GOAL 1:  ENHANCE ECONOMIC OPPORTUNITIES FOR AGRICULTURAL PRODUCERS

Analysis of Results:  This goal is the focus of ARS’ research related to production agriculture, adding quality and value to agricultural products, new products, biobased products and biofuels.  Under Goal 1, 26 Indicators are aligned under 11 Performance Measures.  Because of the adoption of a new ARS Strategic Plan 2003-2007, the Performance Measures and Indicators have changed dramatically from those last reported in the FY 2002 Annual Performance Report and FY 2003 to 2005 Annual Performance Plan.  In addition, the agency made a policy decision to have fewer and broader Indicators then in past Plans and Reports.  As the National Programs become more internally coherent, the agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in all 26 Indicators was completed or substantially completed during FY 2003.  Eighty-one significant accomplishments are reported below.

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

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  Researchers at Wyndmoor, Pennsylvania, proposed a sulfide-free dehairing protocol that utilizes oxidative chemicals which are safer to handle.  The researchers developed oxidative dehairing protocols for use in a tannery and packing plant (i.e., rapid unhairing) and demonstrated that the quality of the leather obtained is not compromised. 

IMPACT/OUTCOME:  These investigations will benefit the tanning and packing industries by eliminating the use of toxic sulfide and its presence in waste effluent streams.

ACCOMPLISHMENTS:  Fiber quality and bale weight are both reduced by a commonly used cleaning machine known as a saw-type lint cleaner, thus a better machine is needed.  Field testing of a USDA-patented, improved lint cleaner, which reduces fiber loss about 50 percent, was completed.  The cleaner was licensed to Continental Eagle Gin Co., and tested in conjunction with the Cotton Ginning Research Unit in a commercial gin; 23 units are now in use in commercial gins worldwide.  A second new, patented lint cleaner was successfully field tested with 5,000 bales at a commercial gin in Arkansas.  The new lint cleaner is currently available for licensing by private industry.

IMPACT/OUTCOME:  These improved units will increase bale weight by 8 pounds or $6 per bale.  The new lint cleaner increased bale weight by 10 pounds per bale and produced even cleaner cotton.

ACCOMPLISHMENTS:  Japan wants to import rice straw from the United States for cattle feed but demands that the straw be free of disease causing agents.  A scientist at the Southern Regional Research Center has invented a process for sterilizing rice straw and is entering into a cooperative research and development agreement (CRADA) with an industry partner to pursue commercialization.  Research is underway to make the process continuous and scale it up for a commercial operation. 

IMPACT/OUTCOME:  This process will allow the U.S. to export rice straw to Japan which currently imports two million tons of forage other than that from rice. 

develop new or improved methods to measure or predict quality.

ACCOMPLISHMENTS:  Scientists in Athens, Georgia, worked cooperatively with MEDCO in St. Louis, Missouri, to field test a detection procedure known as near infrared spectroscopy for identifying cotton stickiness before cotton reaches critical fiber processing steps and developing remediation strategies during harvesting and in the gin.  An instrument was developed that uses the near infrared region to measure stickiness in cotton in the gin and spinning plant.

IMPACT/OUTCOME:  This accomplishment will affect the industry at every level and provide gins and spinning plants with the information needed to identify sticky bales and implement measures to remediate the problem.

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

ACCOMPLISHMENTS:  Researchers at Wyndmoor, Pennsylvania, applied tocopherol (vitamin E) and its derivatives to the grain layer of leather.  Leather treated with tocopherol showed significant improvement in mechanical strength and softness and, more importantly, increased strength retention and color fading resistance against ultra-violet radiation and heat. 

IMPACT/OUTCOME:  The research results may benefit the leather industry in the production of high quality, durable upholstery leather, thereby contributing to the viability of the domestic tanning industry and its markets.

ACCOMPLISHMENTS:  In collaboration with scientists at the USDA Forest Service, Forest Products Laboratory, ARS scientists at the U.S. Dairy Forage Research Center in Madison, Wisconsin, examined the adhesive properties of the residues of biomass fermentations produced by bacteria that produce a sticky cell coating during fermentation. They showed that the fermentation residues produced by several Ruminococcus bacterial strains could partially replace phenol-formaldehyde resins (at up to 73 percent on a dry weight basis) as an adhesive for plywood construction.  They also demonstrated adhesive properties of the fermentation residue of alfalfa fiber, a more industrially relevant substrate.

