morphology to locate a suitable site on which to probe.  This is information that will be useful to plant breeders.

ACCOMPLISHMENTS:  The pink hibiscus mealybug, which attacks hundreds of species of ornamental and agricultural crops, has recently invaded California and Florida.  A parasitoid (Allotropa mecrida) of the mealybug was shown to be specific to this pest.  An Egyptian biotype of A. mecrida was tested by ARS scientists in Newark, Delaware, against six species of U.S. mealybugs, and found to be specific to the target mealybug.

IMPACT/OUTCOME:  This information will be submitted to the California Department of Food and Agriculture and the Animal and Plant Health Inspection Service (APHIS), enabling the completion of an environmental assessment required for the release of the parasitoid for biological control.

ACCOMPLISHMENTS:  At the Beneficial Insects Introduction Laboratory at Newark, Delaware, insect attractants (pheromones) were isolated and used successfully in a trap lure for detecting potentially invasive species closely related to the gypsy moth.  Also, a sex pheromone from a parasitoid wasp (Glyptapanteles flavicoxis) of the gypsy moth was isolated.  Similarly, this laboratory discovered trees that are highly attractive to adult Asian longhorned beetles (ALB) – potentially a $670 billion pest of maples and other shade and forest trees.  Other chemicals associated with ALB egg masses were found to repel ALB egg laying.  The beetle can now be detected (through cooperation with Pryor Knowledge Systems and the State University of New York at Syracuse) using an acoustic device with modified neural network software.  

IMPACT/OUTCOME:  The gypsy moth pheromone can be used by APHIS for detection of potentially invasive species at ports.  Scientists also will be able to use the parasitoid wasp pheromone to determine establishment and effectiveness of the biocontrol agent.  Trees discovered to be highly attractive (i.e., sentinel trees) to ALB might be used by APHIS for monitoring, or perhaps in an attract-and-kill strategy, in support of the eradication program.  Chemicals that repel ALB egg laying may be useful in controlling the spread of beetles, and might be wedded in a repel-and-attract strategy with the sentinel trees.  The acoustic devices performed well under natural field conditions in New York City.  Two have now been purchased by APHIS.

ACCOMPLISHMENTS:  Scientists at the Biological Control of Insects Research Unit in Columbia, Missouri, found cell lines with improved resistance to selected baculoviruses.  Insect cell cultures were exposed over numerous passages to selected baculoviruses, then tested for their sensitivity to the virus.

IMPACT/OUTCOME:  Scientists can use these cell lines to better understand the mechanism of insect resistance to viruses.

develop methods for manipulating the genomes of insect pests and associated organisms including genomic sequencing and for transferring genes into insect cells to be used in biologically-based control strategies.

ACCOMPLISHMENTS:  Scientists at the Exotic and Invasive Diseases and Pests Research Unit in Parlier, California, have shown that grapevines treated with Messenger, a commercially available harpin-containing product, showed lower Pierce’s disease incidence than those in untreated control grapevines.  Also, a biologically active factor in the causative bacterium [Xylella fastidiosa (Xf)] that induces chlorosis in Chenopodium species was partially purified and characterized.

IMPACT/OUTCOME:  The harpin-containing product finding suggests that resistance to infection by the causative bacterium Xf may be induced in grapevines.  The characterized protein is a potential candidate as a virulence/pathogenicity factor in Xf, which can be studied by genomic methods capitalizing on the sequencing of the Xf genome.

ACCOMPLISHMENTS:  Scientists at the Biological Control of Insects Research Unit in Columbia, Missouri, transferred DNA to several cell lines and observed for expression of red fluorescence to provide a better understanding of baculovirus host range.  When testing for resistance of a modified baculovirus (AcMNPV) following exposure to ultraviolet light (UV-B), red fluorescence of the protein occurred.  Although there was not a significant increase in resistance to UV-B, several modified viruses were better than the parental wild type virus following exposure to UV-B.

IMPACT/OUTCOME:  These experiments provide a tool for elucidating resistance at the cellular level, and demonstrate that gene fusion to the polyhedrin gene is feasible and could provide a useful means for testing other genes for their UV protective effect or for reduction in the time required for activity.

develop and demonstrate improved cultural, chemical, and biological methods for control and management of soil-borne diseases.

ACCOMPLISHMENTS:  Scientists at Salinas, California, completed evaluations of commercially available strawberry cultivars under strict organic production conditions and identified three cultivars as highest performing.

IMPACT/OUTCOME:  This information was transferred to growers by working with a farm advisor and the California Cooperative Extension Service, enabling growers to make informed cultivar choices based on yield and quality.

ACCOMPLISHMENTS:  Researchers at Ft. Pierce, Florida, conducted large scale demonstration trials on commercial vegetable farms that validated use of Telone 35, applied using a deep placement coulter system, with the herbicides pebulate, napropamide and/or trifluralin provided levels of weed and disease control similar to soil fumigation with methyl bromide/chloropicrin without injury to the plants.

IMPACT/OUTCOME:  These trials demonstrated that it is feasible to adopt chemical alternatives to methyl bromide without causing major vegetable production disruptions. 

develop and demonstrate improved methods for applying fumigants to minimize the hazard to workers and the general public.

ACCOMPLISHMENTS:  Experiments at Riverside, California, demonstrated that commonly used agrochemicals, including fertilizers and nitrification inhibitors, could be used to rapidly degrade soil fumigants.

IMPACT/OUTCOME:  These experiments could lead to new approaches to minimize emissions and prevent leaching of fumigants in agricultural systems.

develop biologically-based integrated weed management systems.

ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland, in collaboration with the Maryland Department of Natural Resources, Wildlife and Heritage Division, Annapolis, Maryland, determined the distribution and host-specificity of Aceria anthocoptes, a microscopic mite that attacks Canada thistle, Cirsium arvense.  The mite was discovered in the United States during the previous year.  The survey indicated that the mite is widely distributed, being present in the mid-Atlantic and North Central regions, and is highly species-specific, having only Canada thistle as its host. 

