Analysis of Results: 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, 72 Indicators are aligned under 9 Performance Goals. Because of the unique and dynamic nature of research, several Indicators were added to the Report that did not first appear in the Annual Performance Plan for FY 2000. This was done to ensure that significant accomplishments that were not anticipated last year were reported. While it is not possible to report research accomplishments numerically, the progress projected in all 71 Indicators was completed or substantially completed during FY 2000.

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.

During FY 2000, ARSwill

ACCOMPLISHMENTS: Using wild perennial sunflower as a germplasm source, scientists transferred genes for broomrape resistance into intermediate breeding lines. These intermediate sunflower lines were provided to cooperators in Spain for development into cultivated, broomrape-resistant sunflower.

IMPACT/OUTCOME: A new race of broomrape, a parasitic disease of sunflower, has emerged in Southern Europe and Turkey, and no current sunflower hybrids have resistance. The release of sunflower germplasm with resistance to this new virulent race of broomrape provides an important weapon to sunflower breeders in countries where the disease threatens the future of the sunflower industry. The germplasm ensures that U.S. farmers will have a source of resistance to this parasitic pest in the event of its accidental introduction into the U.S.

ACCOMPLISHMENTS: ARS researchers developed and released female and male sunflower lines that can be used to produce the NuSun sunflower hybrid. The new sunflower has an oil composition with improved health benefits and excellent stability under frying conditions.

IMPACT/OUTCOME:The release of female and male sunflower germplasm lines with the NuSun trait will allow seed companies to develop NuSun hybrids with precise fatty acid composition for planting by farmers. Sunflower hybrids produced by these lines have excellent disease resistance, high yield, and acceptable oil content, all of which will benefit both producers and processors.

expand and diversify the ARS sunflower collection through additions of under-represented species from Mexico and the U.S.

ACCOMPLISHMENTS: An ARS botanist conducted an exploration in Arizona, Utah, and Nevada, collecting several wild sunflower species. Two of the species, Helianthus anomalus and Helianthus deserticola had been seriously under represented in the ARS sunflower germplasm collection.

IMPACT/OUTCOME: The addition of these new accessions to the sunflower germplasm collection at Ames, Iowa, will provide a potential new source of genes for drought tolerance in sunflower.

ACCOMPLISHMENTS: ARS scientists and cooperators at the University of Arizona conducted large scale field screening of over 100 peanut breeding populations for resistance to aflatoxin contamination, and identified 17 lines that showed at least a 50 percent reduction in aflatoxin contamination.

IMPACT/OUTCOME: The results demonstrated that reduction of aflatoxin contamination in peanut is possible through selective breeding with available peanut germplasm. This will stimulate additional breeding efforts that are likely to reduce aflatoxin contamination even further.

ACCOMPLISHMENTS: ARS scientists and cooperators at the University of Georgia developed alternative weed management systems in peanut production. One system involves cultural practices: narrow rows to improve peanut•s competitive ability; and stale seedbed tillage, which reduce numbers of weed seeds in soil before planting. A second system is strip-tillage, wherein densities of some weeds were less than in conventional tillage, but inability to control other weeds actually increased dependence on herbicides. Another accomplishment was alternative applications of dinitroaniline herbicides in reduced tillage systems and leadership in the effort to amend herbicide registrations to allow these new uses.

IMPACT/OUTCOME: Peanut growers who use narrow rows and stale seedbeds reduce the need for commonly used late season herbicides. Cost of implementing these alternatives is minimal since no additional inputs are required and, depending on weed species composition, growers save $20/A by using less herbicide. Strip tillage simplifies crop production and spreads workloads through the season, which compensates for higher weed control costs. In this latter system, growers were warned to expect difficulties in managing Texas panicum and common bermuda grass.

ACCOMPLISHMENTS: ARS researchers developed an advanced generation peanut breeding line with a high level of resistance to the peanut root-knot nematode.

IMPACT/OUTCOME: The peanut root-knot nematode is a significant economic pathogen of peanut in the Southeast. This is the first discovery of peanut genetic material with resistance to both the root-knot nematode and tomato spotted wilt virus, another serious disease of peanut in this region.

ACCOMPLISHMENTS: ARS scientists released a high yielding experimental soybean line, LG96-1797. Researchers also identified several high protein experimental lines and evaluated primitive soybean germplasm, finding large differences in isoflavone contents among lines.

IMPACT/OUTCOME: Soybean line LG96-1797 was derived from exotic germplasm not found in the pedigrees of current commercial cultivars. Although this line does not exceed the yield of present high-yielding cultivars, its value lies in the genetic diversity it adds to soybean production. The identification of experimental lines with high protein or variability in isoflavones, thought to be dietary protectants in human health, indicates the potential for improvement of these two quality factors.

ACCOMPLISHMENTS: In Northern Utah, the ARS Logan laboratory demonstrated the value of the blue orchard bee for pollination of commercial cherry. Yield more than doubled compared with using honey bees. Blue orchard bee pollination was facilitated by use of a new nesting material and nest design, for which ARS has received conditional patent approval. In field trials, ARS also demonstrated the use of meadowfoam, an oil-seed crop produced in the Willamette Valley of Oregon, as a forage crop to increase populations of the blue orchard bee for use in California cherries and almonds.

In an effort to reduce 20 to 60 percent losses of bees routinely suffered by alfalfa seed producers each year, ARS entered into a collaborative research effort with BASF (formerly, American Cyanamid) directed toward the development of alternatives to methyl bromide for the management of chalk brood (a fungal disease of all bees) in commercial populations of the alfalfa leafcutting bee.

In the Walla Walla, Washington seed alfalfa region, ARS documented a dramatic one-year increase in nesting densities of the alkali bee. Hybrid onion planted adjoining an alkali bee nesting bed was used exclusively by alkali bees (alfalfa•s best native pollinator) for nectar. Seed production will be evaluated this fall to determine if onion is a profitable nectar crop to supplement the needs of this bee.

Having established that the sunflower leafcutter bee is a much more efficient sunflower pollinator in cages (on seeds produced per bee basis) research, in collaboration with Pioneer Hybrid International, focused on the optimal number of bees per plant to include in each cage. Results will be used to set bee stocking rates for seed producers.

IMPACT/OUTCOME: The ARS Logan laboratory initiated a 5-year collaborative project with USDI-BLM to assess pollinator diversity patterns in the Grand Staircase-Escalante National Monument. This project will provide baseline data for monitoring ecosystem health through the use of bee pollinators as indicator species.

ACCOMPLISHMENTS: ARS scientists at Beltsville, Maryland, have developed a DNA based assay to diagnose and quantitate O. ostertagi infections in cattle from fecal eggs. In the past, testing began on the molecular assay on fecal samples collected from cattle grazing infected pastures to validate the use of the assay under field conditions.

IMPACT/OUTCOME: Once validated, this assay will be used to identify individual members of the herd which account for the majority of parasite transmission, thus allowing for targeted parasite control programs. This assay will be used by industry scientists as a faster and more quantitative method to determine the efficacy of drug treatments for parasite control.

ACCOMPLISHMENTS: In a collaborative effort involving USDA-ARS, New Mexico State University, and the University of California, Los Angeles, genes controlling stomatal conductance in Pima cotton have been localized in two chromosomal regions. The genes provide heat tolerance for this crop, whose yields are generally limited because of excessive heat in its growing areas.

IMPACT/OUTCOME: Pima cotton is grown on about 300,000 acres in the Southwestern U.S. and is severely limited by heat. This research provides a new method to incorporate heat tolerance in varieties much faster than would occur otherwise. Yield increases of 25 percent or more are possible.