IMPACT/OUTCOME:  These residues have potential as adhesives or adhesive extenders in wood construction applications.

ACCOMPLISHMENTS:  In response to the need to utilize surplus commodity starches and add value to underutilized agricultural fibers, researchers at the Western Regional Research Center developed novel wheat starch- and straw-based industrial packaging materials.  Wheat starch was incorporated into starch-based single-use food wraps, plates and trays, allowing CRADA partner, EarthShell, Inc., to create industrial packaging products that are less expensive and more flexible than their present starch-based industrial materials. More specifically, basic knowledge of the structure/properties relationship of wheat starch and its associated trace proteins was applied to allow EarthShell to cut material costs by more than 50 percent.

IMPACT/OUTCOME:  This breakthrough will enable starch-based packaging to take a more competitive position in the $8 billion single-use packaging market, and will potentially improve the rural economy by expanding the non-food markets for wheat starch and fiber.

ACCOMPLISHMENTS:  Broiler litter and broiler cake were dried, milled, pelletized, steam activated, and evaluated for adsorption of several different metal ions by scientists at the Southern Regional Research Center (SRRC), New Orleans, Louisiana, in cooperation with scientists at Tulane University, New Orleans, Louisiana.  These activated carbons absorbed more metal ions than any commercial activated carbon or most commercial cation exchange resins.  A patent application on this technology is currently being prepared.  Several poultry containment facility operators, a fertilizer company, AgriRecycle, in Delaware and Resource Conservation and Development Coordinators in Southern Mississippi are interested in this new technology.

IMPACT/OUTCOME:   Activated carbon production from broiler litter and broiler cakes can add value to animal waste and provide an efficient and cost effective metal ion adsorbent that could compete with commercial carbons in the marketplace.

ACCOMPLISHMENTS:  Two types of modified cotton gauze were designed, prepared, and assayed by scientists at the SRRC in New Orleans, Louisiana, in collaboration with The Wound Healing Institute, Medical College of Virginia.  A Phase I Small Business Innovation Research/National Institutes of Health (SBIR/NIH) grant was funded for work with Tissue Technologies to place the two types of gauze in development.  Subsequent success of this work has resulted in filing a grant proposal for a Phase II SBIR/NIH grant which would create funding to place the gauzes in manufacturing and clinical trials.  This grant proposal has recently received a high score and is likely to be funded. 

IMPACT/OUTCOME:  The impact of this research will benefit the consumer, providing high-tech wound dressings, and the cotton farmer and American textile industry by increasing value-added cotton product sales in the United States.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  Scientists at Beltsville, Maryland, developed a rapid, automated procedure for non-destructively identifying scab-damaged wheat, based on near infrared (NIR) reflectance.  Using hundreds of hard red spring wheat samples, they identified a broad absorption band whose slope can be used as a classifier at 95 percent or better accuracy.

IMPACT/OUTCOME:  This technology, which can provide high speed commercial sorting, has potential for application by plant breeders and Federal grain inspectors.

ACCOMPLISHMENTS:  An Alkaline Water Retention Capacity (AWRC) test has been applied at the Soft Wheat Quality Laboratory (SWQL) in Wooster, Ohio, to predict the pastry baking quality of soft wheat test lines for 50 years.  Selection pressure over that time has reduced the response of contemporary soft wheat test lines to the test.  The SWQL studied the effect on pastry prediction of replacing the AWRC with a regression of protein content, kernel softness, and (50 percent) sucrose retention capacity, and has implemented the new prediction into SWQL's developmental test line evaluation program.  The new pastry quality prediction has proven to be considerably superior to the previous procedure. 

IMPACT/OUTCOME:  Soft wheat breeders now have more confidence in the SWQL’s soft wheat pastry baking score at up to three generations earlier than previously possible.  Millers and bakers can rely on this prediction of baking quality by employing the same principle without having to perform as much costly test baking.

ACCOMPLISHMENTS:  Engineers at Manhattan, Kansas, found that the data generated by the Perten SKCS 4100, an instrument developed by ARS and used by many grain millers and handlers, can be processed for detecting live and dead internal insects in whole wheat kernels.  The software has been transferred to a commercial miller for field testing.  Other grain processors throughout the country have expressed an interest in this technology.