IMPACT/OUTCOME:  Canada thistle is one of the most widespread and damaging invasive weeds in North America.  Currently, there are no affordable control methods for this weed.  However, an effective biological control agent would save growers and natural area managers millions of dollars per year.  The study demonstrates that, while Aceria anthocoptes is highly host-specific, it is already relatively abundant in the United States.  Since, the mite may function as a vector of plant viruses, additional research is being conducted to clarify this point.

ACCOMPLISHMENTS:  The Australian invasive tree, Melaleuca quinquenervia, is the most serious threat to the Florida Everglades and is spreading rapidly.  There are no affordable and environmentally friendly methods to control melaleuca.  Biological control using host-specific natural enemies from Australia offers the only possibility of controlling the tree by reducing its ability to produce massive amounts of seeds.  ARS scientists at Fort Lauderdale, Florida, in collaboration with Florida Department of Environmental Protection, U.S. Army Engineers, and South Florida Water Management District personnel, released a sap-sucking psyllid bug, Boreioglycaspis melaleucae, that is complementing damage caused by the tip-feeding weevil, Oxyops vitiosa, released during FY 1997.  Over 150,000 psyllids were released and are spreading rapidly.

IMPACT/OUTCOME:  Young psyllids suck plant juices and inject saliva that kills the leaf tissue so that small plants die 2 months after infestation, and before they set seed.  The combination of the psyllid and weevil should contribute significantly to control of this invasive weed, which will improve significantly the ecology of the Everglades.

ACCOMPLISHMENTS:  Intercrossing between rice and red rice, a dominant weed in the southern United States, may become problematic when herbicide-resistant rice systems come into use.  DNA/PCR microsatellite fingerprinting analyses were conducted to quantify rates of outcrossing between three imidasolinone-resistant rice cultivars and red rice at the Dale Bumpers National Rice Research Center, Stuttgart, Arizona, in cooperation with the University of Arkansas.  Outcrossing between these imidazolinone-resistant rice cultivars and red rice was found to occur at very low levels and lessened with decreasing synchronization of flowering under field conditions.  

IMPACT/OUTCOME:  A key management consideration in herbicide-resistant rice systems may be to plant rice cultivars that are least likely to flower during the same period as the infesting population of red rice.  This may result in reducing the rate of herbicide resistance to improve management of red rice, saving growers millions of dollars per year.

ACCOMPLISHMENTS:  Reductions in tillage frequencies brought on by expansions in farm size has resulted in increased weed problems.  ARS scientists at New Orleans, Louisiana, in cooperation with the Louisiana State University Agricultural Center and various industry partners, conducted field studies designed to evaluate the effectiveness of several new herbicides, including clomazone and sulfentrazone, for controlling problem weeds in the sugarcane crop. 

IMPACT/OUTCOME:  The demonstration of effective weed control led to a full Federal label for use of clomazone in sugarcane for bermudagrass, itchgrass, and johnsongrass control and a Section 18, "Emergency Use" registration of sulfentrazone for morning glory and nutsedge control the 2001-2002 growing season.  Use of these herbicides will result in increased control of these problematic weeds, and will reduce the sugarcane industry’s dependence on the herbicides atrazine and 2, 4-D, both of which have been identified as threats to the environment.

ACCOMPLISHMENTS:  No-till soybean production requires the use of effective herbicides combined with rapid soybean canopy closure for optimum weed management.  ARS scientists in Urbana, Illinois, designed a study to determine if combining fungicide seed treatments, reducing dosages of herbicide, and various soybean seeding rates affected weed management and soybean yield.  Results showed that increased seeding rates reduced time to canopy closure and increased yields, whereas use of a fungicide seed treatment improved stands and reduced canopy closure in about a third of the environments evaluated. 

IMPACT/OUTCOME:  In most environments, reduced herbicide dosages provided adequate weed control and maintained high yields.  These findings show the potential for combining fungicides and high soybean seeding rates to allow effective weed management, even with reduced herbicide inputs.

make control measures available for suppressing tall whitetop, an exotic invasive weed that threatens temperate desert rangelands in the Western United States.

ACCOMPLISHMENTS:  Biological control of whitetop, a highly invasive exotic weed, is a high priority in several Western States, however, no economical or environmentally compatible strategies are available for whitetop control.  ARS scenists at Sidney, Montana, conducted pathogenicity testing on fungal cultures from field-collected diseased whitetop plants.  They found that the isolates are virulent against whitetop.

IMPACT/OUTCOME:  If the fungal isolates prove highly virulent in the field, they may limit the rapid spread of whitetop and be compatible with introduction of classical biological control agents being sought in Europe.

acquire and test in quarantine a biological control agent for Yellow starthistle, a widespread weed that is infesting Western rangeland.

ACCOMPLISHMENTS:  Several insects have already been established on Yellow starthistle, but their effect is variable.  ARS scientists in Montpellier, France, have found several new potential biological control agents for Yellow starthistle.  Scientists at Albany, California, have established a colony of the most recent natural enemy, Ceratapion basicone, for host-specificity testing.

IMPACT/OUTCOME:  Several years more research are needed to establish the specificity of C. basicone.  If it is sufficiently specific to Yellow starthistle, it will be released in the field and evaluated against target and non-target species.

develop improved methods for biological controls of invasive weeds on rangelands.

ACCOMPLISHMENTS:  Saltcedar, an invasive shrub from Eurasia, infests many Western U.S. waterways and stream banks where it causes both economic and environmental losses.  Detailed studies were conducted by ARS scientists at the Western Regional Research Center, Albany, California, on saltcedar and native plant (cottonwoods and willows) seed germination and establishment.  Biological control agents have also been discovered, released, and being evaluated.

IMPACT/OUTCOME:  Saltcedar seed was found to be extremely viable, but short-lived, and able to establish with overbank flooding throughout the summer, whereas the native seeds are only produced early in the season and not able to compete with saltcedar later in the year.  This research is important as it will interface with on-going investigations of biological control and will provide revegetation strategies for land managers that are interested in removing and replacing saltcedar.

demonstrate new methods to reduce leafy spurge, an invasive weed, on rangeland in the Central Great Plains to enable the native species to reestablish.