ACCOMPLISHMENTS: The effect of red or green mulch (which reflect colored light into the canopy) was exerted directly on cotton bolls rather than leaves. Covering bolls with aluminum foil removed the fiber-enhancing effect. Cotton fibers over red or green mulch were up to 4 mm (5/32 inch) longer, and slightly finer, than controls. The effect of green mulch indicates that reflected light onto bolls from nearby green leaves can have a major effect on fiber length.

IMPACT/OUTCOME: U.S. cotton mills utilize about 11 million bales of U.S.-produced cotton each year. Increased fiber length will greatly improve spinning efficiency in cotton mills, especially with new high-speed machinery. This trait will add greatly to the global competitiveness of both the U.S. cotton farmer and the U.S. cotton mills, which use the majority of U.S. produced fiber.

During FY 2000, ARS will develop microorganisms and determine optimum conditions to preserve protein in silage to conserve forage for livestock.

ACCOMPLISHMENTS: The U.S. Dairy Forage Research Center, Madison, Wisconsin, refocused on the source of protein rather than the development of organisms. Researchers found that protein in red clover conserved in silage was utilized more efficiently than protein in alfalfa conserved in silage.

IMPACT/OUTCOME: This improvement in nitrogen efficiency applied to only the first half of lactation (when cows need more protein) reduces nitrogen excretion 1.5 ton per year for a 100 cow herd.

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.).

During FY 2000, ARS will

continue to monitor the resistance of insect pest populations to transgenic plants that contain the toxin gene from Bacillus thuringiensis (bt). This activity is part of a long-term strategy to keep transgenic pest resistant crops effective, so they can continue to be used in IPM strategies to reduce chemical pesticide use.

ACCOMPLISHMENTS: Bt cotton has proven effective in controlling cotton bollworms. However, the potential development of resistance is a growing concern. ARS scientists at Stoneville, Mississippi, developed a more rapid and sensitive bioassay procedure to better identify cotton bollworms with resistance to Bt cotton. The bioassay requires only a minimum of five insects collected from the field to identity resistance genes. The scientists demonstrated that commercial cultivars of transgenic Bt cotton do not provide the same level of activity against caterpillar pests since the amount of Bt present in the plant is cultivar dependent.

IMPACT/OUTCOME: The U.S. Department of Agriculture•s Agricultural Research Service has been the agency responsible for conducting a Bt resistance-monitoring program in the Southern U.S. The new resistance monitoring bioassay developed by ARS is an essential tool for the resistance-monitoring program and for the early detection of Bt resistance in cotton bollworm populations from the 12 cotton-growing states located in the Southern U.S. The utility of the system has been demonstrated as reliable both abroad (cotton in Australia) and in the Southern U.S. so that alternative tactics can be used in areas where resistance to Bt transgenic cotton appears. The technology will help growers in their cultivar selections as well as providing insight into population dynamics of migratory moths in transgenic crops.

ACCOMPLISHMENTS: Corn rootworms are the targets of almost half of the insecticides used in row crops. ARS• 5-year areawide IPM program in Indiana, Illinois, Kansas, Iowa, and Texas, using an adult corn rootworm attack and kill technology, reduces corn root worm more than 70-90 percent in most of the test sites. In FY 2000, new baits and trapping systems were evaluated at the five primary sites which showed substantial Western corn rootworm population reductions across the Midwest demonstration sites. A number of corn growers have expressed interest in undertaking their own programs using the adult attracticide technology.

IMPACT/OUTCOME: A 90 percent reduction in the amount of prophylactic soil insecticide applied to U.S. corn grown in the Midwest U.S. can result in $300 million estimated savings. The program led by ARS out of Brookings, South Dakota was initiated in 1996 with substantial partner involvement from the University of Illinois, Purdue University, Iowa State University, South Dakota State University, Kansas State University, University of Nebraska, Texas A&M, and corn growers. The team received a USDA-ARS Technology Transfer award for this National IPM program across the U.S. corn belt. Program expansion and technology transfer has been particularly significant in Kansas and Texas, thus far.

ACCOMPLISHMENTS: The areawide pest management for codling moth has now successfully completed its final year. The Western Region of the Nation includes 54 percent of U.S. apple production acres and 97 percent of pear production. The codling moth is the key pest of pears and apples in that area. Traditional pest control methods, chiefly multiple sprays with organophosphate insecticides, which are at-risk pesticides, have led to the development of resistant strains of codling moth, reduced populations of beneficial insects, increased secondary pest outbreaks, and increased concerns over farm worker safety. ARS scientists at Wapato, Washington have led an areawide management partnership program since 1995 across the three State area of Washington, Oregon, and California using mating disruption, sanitation, natural enemies, and early season Bt sprays. Since the beginning of the program, insecticide use has significantly declined with some orchard growers not having sprayed for codling moth or other orchard pests, a decline of as much as 70 percent - 90 percent being realized.

IMPACT/OUTCOME: In 1995, there were 68 growers and 3,109 acres (five sites) in the program. In 1999, more than 600 growers and 21,000 acres (22 sites) had entered the program. The technology has now been accepted by many growers across the region. In Washington State alone, the number of acres within and outside the program has increased from 24,000 in 1997 to more than 60,000 in 1999, and in the three state area the number of acres grew to over 125,000 in 2000 under the technology, and several thousands of acres in California and Colorado. It is estimated that the orchard growers realize a savings of $400 per acre using mating disruption at the main tactic, since the use of the primary insecticide, Guthion, has decreased. ARS research and technology transfer partners were significant and included Washington State University, Oregon State University, the University of California, and numerous growers and consultants.

ACCOMPLISHMENTS: Scientists at the National Products Utilization Research Unit, Oxford, Mississippi, have selected one of several natural product-based blue-green algaecides for further testing and development.

IMPACT/OUTCOME: Potential not demonstrated.

ACCOMPLISHMENTS: In the U.S., the Asian longhorned beetle (ALB) was first found infesting trees in New York in 1996 and in Chicago in 1998. If the ALB spreads unchecked into U.S. urban and forest landscapes, it could cause billions of dollars in damage to ornamental and forest trees and to the maple syrup, lumber, and tourism industries. ARS scientists at Beltsville, Maryland, have discovered and synthesized a potential attractant for the ALB. The scientists are proceeding with evaluations of the attractant to ascertain its usefulness and with pursuing a patent on the attractant.

IMPACT/OUTCOME: A useful attractant for the Asian longhorned beetle could be developed into a detection and survey tool as a means to intercept and destroy the pest, if it proves to be effective over a reasonable distance in the field.

ACCOMPLISHMENTS: The goal of this effort has been to develop a new effective, nonpolluting attracticide pest management strategy for control of adult corn rootworms. Scientists at Beltsville, Maryland, have developed a new bait derived from Hawkesbury watermelon. The bait has undergone successful areawide testing and is undergoing commercial development. Based on field trials, the use of the bait is being expanded to more than 50,000 acres on corn and soybeans in the Midwest, including Texas, Kansas, Iowa, Illinois, Indiana, Nebraska, and South Dakota.

IMPACT/OUTCOME: The new product, commercially identified as Invite, and marketed by Florida Food Products, AgroTech, Inc., adds another new attracticide product for control of adult corn rootworm. Two patents have been awarded for the new bait system and it has been licensed by industry. Full commercialization of this technology should result in widespread use of the bait in formulations for control of corn rootworms, and reduce by 90 percent the amount of soil insecticides being applied to soil for corn rootworm control.

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.