IMPACT/OUTCOME:  This technology provides the wheat milling and handling industries, as well as the Food Grain Inspection Service (FGIS), a rapid and automated method for detecting internal insects in wheat kernels. 

will develop functional food ingredients and/or products.

ACCOMPLISHMENTS:  Years of cooperative work between the Citrus and Subtropical Products Laboratory, Winter Haven, Florida, and the University of Florida Gulf Coast Research and Education Center, Bradenton, Florida, has resulted in the planned release of a premium high lycopene tomato selection with superior flavor.  This was accomplished through many seasons of analytical flavor and sensory analyses of tomato lines, including those with high lycopene, resulting in a final selection this year.

IMPACT/OUTCOME:  This new line should boost Florida's struggling tomato industry by giving growers a horticulturally acceptable, flavorful tomato with added health benefits that should compete well in the domestic market.

ACCOMPLISHMENTS:  Researchers at Wyndmoor, Pennsylvania, in collaboration with a university partner (Chungnam University, Republic of Korea), discovered a new method to produce structured lipids.  To accomplish this, they developed a process that uses a combination of physical fractionation and enzymatic steps; a patent was granted on this technology. 

IMPACT/OUTCOME:  Successful adoption of this technology will provide hypercholesterolemic individuals with products that have beneficial cholesterol lowering effects.

ACCOMPLISHMENTS:  New food ingredients were prepared at NCAUR, Peoria, Illinois, that have useful textural qualities related to food calorie replacement properties.  Specific food products were prepared having increased nutritional qualities.  Technology transfer was completed with the creation of a new company, Fibergel Technologies.   

IMPACT/OUTCOME:  Worldwide dietary improvements and an increased foreign market will result from products developed by ARS from this new technology.

ACCOMPLISHMENTS:  Breads containing wheat, soy flours, and other ingredients were prepared at NCAUR, Peoria, Illinois, and evaluated by a trained taste panel to measure the level of undesirable "beany" flavor of soy versus good grain flavors.  Whole wheat breads containing up to 30 to 40 percent soy flour having very little beany flavor were prepared by adding highly active yeast, ascorbic acid, and sugar. 

IMPACT/OUTCOME:  The U.S. baking industry, food pantries, and American public should benefit from such inexpensive, nutritious, heart-healthy bread.

ACCOMPLISHMENTS:  Economical rice bread products are needed for consumers with celiac sprue disease and other disorders that prevent consumption of gluten-containing grain (e.g., wheat) products.  A scientist at the Southern Regional Research Center has developed formulations for rice bread using a home bread machine.  A prototype rice bread was developed with desirable flavor and texture. 

IMPACT/OUTCOME:  The new formulations will benefit those with celiac sprue and other intestinal diseases by allowing the consumer to readily and economically (ingredient cost $0.30) prepare a gluten free bread.

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

ACCOMPLISHMENTS:  Scientists at Kearneysville, West Virginia, and Beltsville, Maryland, developed a new strategy for controlling postharvest decay without the use of fungicides.  The results showed that a combination of heat treatment and various biocontrol agents significantly reduced postharvest fungal decay of apples. 

IMPACT/OUTCOME:  This control strategy could potentially be used by the apple industry to reduce the use of postharvest fungicides.

ACCOMPLISHMENTS:  ARS scientists at Athens, Georgia, in cooperation with engineers from Stork-Gamco Equipment Company, conducted studies using a European style electric stimulator designed to deplete energy from poultry muscle fiber and allow earlier breast muscle removal while optimizing the texture of the cooked meat.  The European style stimulator was successfully tested on the pilot plant processing line at the Russell Research Center.

IMPACT/OUTCOME:  The Stork-Gamco stimulator can be used in either European or U.S. processing plants to significantly reduce processing costs while optimizing the textural characteristics of the ready-to-eat breast meat.

ACCOMPLISHMENTS:  Working with the Dried Fruit Association (DFA) of California, researchers at the Western Regional Research Center (WRRC) have developed a method to detect the pits and remove them from the process stream.  A prototype device was assembled implementing the method.

IMPACT/OUTCOME:  Once adapted for a processing plant environment, this device could reduce the number of pits in the final product, increasing product quality.

ACCOMPLISHMENTS:  Working with the California Cooperative Rice Research Foundation, researchers at WRRC developed a method to detect the fissures in rice without removing the shell.  This method was adapted to form the basis for an automated sorting device.