ACCOMPLISHMENTS:  Successful biological control of the invasive exotic weed leafy spurge may be enhanced by the combination and interaction of specific herbivorous insects and plant pathogens. Researchers from the USDA-ARS Northern Plains Agricultural Laboratory in Sidney, Montana, investigated the bacterial community associated with highly successful leafy spurge biological control sites at Theodore Roosevelt National Park in Medora, North Dakota. These studies showed that the dominant members of the bacterial community being vectored by the leafy spurge flea beetles were gram positive, belonging largely to the Coryneform group.

IMPACT/OUTCOME:  The identification and evaluation of the biological control potential of bacteria species isolated at sites where flea beetles have the greatest impact on leafy spurge may lead to the development of microbial biological control agents that work with insects to significantly decrease the spread and establishment of leafy spurge on rangelands.

develop alternative weed management systems for irrigated peanuts with less dependence on herbicides.

ACCOMPLISHMENTS:  Adoption of reduced peanut tillage in the southeast coastal plain has increased over the last several years in an effort to reduce production costs and increase timeliness of crop production operations.  A multi-year study was initiated to evaluate changes of composition in weed species and management costs in various reduced tillage systems that include peanut and cotton.  In the third year of this study, perennial weeds in the reduced tillage systems has ocurred, causing significantly higher management costs. 

IMPACT/OUTCOME:  Reduced tillage and labor costs appeared to be a major advantage of reduced tillage systems, which are being increasingly adopted.  However, this research shows that growers need to be aware that reduced tillage systems may affect the weed species composition, shifting from annual weeds to more difficult to control perennial weeds previously held in check by tillage operations, so that weed management costs may increase in these systems.  Additional research to address this issue is planned.

During FY 2003, ARS will

continue to develop and test improved traps and methods for the accurate and rapid survey of mosquitoes and other flies that vector animal and human diseases.

characterize the molecular and physiological basis of vector susceptibility to vesicular stomatitis, bluetongue and other viruses affecting U.S. livestock.

develop the technology for producing male-only lines of genetically transformed screwworms to be used in the APHIS eradication campaign.

identify and test for the Department of Defense candidate mosquito repellents to replace DEET.  Identify novel compounds and methods that can be used in attracting or repelling arthropods of veterinary medical or structural significance.

develop improved methods for control and management of disease losses in plants using improved cultural, chemical, and biological control systems and increased host plant resistance.

develop basic knowledge about the ecology, epidemiology, and genetic variability of plant pathogens to identify potential points of control.

develop improved detection and identification methods for viruses, bacteria, and fungi-causing plant diseases.

describe the genetic variability, epidemiology, and ecology of diseases.

continue to develop and demonstrate insect control technologies as alternatives to pesticides that endanger human health and the environment.

continue development and expansion of areawide pest management programs demonstrating alternatives to at-risk and other environmentally hazardous pesticides.

continue to provide critical identifications of newly found pest species, provide urgently needed taxonomic revisions of critical groups of insects, identify new natural control agents, and produce updated keys to agriculturally important insect groups.

use classical and augmentative biological control approaches along with conserving natural enemies to suppress invasive insect and weed pests with parasites, predators, and pathogens.  This includes using ARS overseas laboratories to collect, evaluate, and ship new exotic biological control agents to ARS quarantine laboratories.  This also includes developing methods to conserve, mass produce, and deliver those that are beneficial; and determining pest and natural enemy biologies (behavior, host range, interactions with plant signaling), persistence, and impact.

develop methods for manipulating the genomes of insect pests and associated organisms (includes genomic sequencing and development of methods for transferring genes into insect cells) to be used in biologically-based control strategies.

develop and/or demonstrate biological or ecologically-based integrated weed management systems for cropping systems and rangelands.

develop and demonstrate improved cultural, chemical, and biological methods for control and management of soil-borne diseases.

develop and demonstrate improved methods for applying fumigants to minimize the hazard to workers and the public.

purify and biochemically characterize the supposedly bluetongue virus receptor in biting midges and determine whether selected species of biting midges are susceptible to infection with vesicular stomatitis virus.

continue work toward developing a genetic sexing strain of screwworms, using both classical, genetic, and transgenic approaches for use in the mass rearing facility in the Program for the Eradication of Screwworms.

identify a replacement repellent for DEET, a replacement fabric impregnate for permethrin, and continue to discover and develop spatial repellents and attractant inhibitors as new technologies for protecting animals and humans from attack by blood-feeding arthropods.

screen a biting midge salivary gland gene library, select potential bluetongue virus receptor genes, and characterize salivary proteins that have an effect on bluetongue virus infectivity.

During FY 2004, ARS will

develop and test improved traps and attractants for the accurate, specific and rapid survey of mosquitoes and other arthropods that cause animal and human diseases.

develop, evaluate, and transfer to  the Department of Defense topical repellents and control systems to protect deployed American military personnel from arthropod vectors of disease.

investigate the physiological basis of vector competence and develop novel methods for controlling arthropods dangerous to animals and humans

evaluate the introduction of mutated algae on wild type counterparts in catfish ponds as a strategy to control off-flavor in catfish.

develop and demonstrate improved cultural, chemical, and biological methods for control and management of soil borne diseases.

develop and demonstrate improved methods for applying fumigants to minimize the hazard to workers and the general public.

develop improved methods for control and management of disease losses in plants using improved cultural, chemical, and biological control systems and increased host plant resistance.

develop basic knowledge about the ecology, epidemiology, and genetic variability of plant pathogens to identify potential points of control.

develop improved detection and identification methods for viruses, bacteria, fungi, and fastidious microbes causing plant diseases.      

identify and characterize genes for disease and pest resistance in crop plants, closely related non-crop species, and alien species to enhance opportunities for developing host plant resistance and incorporate such genes into commercially acceptable varieties.

develop fundamental knowledge about insect biology and ecology that provides the foundation for effective control strategies.

develop Integrated Pest Management (IPM) components and systems for environmentally sound insect pest control.

continue development and expansion of areawide IPM programs.

develop and/or demonstrate biologically- or ecologically-based integrated weed management systems for cropping, rangeland, and natural areas. 

develop and transfer to action agencies technology for exclusion, early detection and eradication, and management of invasive weeds, including those that may be used as biological agents threatening biosecurity. 

expand the areawide pest management program by adding five new projects selected by peer review. 

continue to provide critical identifications of newly found pest species, provide severely needed taxonomic revisions of critical groups of insects, identify new natural control agents, and produce updated keys to agriculturally important insect groups.

use classical and augmentative biological control approaches, together with conserving natural enemies to suppress invasive insect and weed pests with parasites, predators, and pathogens.  This includes using ARS overseas laboratories to collect, evaluate, and ship new exotic biological control agents to ARS quarantine laboratories; development of methods to conserve, mass produce, and deliver those that are beneficial; and determining pest and natural enemy biologies (behavior, host range, interactions with plant signaling), persistence, and impact.