During FY 2000,ARS will

ACCOMPLISHMENTS: Nutritional assessments have been conducted on low phytic-acid corn and barley lines, originally developed by ARS scientists at Aberdeen, Idaho, to reduce phosphorus run-off from animal feedlot operations. Cooperators at the University of Colorado found that human subjects retained 70 percent more zinc from foods prepared with low phytic-acid corn compared to normal corn. Cooperators at Montana State University found that heifers gained up to 33 percent more weight per day when fed low phytic-acid barley compared to normal barley.

IMPACT/OUTCOME: Low phytic-acid corn and barley lines may provide enhanced nutritional value for humans and livestock, as well as improve phosphorus nutrient management.

ACCOMPLISHMENTS: The fungal disease, scab (Fusarium Head Blight) has caused devastating losses to the wheat industry. ARS scientists and university collaborators at Fargo, North Dakota, have incorporated scab resistance from wild relatives of wheat to produce new durum wheat germplasm lines with scab resistance, and released a new hard red spring wheat variety •Alsen• with a higher level of scab resistance. Crown rust is a major disease of oat. Protection against this oat disease has previously depended on a single gene for resistance, which often became ineffective soon after a new oat variety was released. ARS scientists and university cooperators at St. Paul, Minnesota, have now identified a general (nonspecific) type of resistance, conferred by a group of genes, that is effective against many strains of the crown rust organism. The most destructive disease of rice in California is stem rot. ARS scientists at Davis, California, and collaborators at Biggs, California, have identified two DNA markers linked to stem rot resistance from a wild rice species.

IMPACT/OUTCOME: Transfer of the wild grass chromosome segment containing scab resistance into the durum genome was confirmed. The new durum germplasm lines can be used to speed up breeding of new durum wheat varieties with scab resistance. The new bread wheat "Alsen" with increased tolerance to scab will likely be widely adopted by growers in areas previously damaged by scab. (2) General (nonspecific) genes often provide long lasting resistance to crop disease pathogens. DNA markers associated with the durable, general-resistance genes have been identified and can now be used by oat breeders to effectively incorporate crown rust resistance into new oat varieties. (3) Identification of DNA markers linked to stem rot resistance could significantly accelerate the transfer of these genes into high-yielding rice varieties.

ACCOMPLISHMENTS: The ARS National Plant Germplasm System (NPGS) is the premier plant genebank network in the world, managing more than 430,000 different samples invaluable for crop genetic improvement and scientific study. More than 120,000 of these samples (almost 30 percent of the total) were distributed in 2000 in response to more than 3,000 different requests. More than 4,000 different samples were increased in 2000 by controlled field cultivation. More than 80 percent of all the seed-propagated accessions are backed up in security storage at the National Seed Storage Laboratory. In 2000, 9 foreign plant explorations were conducted successfully. More than 600 accessions of cotton were acquired from Uzbekistan, material that may provide critical new genetic diversity for the U.S. cotton crop. The preceding activities enabled the scientific community to gain ready access to a wide diversity of genetic materials for research and crop improvement.

IMPACT/OUTCOME: The website for the NPGS public database, the Germplasm Resources Information Network (GRIN), was queried thousands of times per day through the World Wide Web. An average of more than 450 new "visitors" queried GRIN every day during 2000. This high frequency of usage indicates that this database is a key resource for plant researchers and breeders worldwide.

ACCOMPLISHMENT: The ARS microbial germplasm collections now manage more than 100,000 different strains of bacteria, fungi, and related microbes. The largest collection at Peoria, Illinois, manages more than 80,000 different strains, including germplasm vouchers of patented microbes.

IMPACT/OUTCOME: These microbial collections serve as an important reference standard for microbial identification, as biocontrol agents, and as sources of natural products for pharmaceutical and other industrial uses.

ACCOMPLISHMENTS: Sugarbeet is one of the most important sources of domestic sugar, and a mainstay of the agricultural economy in the Northern Great Plains. Sugar content and disease resistance are key productivity factors for sugarbeets. ARS scientists at East Lansing, Michigan, developed new methods for assaying sugar content of single plants (via High-Performance Liquid Chromatography) and single plant assays for disease resistance to an important sugarbeet seedling disease.

IMPACT/OUTCOME: These new techniques may accelerate the pace of sugarbeet genetic improvement.

ACCOMPLISHMENTS: By evaluating hundreds of cotton germplasm lines, ARS researchers at Starkville, Mississippi, identified non-U.S. germplasm with resistance to tobacco budworm, one of the most serious cotton pests.

IMPACT/OUTCOME: These resistant materials will provide the basis for breeding resistance into cotton germplasm adapted to the U.S.

ACCOMPLISHMENTS: In tomatoes, beta carotene confers superior nutritive properties. ARS scientists at Beltsville, Maryland, identified DNA genetic markers for accurately predicting beta carotene content.

IMPACT/OUTCOME: These markers may improve the efficiency of tomato breeding and hasten the development of tomatoes with superior nutritional content.

ACCOMPLISHMENTS: Nematicides are very expensive, especially for small producers, and those who produce vegetables such as carrots for "organic" or "low-input" niche markets. Consequently, carrots with genetic resistance to nematodes are highly desirable, because the latter pose the largest threat to production worldwide.

IMPACT/OUTCOME: ARS scientists in Madison, Wisconsin, and their university cooperators identified and characterized genes conferring genetic resistance to nematodes in carrots, and began breeding the resistant traits into standard carrot germplasm.

ACCOMPLISHMENTS: At present, herbicides are applied to control weeds prior to flooding rice fields. ARS researchers at Beaumont, Texas, have identified and characterized genes that accelerate seedling growth up to four times.

IMPACT/OUTCOME: When these genes are incorporated into standard germplasm, it may result in more vigorous rice that will become established more quickly, thereby reducing the need for herbicide application.

ACCOMPLISHMENTS: ARS scientists at New Orleans have inserted a bacterial (chloroperoxidase) gene into cotton, to enhance inhibitory activity against A. flavus, which produces aflatoxin contamination in crops. Additionally, the scientists have discovered a new family of proteins in corn kernels that are potential inhibitors of A. flavus growth.

IMPACT/OUTCOME: Experiments to inoculate bolls of the transgenic cotton with A. flavus and then assay for resistance will now be completed. Genes encoding the inhibitory proteins will be exploited by breeding selection and/or transgenic strategies in corn, cotton, and other crops.

ACCOMPLISHMENTS: The value of resistance to insect damage in reducing Aspergillus flavus infection aflatoxin contamination was assessed. Corn inbreds varying in insect resistance were evaluated for aflatoxin accumulation. Hybrids with resistance to southwestern corn borer and fall armyworm sustained less ear damage and less aflatoxin accumulation.

IMPACT/OUTCOME: Results suggest that combining genes for insect resistance and resistance to aflatoxin accumulation will be a productive strategy for developing new corn hybrids that are less vulnerable to aflatoxin accumulation.

ACCOMPLISHMENTS: Quantitative trait loci (QTL) have been found in cattle and pigs. Three chromosomal regions have been identified that affect reproduction in cattle and nine chromosomal regions affecting reproduction in the pig. Four chromosomal regions have been identified to affect carcass composition in the pig and seven chromosomal regions have been identified to affect carcass composition and quality in cattle. The next step will be to identify the genes in these chromosomal regions to improve livestock production.

IMPACT/OUTCOME: The current process to identify these genes takes a long time and considerable resources. New laboratory resources are being developed to reduce the time and cost of this effort. DNA libraries were purchased to sequence a large number of genes and new DNA markers are being developed. Research efforts will also continue to identify additional chromosomal regions that affect reproduction and meat production traits. This research will improve genetic selection programs.