IMPACT/OUTCOME:  Once completed, this device could assist rice breeders in developing new strains of rice that are resistant to fissuring.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at the Wheat, Sorghum, and Forage Research Unit, Lincoln, Nebraska, found that corn grain yield was significantly reduced when corn stover from previous crops was removed. 

IMPACT/OUTCOME:  ARS scientists documented the need to more carefully determine the potential consequences of corn stover removal before the practice is recommended as a way to provide feedstock for biorefineries.

ACCOMPLISHMENTS:  ARS scientists with the U.S. Dairy Forage Research Center in Madison, Wisconsin, evaluated switchgrass populations for agronomic and biofuel traits and found phenotypic variability to be closely associated with the hardiness zone (defined by minimum cold temperatures) and eco-region (defined by historic native vegetation) from which a population was collected.

IMPACT/OUTCOME:  This is the first quantitative data to show that switchgrass properties are affected by the environment in which the plants developed, information that will be useful in determining the potential for using switchgrass as a biofuel crop and in identifying optimal germplasm for breeding, conservation, and production.

ACCOMPLISHMENTS:  The U.S. Dairy Forage Research Center in Madison, Wisconsin, in a specific cooperative agreement with the University of Wisconsin-Madison showed that harvesting corn stover at higher moisture level (~40 percent moisture) and storing the stover in plastic film under non-ensiling conditions economized field operations, increased the rate and efficiency of harvesting, and reduced storage losses of dry matter to under five percent.

IMPACT/OUTCOME:  The research has resulted in a more efficient and economical process for harvest and storage of corn stover to be used as a feedstock for production of ethanol and coproducts.

ACCOMPLISHMENTS:  ARS scientists with the Natural Resource Management Research Unit in Mandan, North Dakota, found that optimal pH and temperature conditions for establishment of big bluestem and switchgrass were 20 C, pH = 7 and 30 C, pH = 6, respectively.  Though very difficult to establish, indiangrass was found to produce three to five times more biomass; biomass of higher quality than either switchgrass or big bluestem.

IMPACT/OUTCOME:  Management technology was devised establishing of warm season grasses on marginal lands and buffer strips that will aid in effective production of biomass either for forage or for conversion to biofuel.

ACCOMPLISHMENTS:  Engineers at the Cotton Production and Processing Research Unit, Cropping Systems Research Laboratory in Lubbock, Texas, conducted studies in cooperation with the USDA-ARS Environmental and Plant Dynamics Research Unit in Phoenix, Arizona, to evaluate performance and emissions of pellet stoves when burning cotton byproduct (COBY) pellets produced from cotton gin trash.  COBY and COBY/Guayule pellets burned in commercial pellet stoves were found to have acceptable exhaust gas emissions and heating values equivalent to other pellet stove fuels. 

IMPACT/OUTCOME:  The findings show that pelletizing cotton gin trash converts a waste product into a reliable and economical heating fuel and provides a source of income for cotton gins.

develop technology that improves the efficiency and economics of ethanol production from biomass.

ACCOMPLISHMENTS:  ARS researchers in the Crop Conversion Science and Engineering Unit at the Eastern Regional Research Center (ERRC) in Wyndmoor, Pennsylvania, discovered the location of the phytosterols contained in corn fiber (a coproduct of ethanol production from corn grain) and developed a process to purify and lower the cost of extracting the healthy, phytosterol rich oil from the corn fiber.

IMPACT/OUTCOME:  This research results in a method of producing corn fiber oil that can make it an economically viable coproduct, and that in turn, can reduce the net cost of ethanol production. 

ACCOMPLISHMENTS:  ARS engineers in the Crop Conversion Science and Engineering Unit at ERRC in Wyndmoor, Pennsylvania, created a base-case state-of-the-art model that can be used to compare the efficiency and economics of conventional ethanol production processes with innovative new unit processes.  They found that recent technology developments can save about 10 cents per gallon of ethanol produced. 

IMPACT/OUTCOME:  The impact of ARS’ research is a model whereby small companies, which design, build, and operate dry-grind corn-to-ethanol plants, can lower their fuel ethanol production costs.

ACCOMPLISHMENTS:  ARS scientists in the Fermentation Biotechnology Research Unit at NCAUR in Peoria, Illinois, developed a process to improve the taste of corn gluten meal.  Spaghetti containing up to 5 percent of this modified corn gluten meal was judged acceptable by a trained taste panel. 