During FY 2005, ARS will

develop and test improved traps and attractants for the accurate, specific and rapid survey of mosquitoes and other arthropods that cause animal and human diseases.

develop, evaluate, and transfer to the Department of Defense topical repellents and control systems to protect deployed American military personnel from arthropod vectors of disease.

investigate the physiological basis of vector competence and develop into novel methods for controlling arthropods dangerous to animals and humans.

develop improved methods for control and management of disease losses in plants using improved cultural, chemical, and biological control systems and increased host plant resistance.

develop basic knowledge about the ecology, epidemiology, and genetic variability of plant pathogens to identify potential points of control.

develop improved detection and identification methods for viruses, bacteria, fungi, and fastidious microbes causing plant diseases.            

identify and characterize genes for disease and pest resistance in crop plants, closely related non-crop species, and alien species to enhance opportunities for developing host plant resistance and incorporate such genes into commercially acceptable varieties.

develop fundamental knowledge about insect biology and ecology that provides the foundation for effective control strategies.

develop Integrated Pest Management (IPM) components and systems for environmentally sound insect pest control.

continue development and expansion of areawide IPM programs.

develop and/or demonstrate biologically- or ecologically-based integrated weed management systems for cropping, rangeland, and natural areas. 

develop and transfer to action agencies technology for exclusion, early detection and eradication, and management of invasive weeds, including those that may be used as biological agents threatening biosecurity.

expand the areawide pest management program by adding five new projects selected by peer review. 

continue to provide critical identifications of newly found pest species, provide severely needed taxonomic revisions of critical groups of insects, identify new natural control agents, and produce updated keys to agriculturally important insect groups.

use classical and augmentative biological control approaches, together with conserving natural enemies to suppress invasive insect and weed pests with parasites, predators, and pathogens.  This includes using ARS overseas laboratories to collect, evaluate, and ship new exotic biological control agents to ARS quarantine laboratories; development of methods to conserve, mass produce, and deliver those that are beneficial; and determining pest and natural enemy biologies (behavior, host range, interactions with plant signaling), persistence, and impact.

PERFORMANCE GOAL 2.1.2.2:  Demonstrate scientific measures, practices, and systems to achieve humane care of food animals.

Indicators:

During FY 2002, ARS will

devise practical approaches to prevent piglet hypothermia and improve survival within production settings.

ACCOMPLISHMENTS:  Demonstrated that maintaining the piglet in warm environments or pre-treatment with aspire-like compounds will prevent hypothermia and improve survival.

IMPACT/OUTCOME:  The research was published in scientific journals and presented at a national pork industry meeting.  The technology will reduce baby pig mortality.

complete evaluation of a swine growth model in a production setting using a respiration sensor to indicate stress.

ACCOMPLISHMENTS:  ARS scientists at the Biological Engineering Research Unit, Clay Center, Nebraska, updated the swine growth model to accommodate new leaner genetic lines of swine.

IMPACT/OUTCOME:  The research was published and technology was transferred and made available for producer use.  This information can be used to reduce stress in lean pigs.

During FY 2003, ARS will develop a fear and anxiety model for use in evaluating stresses of transported cattle, and the social and housing preferences of swine.

During FY 2004, ARS will evaluate immunological indicators of well-being on piglets of sows in groups and stall gestation housing.

During FY 2005, ARS will evaluate immunological indicators of well-being on piglets of sows in groups and stall gestation housing.

STRATEGY 2.1.3:  Germplasm resources and genomics:  Acquire, preserve, evaluate, describe, and enhance genetic resources and develop new knowledge and technologies to increase the productive capacity and usefulness of plants, animals, and other organisms. 
 

PERFORMANCE GOAL 2.1.3.1:  Collections of well-documented germplasms of importance to U.S. agricultural security are readily available to scientists and breeders for research and development.

Indicators:

During FY 2002, ARS will

develop wild alfalfa accessions from China as a possible cultivated crop and begin field evaluations for productivity and survivability.

ACCOMPLISHMENTS:  Scientists from Beltsville, Maryland, collected two rare, wild relatives of cultivated alfalfa.  One was found in an alpine zone and the other in an arid zone.  Both show high tolerance to stressful environments.  Symbiotic rhizobia was also collected from the root zones of the wild relatives, and one species of Rhizobium has been isolated.

IMPACT/OUTCOME:  Field evaluations indicate that the newly found plants have potential as a forage crop for extreme climates.  These plants could provide genetic material for breeding programs to improve existing varieties of cultivated alfalfa by increasing yield and persistence and resistance to insects and disease.

complete the identification in Turkey of natural enemies of Yellow starthistle, a major invasive weed, and ship promising species to the U.S. for quarantine evaluation.

ACCOMPLISHMENTS:  Scientists from Albany, California, found an insect, Ceratapion basicorne, that appears to have the potential for biological control of Yellow starthistle.  A colony of these insects has been established in the laboratory quarantine facility and initial tests completed to assess the insect’s suitability as a biological control agent.  

IMPACT/OUTCOME:  Yellow starthistle is poisonous to horses and injurious to other animals.  It is the most widespread weed in California, covering 20 million acres.  A safe, affordable, effective biological control method would play a key role in restoring these lands ecologically and reducing economic losses.

identify threatened germplasm in natural habitats and in genebanks as a vital first step for conserving these genetic resources.

ACCOMPLISHMENTS:  USDA/ARS scientists and Paraguayan counterparts collected wild and cultivated peanuts in Paraguay in May 2002.  Half of the germplasm was incorporated into Paraguay’s national genebank, and the remainder into the U.S. National Plant Germplasm System.