During FY 2000,ARS will

ACCOMPLISHMENTS: More than 80,000 gene sequences were characterized and 46 gene libraries created in FY 2000 in cooperation with scientists from several universities and industry.

IMPACT/OUTCOME: These sequences are being accessed by public and private researchers for research and development of economically important products, which may reach the marketplace in the next 5 to 10 years.

determine the nucleotide sequence of nearly the entire genome of a mustard plant (Arabidopsis), an important "model species" for understanding plant genomesin conjunction with university and private sector partners supported by ARS, the National Science Foundation, and Department of Energy. This also will provide substantial progress in sequencing the rice genome. Because the DNA sequence of many agronomically-important genes is similar among species, this knowledge may help to identify similar ones in major crops, thus accelerating the progress of crop improvement.

ACCOMPLISHMENTS: At the end of 2000, an international scientific team that included ARS researchers in Albany, California, finished the first essentially complete genome sequence for a plant, Arabidopsis, an experimental "model plant." It was sequenced first because of its small genome and rapid life cycle.

IMPACT/OUTCOME: Knowledge of the Arabidopsis genome is already helping to elucidate the structure and function of crop genomes and their constituent genes.

ACCOMPLISHMENTS: With the ARS Center for Agricultural Bioinformatics at Cornell University, Ithaca, New York, serving as a hub, this ARS national program has expanded its institutional network for developing and maintaining crop genome databases and bioinformatics tools to encompass strong partnerships with the University of Minnesota, the University of California-Davis, and the Cold Spring Harbor Laboratory.

IMPACT/OUTCOME: At Ithaca, ARS scientists established a new worldwide web server to distribute genetic and genomic information for more than a dozen crops and model plant species as widely as possible to the scientific community.

ACCOMPLISHMENTS: ARS scientists and collaborators at Cornell University, Ithaca, New York, developed more efficient means for genetically mapping agriculturally-important traits. Often, mapping the genomic location of the genes that govern a trait serves as a vital prerequisite for genetic improvement of the trait. A new software tool was developed, MapPop, that enables high-quality genetic mapping with smaller-scale genetic studies.

IMPACT/OUTCOME: This new tool and approach may tangibly accelerate the generation of genetic data integral to the progress of crop genetic improvement.

ACCOMPLISHMENTS: The size and complexity of soybean•s genome preclude it from being completely characterized in the near future. ARS scientists in Ames, Iowa, correlated information in the ARS soybean genome database with genomic data from the model plant Arabidopsis, the first plant genome to be completely sequenced.

IMPACT/OUTCOME: The arrangement of genes on the preceding two genomes was somewhat similar, indicating that information derived from the Arabidopsis genome may help accelerate genetic research and crop improvement in soybean, a major crop worldwide.

ACCOMPLISHMENTS: Additional DNA markers have been added to the poultry map and a complete description of the map is available on the web (http://poultry.mph.msu.edu/). The total number of markers exceeds 1,500 and 200 of these markers represent genes.

IMPACT/OUTCOME: The DNA markers are being used to identify chromosomal regions that affect susceptibility to Marek•s disease. A gene that interacts with the virus has been identified as Growth Hormone and a certain form of this gene appears to make the chicken more resistant to the virus.

ACCOMPLISHMENTS: ARS scientists at East Lansing, Michigan, have sequenced 175,000 bases of DNA from a serotype 1 Marek•s disease virus (MDV), thus providing a crucially important roadmap for understanding viral gene function as a first important step toward better diagnosis of MDV in commercial meat-type chickens. Molecular DNA sequencing of the serotype 1 MDV was transferred to academia and the poultry industry through a publication to enhance the global effort to elucidate the function of various viral genes and the epidemiology of MDV infection.

IMPACT/OUTCOME: The entire DNA sequence of the MDV will provide a crucial first step toward the development of novel molecular vaccines for MDV. Furthermore, the DNA sequence information of MDV will enhance understanding of the immunology of MDV infection that may prove useful to control other types of viruses important to the U.S. poultry industry.

ACCOMPLISHMENTS: ARS scientists at East Lansing, Michigan, compared the DNA sequences of various isolates of avian leukosis virus subgroup J (ALV-J) and observed numerous mutations scattered throughout the genomes. These findings suggest that variations in these regions may alter the ability of the infected host to neutralize the virus and emphasize the importance of virus antigenic variants that may confound diagnosis and vaccine strategies for control of ALV-J virus infection.

IMPACT/OUTCOME: DNA sequence information from the ADOL-Hc1 virus strain, the U.S. prototype of ALV-J, and development of several recombinant baculovirus and fowlpox viruses containing the inserted ALV-J gene allowed the expression of recombinant ALV-J protein and the development of a sensitive assay for detection of ALV-J outbreaks in commercial meat-type chickens. Recombinant ALV-J viral antigen expressed in the baculovirus vector has been used in a commercial diagnostic kit for detection of antibody to ALV-J (U.S. Patent #6,146,641).

During FY 2000, ARS will

ACCOMPLISHMENTS: The ARS Baton Rouge laboratory released Russian honey bees that showed resistance to mites from quarantine to the beekeeping industry, in cooperation with Bernard Apiaries in Breaux Bridge, Louisiana. The purpose is to begin to introduce mite-resistant stock into commercial honey bees.

IMPACT/OUTCOME: A new mite-resistant trait was discovered in a selected line of honey bees; the trait suppresses mite reproduction in the first offspring of a queen rather than (as previously) after a six-week delay. With this trait it may be possible to predict mite-resistance in a colony as soon as 17 days after a queen begins to lay eggs. This should greatly speed up breeding of resistance traits.

ACCOMPLISHMENTS: ARS researchers and university cooperators at East Lansing, Michigan, released a high-yielding, black seeded dry bean incorporating resistance to a variety of fungal diseases, including white mold, the most serious disease of the crop in the Great Lakes region.

IMPACT/OUTCOME: Cultivation of this bean may reduce fungicide use, while increasing profits for small producers who generally rely on good yields to offset profit risks.

ACCOMPLISHMENTS: The farmgate value of potatoes is worth several billions of dollars in the U.S., but cost of production is high because of diseases, pests, and suboptimal quality. ARS researchers at Prosser, Washington, and university cooperators in the Pacific Northwest released several superior potato varieties that should increase producer profitability.

IMPACT/OUTCOME: Bannock Russet and Gem Russet have improved disease resistance and yield. They are suitable for the French fry and fresh markets. Idarose is a superior red-skinned variety for boiling and salad purposes.

ACCOMPLISHMENTS: Two new woody ornamental landscape plants, a lilac and a redbud, were developed by researchers at Washington, D.C., and released to nurseries for propagation. The redbud is seedless, and the lilac is better adapted to warmer climates.

IMPACT/OUTCOME: Both new varieties can be propagated readily by standard techniques, and will furnish U.S. gardeners a wider diversity of well-adapted landscape plants.

ACCOMPLISHMENTS: Continued improvement in yield of soybeans is needed to enable U.S. farmers to maintain a competitive edge in world markets. In 1999 field trials, ARS researchers in Wooster, Ohio, found that a newly released semi-dwarf soybean cultivar topped the maximum yield trials at 97 bushels per acre.

IMPACT/OUTCOME: The results confirmed the potential of a well-managed subirrigation/drainage system, when used in combination with a high yield soybean cultivar, to produce consistent yields of 70 to 80 bushels per acre.