IMPACT/OUTCOME:  This technology provides food products with improved nutritional value to consumers while creating new markets for ethanol coproducts.

ACCOMPLISHMENTS:  By using directed molecular evolution, ARS researchers in the Bioproduct Chemistry and Engineering Research Unit at the Western Regional Research Center in Albany, California, found new enzymes for conversion of starch to glucose that are nearly 50 times more reactive than the original enzymes. 

IMPACT/OUTCOME:  Enzymes that enable the conversion of starch to glucose at lower temperatures (cold hydrolysis), will improve energy efficiency and reduce the cost of fuel ethanol production.

ACCOMPLISHMENTS:  ARS scientists in the Crop Conversion Science and Engineering Research Unit at ERRC in Wyndmoor, Pennsylvania, have developed enzymatic milling procedures adapted to the dry grind ethanol process for the purpose of recovering additional high value coproducts.

IMPACT/OUTCOME:  Enzymatic milling should improve the efficiency of dry-grind ethanol production, and by increasing the value of coproducts, should improve its economics.

develop technology to improve biodiesel quality and performance and the efficiency and economics of biodiesel production.

ACCOMPLISHMENTS:  ARS scientists of the Fats, Oils, and Animal Coproducts Research Unit at the ERRC in Wyndmoor, Pennsylvania, in collaboration with the Center's cost engineer developed quantitative computer models for use in estimating the effects that facility design, production process, and feedstock have on the cost of biodiesel production.

IMPACT/OUTCOME:  The computer models, which were developed, should eliminate trial and error and help increase the efficiency of biodiesel production.

ACCOMPLISHMENTS:  ARS scientists of the Fats, Oils, and Animal Coproducts Research Unit in Wyndmoor, Pennsylvania, developed and optimized a process to produce biodiesel directly in oilseeds.  The process eliminates the need to use the EPA regulated organic solvents required in the current biodiesel production process.

IMPACT/OUTCOME:  ARS scientists developed an environmentally friendly process that reduces the cost of producing biodiesel.

ACCOMPLISHMENTS:  ARS scientists with the Food and Industrial Oil Research Unit at the NCAUR, Peoria, Illinois, developed a spectroscopic method for determining the fatty acid composition of biodiesel fuel.  Results with this new method are in agreement with measurements made with the slower, more expensive chromatographic method normally used. 

IMPACT/OUTCOME:  Research has resulted in a quicker and less expensive measurement technology to determine fatty acid composition and to assess the quality of biodiesel fuel.

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

Indicators:

During FY 2003, ARS will

develop information on measures of animal well-being, strategies to reduce stress, and systems to improve food animal production.

ACCOMPLISHMENTS:  ARS conducted research on toll like receptors and acute phase proteins at West Lafayette, Indiana, and tumor necrosis factor-alpha at Columbia, Missouri, that demonstrated the importance and ability of these components of the immune system to withstand stress and disease when animals are distressed.

IMPACT/OUTCOME:  This accomplishment is useful to livestock producers to reduce mortalities and reduce susceptibility of distressed animals to disease and the loss of production from stress.

ACCOMPLISHMENTS:  ARS and Mississippi State collaborators demonstrated that higher air velocity improves performance of broilers over 28 days of age.

IMPACT/OUTCOME:  This accomplishment provides the basis for poultry producers to produce larger-sized broilers more efficiently.

ACCOMPLISHMENTS:  ARS scientists at Clay Center, Nebraska, found respiration rate the best indicator of heat-stress for both cattle and swine.

IMPACT/OUTCOME:  A “livestock safety monitor” has been built and the design was transferred to customers for early warning of high temperature events.

conduct research contributing to development of genetically improved aquatic stocks; biologics, medicines, and practices to improve fish health; and research to enhance economic and environmental sustainability.

ACCOMPLISHMENTS:  ARS initiated a breeding project for North American Atlantic salmon at Orono/Franklin, Maine, established the basis for a breeding plan for rainbow trout at Leetown, West Virginia, and increased knowledge of genes in the genomes of channel catfish and rainbow trout at Stoneville, Mississippi, and Leetown, West Virginia.  The USDA 103 select line of channel catfish released to the industry in 2001 was further improved for multiple economically important traits.

IMPACT/OUTCOME:  These genetic improvement accomplishments of aquatic species contribute to further enhancement of economically important traits in the USDA 103 line of catfish and represent progress toward developing improved lines of rainbow trout and North American Atlantic salmon.