IMPACT/OUTCOME:  New genetic material of wild perennial peanuts may assist breeders in developing and selecting improved lines and cultivars of forage peanuts, with potential for use in turf, erosion control, ornamentals, and feed for domestic animals and wildlife.

ACCOMPLISHMENTS:  The Ornamental Plant Germplasm Center (OPGC) at Ohio State University in Columbus became fully operational during FY 2002.  To handle incoming samples, the seed storage facilities were improved and a seed multiplication program initiated with both field pollination cages and greenhouse plantings.

IMPACT/OUTCOME:  More than 950 samples of herbaceous ornamental germplasm were incorporated into the OPGC, where they are readily available for distribution to researchers worldwide for crop improvement and basic biological studies. 

ACCOMPLISHMENTS:  ARS researchers coordinated and assisted in the development, review, funding and execution of 26 plant explorations in 19 different foreign countries and 8 explorations in areas of the United States. 

IMPACT/OUTCOME:  The plant explorations acquired germplasm that has been incorporated into the NPGS, where it is safeguarded and accessible to researchers worldwide. Non-monetary benefit sharing associated with several foreign plant explorations has enabled USDA to obtain access to genetic resources despite challenging conditions. 

improve methods for preserving beneficial microbes, insects, and wild relatives of crops in native habitats.

ACCOMPLISHMENTS:  In cooperation with scientific counterparts in Paraguay, Bolivia, and Guatemala, ARS scientists completed inventories of wild crop relatives in native areas.

IMPACT/OUTCOME:  The completed inventories furnished the initial field data required to set priorities for conservation of important crop wild relatives in those nations.  With the data, conservation planners can begin to compile more specific plans for priority on-site conservation efforts.

perfect methods for maintaining germplasm in long term under conditions (low temperature and/or controlled atmosphere) that ensure viability, health, genetic integrity, and uniformity, as well as providing a sufficient supply for research and breeding.

ACCOMPLISHMENTS:  Research conducted by USDA/ARS researchers with support of a grant from the USDA Foreign Agricultural Service evaluated factors affecting successful implementation of preservation protocols (storage conditions, optimal plant organ or tissues) for plant germplasm.  USDA/ARS scientists and cooperators spent 4-5 days in each participating laboratory in Scotland, Germany, Poland, and Kazakhstan where they demonstrated methods, and suggested improvements to existing procedures.

IMPACT/OUTCOME:  For each laboratory, deficiencies in standard preservation methods and the means for correctly instituting the protocols were investigated.  A second set of experiments will be performed with the corrected protocols to ensure that the methods are effective.

ACCOMPLISHMENTS:  Long-term preservation protocols are needed for clonally propagated germplasm to reduce costs of maintaining materials in field orchards and to protect germplasm from natural catastrophes.  ARS researchers evaluated dormant vegetative buds of more than 1,000 samples of apple, and more than 40 of its wild relatives for survival following desiccation, initial exposure to liquid nitrogen, and eight years of storage at about -120C at the USDA/ARS National Center for Genetic Resources Preservation.  About 90 percent of the accessions and nearly 60 percent of the species tested were cryopreserved successfully, and most showed little change in viability over the eight years of storage.

IMPACT/OUTCOME:  Some of the underlying mechanisms of tolerance to cryoexposure were elucidated, which may help with establishing a genetically representative, cryopreserved apple germplasm collection.  That knowledge is applicable to developing preservation protocol for other fruit and nut germplasm.

ACCOMPLISHMENTS:  Long-term preservation of Cuphea germplasm has not been possible because some species are killed by -18C storage conditions.  ARS researchers at Ft. Collins, Colorado, demonstrated that sensitivity to freezing damage in seeds of different Cuphea species was correlated with the fatty acid composition and melting temperature of the storage lipids, with seeds dying if they are hydrated before the intracellular storage lipids are melted.

IMPACT/OUTCOME:  This research showed that a simple heat pulse that melted seed lipids before seed storage prevented any measurable damage to the seeds.  The findings are potentially applicable to many other seed species that produce saturated lipids and are difficult to store.

evaluate protocols for storing DNA or nuclei isolated from plant and insect cells.

ACCOMPLISHMENTS:  None at present. This high risk, exploratory research was accorded relatively low priority by OSQR review panels, so it has not yet been addressed.  

IMPACT/OUTCOME:  None at present.

develop methods for maintaining injurious microbial and insect germplasm in combination with the host plants they attack.

ACCOMPLISHMENTS:  ARS researchers and cooperators at the University of Hawaii developed a rapid detection assay for the strain of the bacterium, Ralstonia solanacearum, which causes ginger wilt.  The virulence and host range of sixteen local ginger wilt strains were tested and the genetic diversity of fifty-five local strains was analyzed.  The specificity of a panel of eight selected monoclonal antibodies (MAbs) was tested and the two most appropriate MAbs for ginger wilt strains in Hawaii were selected. 

IMPACT/OUTCOME:  The preceding research yielded a rapid diagnostic ELISA test for ginger wilt, and furnished a foundation for developing an enrichment trapping/immunodiagnostic procedure and evaluation system for detecting R. solanacearum in soil extracts.

identify sources of new genetic variability and conduct genetic studies to detect novel genes for crop improvement.

ACCOMPLISHMENTS:  ARS scientists in College Station, Texas, conducted a wide-scale sampling of genetic variability in natural stands of pecan by measuring leaflet area, trunk diameter, and leaf mineral content.

IMPACT/OUTCOME:  Variation in leaflet area, trunk diameter, and leaf mineral content was correlated to various degrees with ecogeographical distribution of the trees sampled.  Populations from west Texas and Mexico appeared to be the most genetically divergent.  These results may help improve the efficiency of breeding regionally adapted pecan rootstocks.

develop more efficient and effective means for multiplying germplasm stored in genebanks and for monitoring its viability, health, and genetic content.

ACCOMPLISHMENTS:  High variation in the number of progeny produced per plant in a population may lead to lower effective population size and susceptibility to random genetic drift, which must be minimized for optimal germplasm conservation.  ARS researchers in Pullman, Washington, developed a cost effective field grow-out method that maximizes the effective population size.