ACCOMPLISHMENTS: Peaches in the Southeastern U.S. are generally grown by small producers in relatively small volumes.

IMPACT/OUTCOME: The profitability of southeastern growers may be enhanced by •Gulfprince• an early season peach with superior quality and shipping characteristics that was bred by ARS researchers and their university cooperators at Byron, Georgia.

ACCOMPLISHMENTS: Grain legumes are important rotational crops in cereal-based cropping systems of the U.S. Pacific Northwest. But many diseases, insect pests, and environmental stresses reduce seed yield and quality. ARS scientists in Pullman, Washington, released two new varieties of pea, two of lentils, and a new variety of chickpeas.

IMPACT/OUTCOME: These superior new varieties incorporate high yields and disease resistance.

ACCOMPLISHMENTS: Plum pox virus, the most serious virus disease of plums and other stone fruit, recently entered the U.S. and may threaten the U.S. stone fruit industry. ARS researchers at Kearneysville, West Virginia, genetically-engineered plums for resistance to that virus.

IMPACT/OUTCOME: These resistant varieties will provide producers with the means to combat that disease.

ACCOMPLISHMENTS: ARS researchers at Raleigh, North Carolina, developed soybeans with high concentrations of oleic acid, i.e., with highly unsaturated oil, using traditional breeding methods. Highly unsaturated oil is considered healthier than highly saturated oils.

IMPACT/OUTCOME: Such varieties bred by traditional approaches may enable U.S. farmers to remain competitive in exporting soybeans to nations that restrict use of transgenic crops.

ACCOMPLISHMENTS:Fusarium head blight (scab) has devastated the hard red spring wheat producing areas of the Northern Great Plains. ARS researchers and university cooperators at Fargo, North Dakota, released the scab-tolerant variety •Alsen•, which has high yields and greater scab resistance than current varieties.

IMPACT/OUTCOME: •Alsen• wheat will likely be widely produced in regions previously devastated by scab.

ACCOMPLISHMENTS: The U.S. frying industry requires sunflower oil with 50-60 percent monosaturated fatty acid, which ideally is produced by a sunflower hybrid having high yield and superior agronomic properties. ARS researchers in Fargo, North Dakota developed a hybrid sunflower with the desired fatty acid profile, high yield, and disease resistance.

IMPACT/OUTCOME: The germplasm was released to private and public breeding programs for varietal development.

ACCOMPLISHMENTS: ARS scientists at Fresno, California, are releasing a new white seedless muscat table grape.

IMPACT/OUTCOME: A series of seedless cultivars ripening from early to late with white, red, or black skin color are needed to provide a continuous supply throughout the year for the consumer. A limited number of good seedless table grape cultivars are currently available to grape growers. The development of seedless grape varieties with naturally large size will reduce production costs and provide the type of grapes consumers want. ARS seedless table grapes have had a significant impact nationally such as 'Flame Seedless', the first ARS seedless grape released in 1973, which is now the second most important table grape grown in California, and "Crimson Seedless" which is the fourth leading variety.

ACCOMPLISHMENTS: ARS scientists at Fresno, California, are releasing a new blue/black seedless Concord flavored grape.

IMPACT/OUTCOME: A series of seedless cultivars ripening from early to late with white, red, or black skin color are needed to provide a continuous supply throughout the year for the consumer. A limited number of good seedless table grape cultivars are currently available to grape growers. Since Concord type grapes are not readily cultivated in California, this new variety will allow for the production of a seedless Concord variety adapted to California conditions.

ACCOMPLISHMENTS: ARS scientists in Corvallis, Oregon, working jointly with Washington State University released •Puget Summer• strawberry, developed from a cross made by ARS in Corvallis. This new strawberry variety, in concert with recent releases of •Firecracker• and •Independence• by ARS in Corvallis, Oregon, provides three new late ripening cultivars for the Pacific Northwest. ARS scientists in Chatsworth, New Jersey, released •Cara•s Choice• and •Hannah•s Choice•, two new highbush blueberry cultivars for the pick-your-own and home garden markets. ARS researchers in Poplarville, Mississippi, released •Biloxi•, an early, low chill highbush blueberry for the Gulf Coast Region.

IMPACT/OUTCOME: New strawberry cultivars released in the Pacific Northwest will extend what has been a fairly short season for the industry that has faced challenges in recent years, while depending primarily on high quality fruit for processing. Season extension has been a goal of breeding and production research in the Pacific Northwest strawberry industry. New blueberry varieties released by ARS in Chatsworth are high quality with advances in sweetness, firmness and flavor not available in commercial cultivars. These new varieties will increase public awareness of blueberry as a quality fruit and lead to greater consumption of blueberries as a healthful part of the diet. The new early, highbush blueberry from Poplarville will assist the expanding blueberry industry of the Gulf Coast Region to expand into new areas.

During FY 2000, ARS will

ACCOMPLISHMENTS: Scientists at the Catfish Genetics Research Unit, Stoneville, Mississippi, completed a catfish genetic linkage map with 264 markers.

IMPACT/OUTCOME: This map will be useful for selection of traits that are difficult to measure, such as disease resistance and fillet yield.

ACCOMPLISHMENTS: The "Test Day Model" was put on hold until the Council on Dairy Cattle Breeding and the Cornell Research Foundation negotiate the use of a patent.

IMPACT/OUTCOME: Impact not measurable.

ACCOMPLISHMENTS: ARS scientists constructed a library of over 1,400 soybean genes that are expressed two days after infection by the soybean cyst nematode race 3. Over 1,000 of the genes were sequenced in an attempt to identify their function. In a complementary approach, DNA markers were developed which map a trait closely linked to soybean cyst nematode resistance.

IMPACT/OUTCOME: The library of genes will be applied to microchip DNA array technology, in which thousands of soybean genes can be monitored for their response to soybean cyst nematode invasion. This will allow researchers to identify genes that are involved in resistance to the soybean cyst nematode. Until these genes are positively identified, the use of new DNA markers can be used by breeders to develop soybeans with improved resistance to this pest.

ACCOMPLISHMENTS: DNA markers have been found on chicken chromosome 1 that are associated with resistance to avian coccidiosis. The markers are currently being evaluated in industry populations. Additional research efforts are designed to identify the gene on chromosome 1 that influences resistance to coccidiosis and identify additional chromosomal regions that confer resistance.

IMPACT/OUTCOME: Avian coccidioses cost the U.S. poultry industry more than $700 million per year by reducing growth and feed efficiency in chickens. DNA markers will be used to select chickens that are less susceptible to coccidioses and therefore decrease the number of chickens that will get sick. DNA markers will also be used to identify genes that influence resistance to coccidioses and this information will be used to develop therapeutic agents.

ACCOMPLISHMENTS: ARS has focused on DNA sequencing as a practical tool to study problems such as: the effect of horizontal movement of genetic elements in the microbial environment; understanding the development of antibiotic or antimicrobial resistance, or resistance to stress and the development of increased virulence; or to phylogenetically characterize strains in order to develop better identification and differentiation methods. ARS studies genes that are present both on the bacterial chromosome and on DNA elements such as plasmids, transposons, integrons, and bacteriophages in order to achieve these goals.

IMPACT/OUTCOME: A better understanding of the genetic basis for resistance and adaptation of food-borne bacterial pathogens will help ensure the safety of the U.S. food supply.

ACCOMPLISHMENTS: Chicken and pig leptin have not been produced in the laboratory, but antibodies to chicken and pig leptin have been produced which allows researchers to quantify the amount of leptin in different animals and at different stages of growth, development, production, or nutrition.

IMPACT/OUTCOME: Future research will evaluate leptin•s role in nutrient metabolism by using the antibody to leptin and other laboratory methodologies.

ACCOMPLISHMENTS: ARS scientists developed one novel method for large scale screening of pollen mutants by pooling pollen from approximately 100 plants at a time. Numerous unexpected pollen mutant types were identified.

IMPACT/OUTCOME: The identification of pollen mutants will assist researchers in characterizing the individual signaling events that occur during successful pollen germination and fertilization. Knowledge about the genes that control these events can potentially be used in the future to facilitate pollination between distantly related species for the introduction of new genes by natural processes.

ACCOMPLISHMENTS: The multiple genes of the Technology Protection System (TPS) have been assembled in cotton plants, but not all in the same plants. This awaits another round of crossing and selection of progeny that includes all of the genes in one plant.

IMPACT/OUTCOME: TPS has many potential applications, the most valuable of which is the ability to prevent the spread of genes from a genetically engineered crop to closely related wild plants. How to utilize the TPS genes properly is actively under discussion in many quarters.

ACCOMPLISHMENTS: In two growing regions, fiber yield was found to be depressed in low areas of fields that had high soil moisture, soil phosphorus, and organic matter. Fiber maturity (a quality trait) was associated with high soil phosphorus.

IMPACT/OUTCOME: Designing "zoned" harvesting schemes to partially separate high-maturity from low-maturity fiber appears feasible from these data. The benefit is realized in the production of cotton bales of more uniform fiber quality, a high-priority need of cotton mills.

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.

During FY 2000, ARS will

ACCOMPLISHMENTS: Scientists at the Aquatic Animal Health Research Unit, Auburn, Alabama, developed the vaccine Aquavac-ESC that was licensed to Intervet, who made it available to fish farmers for use during the 2000 growing season.

IMPACT/OUTCOME: Estimates indicate that 1 million doses of the vaccine will be sold in the year 2000.

ACCOMPLISHMENTS: Two vaccine trials were carried out to test the efficacy of 2 CSFV E2 subunit/marker vaccines and a live attenuated vaccine against a challenge with virulent CSFV. The live attenuated vaccine proved to be more efficient controlling CSFV in pigs than the subunit/marker vaccines when infection occurred shortly after vaccination.

IMPACT/OUTCOME: These data indicate that attenuated vaccine is an efficacious tool for use in the control of a CSF outbreak. Subunit/marker vaccines might be applied to herds not directly in contact with an outbreak, facilitating differentiation between vaccinated and naturally infected pigs, thus decreasing economic losses due to elimination of uninfected animals.

ACCOMPLISHMENTS: In 1995, VSV-NJ caused outbreaks in Southwestern U.S. This was the first re-emergence of VSV-NJ since 1985. In 1997 and 1998 VSV-IN1 re-emerged in the Southwest after 30 years of absence. Using Reverse Transcriptase - Preliminary Chain Reaction (RT-PCR) DNA sequencing, and phylogenetic analyses combined with epidemiological information (molecular epidemiology), the determination was made that viruses causing the 1995, 1997, and 1998 VS outbreaks were newly introduced ones. They were more similar to viruses circulating in enzootic areas of Southern Mexico than to those causing previous outbreaks in the U.S.

IMPACT/OUTCOME: Rapid detection and characterization methodology for VSV by RT-PCR and direct sequencing is possible. Determining the origin of VSV strains causing outbreaks in the Western U.S. allows attention to be focused on analyzing the factors influencing the introduction of VSV into the U.S., such as environmental, climatological, and vectorial.

ACCOMPLISHMENTS: Developed a vaccine using limited replication competent Venezuelan Equine Encephalitis virus vector containing an avian influenza H5 hemagglutinin gene insert.

IMPACT/OUTCOME: The vaccine vector induced protective immunity in chickens against a highly pathogenic H5 avian influenza virus when given subcutaneously. Since poultry does not have immunity against this vector, the vaccine has the potential for widespread use.

ACCOMPLISHMENTS: DNA was sequenced and nine strains of ALV-J compared from different U.S. poultry flocks isolated in the years 1993 to 1997. Analysis clearly shows that the ALV-J viruses in the U.S. are changing over time. It also suggests that U.S. strains may have evolved independently from the ALV-J viruses in Great Britain. DNA sequencing efforts made it possible to design PCR primers for use in quickly detecting the ALV-J virus in infected birds.

IMPACT/OUTCOME: There are two commercial diagnostic kits for ALV-J on the market. Unfortunately, both of them detect only a subset of the ALV-J field strains, generating both false negative and false positive results. DNA sequencing demonstrated that ALV-J•s are highly variable and explains why the existing commercial kits are unsatisfactory. Vaccine developers and diagnostic kit designers need to target the portions of ALV-J that are constant and not likely to change. The PCR primers were designed to bind to highly conserved regions of the ALV-J genome. Consequently, several poultry breeding companies are using the primers and PCR conditions to aid them in detecting ALV-J positive chicks.

ACCOMPLISHMENTS: Through collaborative research with the National Animal Disease Center, Ames, Iowa, Washington State University, APHIS, MAFF (United Kingdom), and Utah State University (Logan, Utah), the stage 2 OIE (Office of International Epizooties • Assay development and standardization) validation of the third eyelid test was completed and published. The third eyelid test for sheep scrapie is the first and only practical preclinical diagnostic test for a transmissible spongiform encephalopathy worldwide.

IMPACT/OUTCOME: This work represents the next step toward international acceptance of the test. It is being implemented as part of the U.S. national scrapie test validation and eradication program.

ACCOMPLISHMENTS: A vaccine developed by ARS scientists and subsequently evaluated by them and a commercial cooperator was found to be effective and is in the final stages of Federal licensure. Also, a highly sensitive diagnostic test was developed for porcine reproductive and respiratory syndrome (PRRS) during the past year using a powerful molecular technique based on detecting a portion of the nucleic acid core of the PRRS virus.

IMPACT/OUTCOME: Use of the vaccine, which is expected to be marketed later this year, will reduce the clinical impact of PRRS on the U.S. swine industry. In addition, the use of the diagnostic test will allow the early and definitive recognition of epidemics of PRRS and immediate implementation of control strategies to minimize further spread and clinical impacts of the disease.

ACCOMPLISHMENTS: ARS scientists have achieved complete protection against congenital neosporosis in the mouse model by immunization of dams with Neospora caninum antigen prior to mating and subsequent challenge with the parasite. It was determined that this antigen was associated with an insoluble portion of the N. caninum extracts as a first step in purifying the protective component.

IMPACT/OUTCOME: Abortions due to Neospora caninum have a major impact on the dairy and beef cattle industries throughout the world. Knowledge about transmission of this parasite will help producers manage and prevent the disease.

ACCOMPLISHMENTS: ARS scientists identified the period during seed development when a key enzyme for degreening of seed chlorophyll is the most active.

IMPACT/OUTCOME: Knowledge of the period of highest activity of the degreening enzyme will facilitate purification of the enzyme and cloning of the degreening gene, which is necessary for characterizing how the gene works and, finally, for transferring it into canola for evaluation.

ACCOMPLISHMENTS: See Performance Goal 2.1.3.4. Since the elements of the Technology Protection System are not yet assembled into a single plant, and this evaluation could not go forward.

ACCOMPLISHMENTS: In fields with early and late planting dates, boll distribution on the plants was found to be a major contributor to fiber length variability, but not maturity variability. In years with ample mid-season moisture, early planting increased yield and fiber length and maturity.