IMPACT/OUTCOME:  This research provides a sound scientific basis for increasing the number of seeds for populations while minimizing genetic drift, thus enabling efficient and economic strategies for maintaining germplasm collections, especially those of outcrossing grasses.

where appropriate, designate core subsets for crop collections to improve accessibility of the genetic diversity within each crop and their wild relatives.

ACCOMPLISHMENTS:  ARS researchers in Tifton, Georgia, developed and designated a core subset for the USDA/ARS peanut collection.

IMPACT/OUTCOME:  The preceding new core subset had the immediate impact of significantly increasing the number of peanut accessions evaluated for valuable agronomic traits.  This led to the identification of host-plant resistance to several economically important peanut pathogens.

ACCOMPLISHMENTS:  The designated core subsets for apple and its wild ancestor were assessed by ARS scientists and cooperators at Colorado State University for genetic variation in total phenolic content and other antioxidants.

IMPACT/OUTCOME:  Total phenolic content was very diverse in this core subset, suggesting that, for the most part, the initial designation of subset membership captured a broad spectrum of genetic diversity.

During FY 2003, ARS will

evaluate multi-year results concerning differences in tannin and hydrogen cyanide production among Lotus species for potential beneficial effects to grazing animals.

complete publications that document the genetic variation that exists among native grass accessions from preserved remnant prairies, and document that in situ preservation of the germplasm using preserved remnant prairies is an effective mechanism for preserving the prairie germplasm.

identify new sources of genetic variability and acquire new accessions to enhance the diversity of plant germplasm collections.

acquire and safeguard additional microbial and insect germplasm to enhance the use of beneficial microbes and insects.

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

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

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

During FY 2004, 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.

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.

ACCOMPLISHMENTS:  ARS researchers at Tifton, Georgia, and cooperators at Sygenta Seeds, Inc. converted the RFLP genetic markers pl and al – which are associated with the content of maysin – to markers based on PCR (polymerase chair reaction).  They made available the relevant primer sequences needed for PCR amplification of the preceding markers.

IMPACT/OUTCOME:  Maysin content corresponds closely to resistance and susceptibility to key corn insect pests such as corn earworm.  PCR amplification is a much more rapid and inexpensive procedure than RFLP analyses or direct biochemical determination of maysin content, so the availability of this primer information could greatly accelerate breeding of insect-resistant corn lines.

incorporate the most modern and effective methods of high volume gene sequencing, genetic mapping, gene expression assays, and related techniques into genomic research programs.

ACCOMPLISHMENTS:  Effector proteins are frequently used by bacteria to disrupt plant metabolism during infection.  ARS researchers and collaborators at Cornell University and the University of Nebraska developed an integrated laboratory-computational approach to identify effector proteins in the DNA sequence of bacterial pathogens in general, and in P. syringae in particular.  This method has been used to identify 23 previously unknown effector proteins in the P. syringae genome, and a patent application is now pending.

IMPACT/OUTCOME:  This new information is being used by plant pathologists to understand the molecular basis of pathogenesis and disease resistance.

ACCOMPLISHMENTS:  ARS researchers at Ithaca, New York, developed bioinformatic tools for annotating, analyzing, and visualizing bioinformatic data.  They designed a program to rapidly analyze nucleotide and amino acid sequence data, including parallel analyses on a supercomputer.

IMPACT/OUTCOME:  These new computer programs analyze nucleotide and amino acid sequence more rapidly, and make more efficient use of available computer hardware and software while doing so.

During FY 2003, ARS will

develop differential display techniques to identify genes that regulate feed intake and energy metabolism of livestock.

correlate changes in body composition with genes associated with lean and fat deposition in swine and milk production of dairy cows.

determine target genes for enhancing mammary gland development in heifers, and to increase persistence of milk production.

demonstrate in transgenic cattle the effectiveness of a gene to prevent Staphylococcus aureus mastitis.

complete the placement of 1,000 markers within known genes on the USDA/ARS channel catfish linkage map using ARS reference populations.

develop at least 200 micro-satellite markers and at least 100 random sequence tag sites for mapping the rainbow trout genome.

identify in alfalfa and Medicago truncatula, DNA-base sequences related to nitrogen and carbon assimilation, plant disease response, and nutritional stress.

exploit genome sequence information to identify valuable genes in germplasm collections.

develop new DNA markers linked to disease resistance and weather stress tolerance to accelerate plant germplasm evaluation and breeding.

During FY 2004, ARS will

develop DNA microarrays for gastro-intestinal (GI) genes in chickens and evaluate the nutritional effects on gene expression.

document the functional genomics of ticks, screwworms, mosquitoes, culicoides and other arthropods detrimental to animal and human health.

characterize and develop specific genetic tools to identify specific genes that mediate improved quality and composition of important agricultural commodities.

sequence and map expressed sequence tags (ESTs) to facilitate germplasm characterization.

develop new genetic tools, particularly DNA markers, to enhance plant breeding.

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.

construct and maintain more precise physical, genetic, and transcript genomic maps to identify the genes underlying key agricultural traits and the genomic location of those genes, and to elucidate comparative gene function, structure, and organization.

exploit genome sequence and gene expression information to identify valuable genes and gene combinations in undeveloped genetic resources.

develop new DNA markers closely associated with resistance to disease, pests, environmental stresses, or with high-value quality traits.

During FY 2005, ARS will

identify new quantitative trait loci (QTL) affecting reproduction and health traits from novel populations of dairy cattle.

document the functional genomics of ticks, screwworms, mosquitoes, culicoides and other arthropods detrimental to animal and human health.

identify sequences in forage plants that control the plant’s ability to adapt to stressful conditions such as disease, aluminum toxicity, salinity, and drought to aid breeders to improve plants that will increase economic and environmental sustainability.

characterize and develop tools to identify specific genes that mediate improved quality and composition of important agricultural commodities.

sequence and map expressed sequence tags (ESTs) to facilitate germplasm characterization.

develop new genetic tools, particularly DNA markers, to enhance plant breeding.

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.

construct and maintain more precise physical, genetic, and transcript genomic maps to identify the genes underlying key agricultural traits and the genomic location of those genes, and to elucidate comparative gene function, structure, and organization.

exploit genome sequence and gene expression information to identify valuable genes and gene combinations in undeveloped genetic resources.

develop new DNA markers closely associated with resistance to disease, pests, or environmental stresses, or with high value quality traits.              