IMPACT/OUTCOME: The data are useful for the modeling (prediction) of fiber quality, which will help cotton mills (users of the fiber) to select the appropriate quality for various spinning processes which have differing needs for raw material inputs.

ACCOMPLISHMENTS: The bovine and ovine u-calpain genes were cloned and placed on the genetic linkage map. DNA markers near the u-calpain gene were used to evaluate u-calpain•s potential effect on meat tenderness. A number of proteases were identified to degrade calpastatin; however, only u-calpain and m-calpain degraded calpastatin in the same manner as during postmortem aging. ARS scientists determined that, under physiological conditions, the rate of proteolysis was reduced, but not completely halted, by increasing the ratio of calpastatin:u-calpain from 2:1 to 4:1.

IMPACT/OUTCOME: These results will lead to a greater understanding and control of biological mechanisms that regulate variation in muscle growth and meat tenderness. ARS scientists determined that variation in muscle shortening, proteolysis of muscle proteins during aging, and connective tissue accounts for 72 percent of the variation in pork tenderness. They also determined that muscle shortening affects meat tenderness, but altering proteolysis of muscle proteins does not.

ACCOMPLISHMENTS: A protocol has been developed with APHIS to complete stage 3 OIE validation (determination of assay performance characteristics) of the third eyelid test.

IMPACT/OUTCOME: These data will provide statistically significant test performance characteristics for the third eyelid test. In addition to aiding in scrapie eradication from the U.S., these data will make the test acceptable internationally for continued quality assurance programs in the U.S. once scrapie is eradicated. Due to the enormous economic impact of transmittable spongiform encephalopathies (TSEs), such as bovine spongiform encephalopathy (mad cow disease), the importance of the eradication of related TSEs, such as scrapie, from the U.S. is clear. The final impact/outcome is improved export advantages for U.S. animal agriculture.

ACCOMPLISHMENTS: Scientist at the Animal Physiology Unit, Columbia, Missouri, in collaboration with scientists at the University of Missouri demonstrated that plasma protein in weanling diets provided protection to infectious disease.

IMPACT/OUTCOME: The research was recognized by NPPC with the 2000 Innovation Award for basic research.

ACCOMPLISHMENTS: Based on DNA sequence data, five sets of polymerase chain reaction (PCR) primers were developed that were specific for the Karnal bunt fungus, Tilletia indica, and three sets were designed specific to Tilletia walkerii, a closely related fungal species of ryegrass that had been indistinguishable previously. Later these tests were used to show that a shipload of wheat exported to the European Union was contaminated with low levels of the ryegrass pathogen, not Karnal bunt, so that negative regulatory action was avoided.

IMPACT/OUTCOME: These tests provide rapid, accurate identification of Karnal bunt contamination in grain, and, equally important, to accurately determine that suspected fungi may be Karnal bunt. This capability will allow international wheat trade to proceed with fewer shipments rejected because of incomplete or mistaken identifications of the fungi.

ACCOMPLISHMENTS: ARS scientists at Ames, Iowa, fed various sources of chloride and sulfate containing chemicals to dry nonpregnant dairy cows and demonstrated that chloride consistently counteracted the effects of dietary potassium that causes a decrease in blood acidity, thus contributing to hypocalcemia (milk fever). Furthermore, this study found that chloride was more effective than sulfate in the prevention of milk fever in peri-parturient cows.

IMPACT/OUTCOME: This new information has resulted in the development of hydrochloric acid treatment of feeds by at least two companies (West Central Corp., Ralston, Iowa, and Nutritech, Abbottsford, British Columbia) and allowed farmers, veterinarians, and nutritionists to more accurately choose the most effective feeds and chloride sources for balancing transition dairy cow rations.

ACCOMPLISHMENTS: ARS researchers at Ames, Iowa, have demonstrated that mild alkalosis can attenuate the action of parathyroid hormone at its target organs (bone and kidney), resulting in decreased production of the active form of vitamin D, bone calcium and phosphorus reabsorption. Collectively, these effects lead to the inability of dairy cows to respond to the high demand for calcium at parturition and ultimate development of peri-parturient hypocalcemia (milk fever).

IMPACT/OUTCOME: This research has provided a more detailed understanding of the pathogenesis of milk fever. The research has also emphasized the importance of dietary methods for reversing alkalosis in order to re-establish target tissue sensitivity to the parathyroid hormone and prevent clinical and sub-clinical hypocalcemia in dairy cows. An enhanced understanding of the effects of dietary factors on the overall health of young and adult dairy cattle will benefit the U.S. producer and consumer.

OBJECTIVE 2.2: Safe food: "Maintain a ... safe supply of food to meet human ... needs ...."

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

During FY 2000, ARS will

ACCOMPLISHMENTS: A preharvest certification program for Trichinella is needed to assure consumers that the pork they buy and bring into their homes is free of this parasite. ARS scientists, together with the pork industry, developed the certification system based on the knowledge of risk factors, detection methods, and good management practices. Certification requires pork producers to meet certain management criteria that eliminate risk of exposure of pigs to the Trichinella parasite.

IMPACT/OUTCOME: This certification program has been adopted by the pork industry, and APHIS and FSIS are currently developing regulations for management of the program. Certification should also help the USDA establish equivalency agreements with foreign markets regarding the safety of U.S. pork.

ACCOMPLISHMENTS: Unfortunately, this Indicator was not achieved; due in part to the retirement of a scientist critical to the research; the restructuring of the project into two separate ones, and refocusing of the scientist working on the biofilm work to research more associated with intervention strategies.

IMPACT/OUTCOME: An understanding of the microbial ecology of biofilm communities associated with poultry products continues to be of significance to the Food Safety National Program, because of its importance with respect to pathogenicity and food quality. Thus, research in this area will continue, albeit at a slower pace than previously envisaged. Expectation is that the Indicator will require at least another 3 years to be achieved.

ACCOMPLISHMENTS: ARS has made several significant advancements in this area. Research has shown that some chemicals used for sanitizing seeds for sprouting are ineffective against the bacteria and/or they damage the seeds leading to a reduction in sprouting. Treatment of seed for 10 minutes with calcium hypochlorite providing 20,000 ppm of free chlorine was highly effective in reducing specific pathogens. Irradiation studies indicate however, that seeds irradiated to 2kGy can inactive > 99 percent of pathogens without significantly affecting yield, and extend shelf-life of sprouts themselves. Gas-phase application of chlorine dioxide showed significant promise for general use by the produce and seeds industry. ARS studies also showed how to increase the efficiency of hydrogen peroxide treatment for removing attached pathogens from apples. Reductions of > 99.99 percent could be readily obtained.

IMPACT/OUTCOME: Information on the efficacy and efficiency of conventional and experimental methods to decontaminate seeds and produce was conveyed to growers, packers, processors, and the FDA. The research has helped meet the goals established by the FDA for several commodities; for example, a 99.999 percent (5 log) reduction target for unpasteurized apple cider, providing the new treatments can be translated into approved and affordable technology.

ACCOMPLISHMENTS: ARS has developed the information that is necessary to obtain an experimental use permit for testing a product utilizing competitive strains of A. flavus and A. parasiticus to prevent contamination of peanuts with aflatoxin.

IMPACT/OUTCOME: A Georgia company is interested in the technology and is moving forward with efforts to license the technology from ARS. An experimental use permit will allow the product to be field tested in more than 10 acres of peanuts per season in order to determine if it will effectively exclude toxin producing fungi from peanuts grown under commercial conditions, and keep the aflatoxin content under the tolerance required by European markets.