PERFORMANCE GOAL 2.1.3.3:  Release of improved germplasm, varieties, and breeds based on effective use of genetic resources.

Indicators:

During FY 2002, ARS will

identify bermuda, fescue, and rye turf-grasses cultivars with improved tolerance to athletic field traffic and diseases, and evaluate management regimes for using these cultivars effectively.

ACCOMPLISHMENTS:  The National Turfgrass Evaluation Program, located at Beltsville, Maryland, coordinates research at cooperating universities in 40 States and 5 Canadian provinces that evaluate the persistence, input requirements, and other qualities of the major turfgrasses.  The program consolidates the results.

IMPACT/OUTCOME:  The data provided aids turf managers in selecting the varieties of Kentucky bluegrass, perennial ryegrass, tall fescue, fineleaf fescue, bent grass, and bermudagrass that are best adapted to their locations and turf needs.  This results in reduced costs and maximizes environmental benefits.

release four or five new cultivars of clover and trefoil better adapted to the Eastern United States.

ACCOMPLISHMENTS:  Scientists at Columbia, Missouri; Fresno, California; and Corvallis, Oregon, worked together to release and register five improved genetic stocks, including two narrowleaf trefoils, a big trefoil, and two birdsfoot trefoils.

IMPACT/OUTCOME:  Trefoils are useful nitrogen‑fixing forage plants that are high in protein, grow on acid soils, and do not cause bloating in livestock.  These new germplasm improvements will make using trefoils more affordable since the plants will be more productive, better adapted to a wider range of conditions, and more persistent.

release germplasm for an alfalfa line with improved pest resistance due to the selection of the genes for high density glandular hairs on the seedpod which protects the plant.

ACCOMPLISHMENTS:  Scientists at Manhattan, Kansas, released a variety of alfalfa with high‑density glandular hairs.

IMPACT/OUTCOME:  The dense hairs on the seedpod prevent certain insects from eating the tissue of the pod and reducing seed production.  Maintaining high levels of seed production with a genetic enhancement instead of using pesticides increases economic and environmental sustainability.

release a new dallisgrass cultivar resistant to ergot disease, and a klein grass cultivar for use in the Southeastern U.S.

ACCOMPLISHMENTS:  A new dallisgrass cultivar is being released by ARS and university scientists at College Station, Texas,  and the Texas and Louisiana Agricultural Experiment Stations.  This new cultivar has significantly improved persistence and yields over common dallisgrass that is grown on hundreds of thousands of acres across the Gulf Coast region.  The release of a new variety of klein grass for use in the Southern Great Plains has been delayed because weather and other problems limited seed production for field testing.

IMPACT/OUTCOME:  Improving the forage yields and persistence of important forage grasses reduces input costs for both seed and livestock production which increases profitability and also helps to maintain good ground cover that protects soil, water, and other natural resources.

release new forage and grain pearl millet hybrids with stable disease resistance and increased yields under non-irrigated conditions.

ACCOMPLISHMENTS:  ARS and University of Georgia scientists at Tifton, Georgia, have released a new pearl millet grain hybrid that has disease resistance and grain yields of 4,000‑5,000 kg/ha.

IMPACT/OUTCOME:  Grain pearl millet meets the need for a locally produced feed grain crop in the Southeast that provides high grain yields without irrigation and does not have aflatoxin problems.   

develop new crops from “wild” plants and microbes, and new genotypes of conventional crops, to further diversify the Nation’s agricultural production base and human diets, and to provide valuable new products (e.g., non-allergenic rubber from guayule latex).

ACCOMPLISHMENTS:  Developed a non-transgenic soybean containing oil that requires less processing (hydrogenation) for food use. 

IMPACT/OUTCOME:  Soybean oil is often hydrogenated in many food applications to improve flavor and functional properties of the oil, a process wherein some of the fatty acids are converted to ‘trans-fat’, which is a health concern.  Oil of this new soybean germplasm has a 3-fold increase in oleic acid concentration, which enables manufacture of high quality food products without oil hydrogenation.  This gives processors added flexibility for achieving better flavor, improved frying stability, and healthier food products.

identify new crops for medicinal uses.

ACCOMPLISHMENTS:  Developed a natural compound from mayapple (Podophyllum peltatum) that inhibits cell growth by affecting the formation of mitotic microtubular organizing centers.   

IMPACT/OUTCOME:  The compound, podophyllotoxin, serves as a biochemical structural backbone for anti-cancer drugs. Cells treated with this natural product formed tubulin in cells, which prevents uncontrolled cell division.  This discovery shows promise as a new and inexpensive natural resource for the development of cancer fighting drugs. 

enhance the genetic base of gene pools through programs of recurrent genetic recombination and selection so they can be more easily used by breeders.

ACCOMPLISHMENTS:  ARS researchers in Stoneville, Mississippi, produced via recombination and selection, a soybean germplasm population with host-plant resistance to Phytophthora root rot and soybean cyst nematode.

IMPACT/OUTCOME:  The preceding line provides new genetic variability in host-plant resistance to these diseases and pests for incorporation into the southern-adapted soybean genepool.

incorporate into genepools new genetic variability continually from germplasm in nature, in genebanks, or in traditional farmers’ fields so as to decrease genetic vulnerability to pests, pathogens, and other threats.

ACCOMPLISHMENTS:  ARS researchers in Stoneville, Mississippi, intercrossed cotton with some of its wild relatives and recovered hybrid plants via an embryo rescue technique. 

IMPACT/OUTCOME:  The preceding wild relatives of cotton are highly resistant to the reniform nematode, which causes significant yield losses in cotton grown in the Southeastern United States.  These interspecific hybrids represent a potential avenue for incorporating new sources of host-plant resistance to this important pest into cotton gene pools adapted to the Southeastern United States.

strengthen breeding and evaluation programs for minor crops, such as certain vegetables and fruits which comprise an important part of the U.S. diet, and for nursery and floral crops, which are of increasing economic importance.

ACCOMPLISHMENTS:  Securing sufficient seed supplies of the lethal yellowing (LY) resistant coconut varieties is a high priority of the tropical landscape nursery industry.  ARS researchers in Miami, Florida, analyzed genetic variation in ornamental coconut germplasm, with special emphasis on the 'Fiji Dwarf' variety that is very ornamental.  Research showed that an open pollinated stand of this variety maintained at modest distance from other varieties will likely yield pure 'Fiji Dwarf' seed nuts, and that contaminants could be identified molecularly using these markers.

IMPACT/OUTCOME:  These results represent a major step forward in breeding LY-resistant ornamental coconuts for the tropical landscape plant industry.

During FY 2003, ARS will

release a new grama grass cultivar for use in the Central Great Plains.

release a new fairway-type crested wheatgrass for use in the Central and Northern Great Plains.

release a switchgrass, big blue stem, and indiangrass germplasm based on collections from remnant prairies for use in the Midwest and Great Plains for USDA Hardiness Zones 4, 5, and 6.

release a new cultivar of kleingrass for use on pastures and grasslands of Texas and possibly other areas of the Southern Great Plains for livestock production and wildlife habitat.

complete the first field studies of maize-tripsacum hybrids to evaluate the impact of Tripsacum dactyloides genomic material on disease and insect resistance, and tolerance to environmental extremes in the Southern Great Plains and Midwest region of the United States.

develop new methods and tools to identify end product traits desired by consumers, such as specialty oils and grain qualities.

strengthen breeding and evaluation programs and identify new sources of diversity for minor crops, such as certain vegetables and fruits, which comprise an important part of the U.S. diet, and for nursery and floral crops, that are of increasing economic, ecological, and social importance.

develop and release germplasm with enhanced resistance to pests, pathogens, and weather damage.

enhance the genetic base through programs of recurrent genetic recombination and selection for viral resistance.

During FY 2004, ARS will

improve understanding and effectiveness of forage selection for establishment, digestibility and pest resistance, and release germplasm and cultivars adapted to the Southeastern environment.

provide increased understanding of plant processes that help grasses adapt to environmental stress, identify the molecular markers controlling these processes, and release improved germplasm and cultivars for use semi-arid lands to improve livestock forage production and turf management.

provide increased understanding of plant processes that aid alfalfa to resist pests and adapt to environmental stress, identify the genes controlling these processes, and release improved germplasm and cultivars.

develop new germplasm resources for commercial use that have significantly enhanced protein and oil quality.

develop new germplasm resources that have significantly enhanced starch and end-use grain quality.

develop new germplasm resources that have enhanced resistance to plant disease and pests.

conduct genetic engineering studies for viral resistance.

develop new crops from "wild" plants and microbes and new genotypes of conventional crops, so as to further diversify the Nation’s agricultural production base and its citizens’ diet, and provide new high-value products.

enhance the genetic base of crop gene pools through programs of recurrent genetic recombination and selection so these gene pools can be more easily used by breeders.

develop new analytical methods and genetic tools to identify end-product traits desired by consumers, such as specialty oils and grain qualities.

continually incorporate into gene pools new genetic variability from germplasm in nature, in gene banks, or in farmers' fields so as to decrease genetic vulnerability to pests, pathogens, and other threats.

strengthen breeding and evaluation programs for minor crops, such as vegetables and fruits of dietary importance, and nursery and floral crops, which are of increasing economic importance.

During FY 2005, ARS will

release improved grasses and forage legumes with higher nutritional quality and stress tolerance.

develop new germplasm resources for commercial use that have significantly enhanced protein and oil quality.

develop new germplasm resources  that have significantly enhanced starch and end-use grain quality.

develop new germplasm resources that have enhanced resistance to plant disease and pests.

conduct genetic engineering studies for viral resistance.

develop new crops from "wild" plants and microbes and new genotypes of conventional crops, so as to further diversify the Nation’s agricultural production base and its citizens’ diet, and provide new high-value products.

enhance the genetic base of crop gene pools through programs of recurrent genetic recombination and selection so these gene pools can be more easily used by breeders.

develop new analytical methods and genetic tools to identify end-product traits desired by consumers, such as specialty oils and grain quality.

continually incorporate into gene pools new genetic variability from germplasm in nature, gene banks, or farmers' fields so as to decrease genetic vulnerability to pests, pathogens, and other threats.

strengthen breeding and evaluation programs for minor crops, such as vegetables and fruits of dietary importance, and for nursery and floral crops, which are of increasing economic importance.

PERFORMANCE GOAL 2.1.3.4:  Improve methods for identifying useful properties of plants, animals, and other organisms, and for manipulating the genes associated with these properties.

Indicators:

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.

determine how antimicrobial resistance is acquired/transmitted/maintained in food producing animals in order to develop technologies/altered management strategies to control its occurrence.

develop information technologies to help control mycotoxins of fungal origin in crops and their food products, including competitive exclusion,  genetic markers, and more rapid methods of identification of  crop-effective sorting technologies.

develop information/technologies to help control toxins of plant origin in feeds and food products.

During FY 2004, ARS will

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 under what circumstances, and determine whether they destroy environmental pathogens including those in biofilms.

determine the key risk factors of human pathogens in foods of animal origin.  Evaluate interventions for their impact, 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.

determine how antimicrobial resistance is acquired/transmitted/maintained in food producing animals in order to develop technologies/altered management strategies to control its occurrence.

develop information technologies to help control mycotoxins of fungal origin in crops and their food products, including competitive exclusion, genetic markers, and more rapid methods of identification of  crop-effective sorting technologies.

develop information/technologies to help control toxins of plant origin in feeds and food products.

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 factors affecting disease spread and development in the United States for risk assessment.

During FY 2005, ARS will

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 under what circumstances, and determine whether they destroy environmental pathogens including those in biofilms.

determine the key risk factors of human pathogens in foods of animal origin.  Evaluate interventions for their impact, 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.

determine how antimicrobial resistance is acquired/transmitted/maintained in food producing animals in order to develop technologies/altered management strategies to control its occurrence.

develop information technologies to help control mycotoxins of fungal origin in crops and their food products, including competitive exclusion, genetic markers, and more rapid methods of identification of  crop-effective sorting technologies.

develop information/technologies to help control toxins of plant origin in feeds and food products.

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 factors affecting disease spread and development in the United States for risk assessment.

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Last Modified: 2/24/2004
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