ACCOMPLISHMENTS: Aflatoxins are extremely toxic substances produced by some strains of Aspergillus flavus and most strains of Aspergillus parasiticus. These fungi are ubiquitous and infect many crops including peanuts, corn, cottonseed, and tree nuts, and even some wild plants growing in noncultivated areas. Both the health risks and the reduced profitability of contaminated crops create a need to prevent the formation of aflatoxins. Strains of A. flavus which do not produce aflatoxin may be used to competitively exclude the toxin producing strains prior to boll development. ARS developed the information necessary for EPA to allow the treatment of up to 20,000 acres of cotton to further assess and confirm the value of this product in preventing aflatoxin in cottonseed in a wide variety of environmental conditions and production practices.

IMPACT/OUTCOME: Use of this product to prevent aflatoxin in cottonseed will help assure its safety for animal feed purposes, in particular cottonseed in dairy cattle feed, and will help to maintain the continued profitability of the crop.

ACCOMPLISHMENTS: A method involving a multiplex polymerase chain reaction (PCR) assay was developed to simplify detection and identification of Escherichia coli O157:H7 in foods, and to also permit detection of low levels of bacteria subjected to cold stress. Primers for a plasmid-encoded hemolysin gene (hly₉₃₃), and chromosomal flagella (fliC_h7; flagellar structural gene of H7 serogroup), Shiga toxins (stx₁, stx₂),and attaching and effacing (eaeA)genes were used in a multiplex PCR for co-amplification of the corresponding DNA sequences from E. coli O157:H7. Sensitivity of the assay was #1 CFU/g of food including ground beef and bovine feces: results could be obtained within 24 h.

IMPACT/OUTCOME: In addition to allowing for rapid detection and identification of low numbers of E. coli O157:H7 in foods and other types of samples, the multiplex PCR can markedly reduce the time required for confirmation of isolated colonies since lengthy biochemical, serological, and toxin testing could justifiably be eliminated. This technology can enhance the ability of regulatory agencies and industry in testing for E. coli O157:H7.

ACCOMPLISHMENTS: ARS has developed a MicroFiltration assay (MFA) for Campylobacter using europium-labeled monoclonal antibodies, and two alternative immunomagnetic beads for the direct detection of C. jejuni. Several new approaches for detecting E. coli O157:H7 have been developed, a 96-well microplate method, a light addressable potentiometric sensor method using streptavidin coated magnetic beads, a time-resolved fluorescence assay using europium, and a immunomagnetic electro-chemiluminescent method.

IMPACT/OUTCOME: These methods represent a new approach to extracting, concentrating, and isolating bacterial pathogens directly from foods. Sensitivities of 10 bacteria per ml using a single antibody or mixture of antibodies can be directly achieved and with inclusion of an enrichment step, sensitivity to 1 bacteria per gram food. These technologies will be directly transferred to regulatory agencies for evaluation and inclusion in their protocols.

ACCOMPLISHMENTS: ARS scientists at Ames, Iowa, in collaborative studies with scientists in APHIS and the Wyoming Fish and Game Department, evaluated the clinical effects and immune responses against the Brucella abortus RB51 vaccine strain in various representative nontarget species of the Greater Yellowstone Area (deer mice, ravens, ground squirrels, coyote, moose, pronghorn, bighorn sheep, and mule deer). The scientists demonstrated that strain RB51 can elicit host immune responses and is safe in these nontarget species. Ongoing studies are evaluating the safety of the RB51 vaccine in pregnant black bears as a model for the endangered grizzly bear.

IMPACT/OUTCOME: These studies provided novel information on the clinical safety and effectiveness of the Brucella abortus strain RB51 vaccine for nontarget species in the Greater Yellowstone Area, thus allowing the vaccine to be used to reduce Brucella infections in free-range elk and bison populations to reduce the risk of transmission from wildlife animals to domestic cattle.

ACCOMPLISHMENTS: ARS researchers at Ames, Iowa, demonstrated that hand vaccination of bison calves with Brucella abortus RB51 strain vaccine significantly enhanced protection against brucellosis. In contrast, ballistic vaccination of bison calves was less effective than hand vaccination. ARS scientists at Ames, Iowa, also showed that the RB51 vaccine was safe for deer mice, ravens, ground squirrels, coyoted moose, pronghorn, bighorn sheep, and mule deer. Some of these nontarget species developed immunity, but no clinical signs of disease.

IMPACT/OUTCOME: These studies provided important background information necessary for initiation of a vaccination program for wild bison and elk within Yellowstone National Park and surrounding areas. The finding of superior effectiveness of hand delivery over ballistic administration for vaccination against brucellosis in wildlife provides important knowledge for future development of optimum vaccination strategy against brucellosis in those areas. Further evaluation of the efficacy of Brucella abortus RB51 vaccine delivery methods to wildlife will enhance its practical utilization in the field. Demonstration of the clinical safety and efficacy of the Brucella abortus RB51 vaccine, as shown by studies conducted in collaboration with scientists from ARS at Ames, Iowa, and APHIS, will enhance the feasibility of developing a vaccination program for free-range bison.

ACCOMPLISHMENTS: ARS scientists at Ames, Iowa, evaluated new vaccines for bovine leptospirosis in collaboration with two industrial partners. In the first project, now nearing completion, vaccines designed by Pfizer Corp. were evaluated for their ability to prevent urinary shedding of virulent Leptospira after live challenge. Data from these studies are still being collected. In the second series of vaccine studies, ARS researchers working on the Spirochete Diseases project in collaboration with a scientist at CSL (Australia) evaluated a novel vaccine formulation against bovine leptospirosis. Results from the first phase of these studies suggested that the vaccine prevents urinary shedding of Leptospira in animals challenged with the live virulent hardjo serovar. In the current phase of these studies, ARS scientists are evaluating whether the CSL vaccine is capable of protecting against reproductive failure (abortion, birth of weak offspring) in pregnant cows.

IMPACT/OUTCOME: Although the initial results are promising, further studies are necessary to address important issues relating to the feasibility of this vaccine to prevent Leptospira infection and colonization of the kidney by the hardjo serovar. Yet to be determined is whether this vaccine is capable of protecting against other species of serovar hardjo (3 different species share this designation) as well as other genotypes. Because all current vaccine formulations are serovar specific and provide minimal protective immunity against other antigenic types of Leptospira, future studies are planned to identify cross-protective antigens for second-generation vaccines that will prevent urinary shedding and infection by these additional serovar types.

ACCOMPLISHMENTS: ARS scientists at Athens, Georgia, identified a novel strain of astrovirus isolated from the thymus of Poult Enteritis Mortality Syndrome (PEMS) infected turkeys and sequenced the entire genome of a nonhuman strain of astrovirus. ARS researchers then verified that this purified astrovirus caused PEMS-like disease in naive turkey poults as characterized by growth depression, mortality, enteritis and immunosuppression. A new diagnostic test, RT-PCR, was developed to identify conserved and divergent regions of the astrovirus genome and this test kit detected astrovirus in commercial turkey flocks.

IMPACT/OUTCOME: These studies indicate an important role of the new astrovirus in PEMS-associated pathology in turkeys. The RT-PCR test was transferred to scientists at Virginia Polytechnical Institute and Texas Veterinary Medical Diagnostic Laboratory and is currently being used to detect astrovirus in commercial flocks. This test will provide new ways to understand the pathogenesis of astrovirus infection (and PEMS infection) that will ultimately increase basic knowledge on the interactions between the turkey immune system and virus infections and enable the development of a vaccine against turkey PEMS.