ACCOMPLISHMENTS:  ARS developed molecular methods to clarify misidentified Flavobacterium columnare at Stuttgart, Arkansas, and rapid detection of Flavobacterium columnare in pond water and eggs at Auburn, Alabama.  A data package was completed on copper sulfate for FDA approval so that copper sulfate can be used for treating sick catfish in earthen ponds.

IMPACT/OUTCOME:  These fish health accomplishments will provide fish farmers with an additional approved medicine to combat disease.

ACCOMPLISHMENTS:  ARS demonstrated that the capability of trout to utilize barley was heritable at Aberdeen, Idaho.  Research was conducted on alternative nutrient sources for hybrid striped bass at Stuttgart, Arkansas, and for spawning flounder and black sea bass at Ft. Pierce, Florida.

IMPACT/OUTCOME:  These nutrition accomplishments contribute to reducing the reliance of aquaculture on fish meal and improve the sustainability of fish farming.

ACCOMPLISHMENTS:  An ARS partner, Freshwater Institute, Shepherdstown, West Virginia, demonstrated a commercially relevant scale recirculating fish farm system continuously produced a ton of marketable coldwater finfish per week, showing a practical land-based alternative to ponds, net pens, or raceways.

IMPACT/OUTCOME:  Domestic and international commercial fish farms producing Atlantic salmon smolts, Artic char, ornamental fish, tilapia, rainbow trout, walleye, yellow perch, and hybrid striped bass have adopted production systems designs and altered management based on this recirculation research.

develop scientific information that contributes to improved efficiency and environmental stewardship of food animal production systems.

ACCOMPLISHMENTS:  Research conducted at the U.S. Dairy Forage Research Center at Madison, Wisconsin, found that reducing the amount of dietary rumen degraded protein of dairy cows from 13.7 to 9.5 percent did not affect milk or protein yield but did result in a 12 percent decrease in urinary nitrogen excretion. 

IMPACT/OUTCOME:  ARS research found that feeding rumen degraded protein in excess of the amount needed by rumen microbes leads to excess urinary nitrogen excretion, contributing to pollution of water and air.  Application of a lower (10 percent) dietary rumen degraded protein requirement in dairy cattle offers a means for reduction in nitrogen excretion. 

ACCOMPLISHMENTS:  ARS researchers at Clay Center, Nebraska, measured plasma urea nitrogen concentrations, a quantitative assessment of inefficient crude protein utilization, and determined that this trait was moderately heritable and not genetically correlated to growth in swine. 

IMPACT/OUTCOME:  ARS researchers have found that swine diets are over formulated with nitrogen crude protein to ensure no deficiencies and accommodate genetic variation in crude protein requirements and utilization.  Plasma urea nitrogen concentrations may be an exploitable quantitative trait to develop animals with greater ability to efficiently utilize dietary crude protein and minimize nutrient excretion.

ACCOMPLISHMENTS:  ARS scientists at the Fort Keogh Livestock and Range Research Laboratory, Miles City, Montana, have found that the overall efficiency of beef production systems can be improved by changing the calving season from spring to summer, thereby allowing better matching of seasonal forage production to animal needs while simultaneously improving rangeland health and productivity.

IMPACT/OUTCOME:  Results of ARS’ research will result in integrated rangeland-based beef production systems that are more economically and environmentally sustainable.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland, revealed differences in the expression of over 430 genes in swine embryos between days 11 and 12 of pregnancy using serial analysis of gene expression techniques. 

IMPACT/OUTCOME:  Swine exhibit high rates (less than 30 percent) of early embryonic mortality in the first two weeks of pregnancy.  This effort is the first step in identifying genes and their function that are critical for porcine embryo development, ultimately leading to increased reproductive rates per female.

ACCOMPLISHMENTS:  Research in the Growth Biology Laboratory at Beltsville, Maryland, showed that expression of the genes encoding fatty acid synthase and acetyl coenzyme A in the liver is altered when young broiler chickens are switched from a high protein to lower protein grower diet. 

IMPACT/OUTCOME:  Although changes in dietary protein levels change metabolism during the starter to grower periods in broiler chickens, there is little information concerning the time and course of the process to adaptation.  Regulating these genes by diet offers the poultry industry the means to selectively reduce unwanted fat accretion in birds.

ACCOMPLISHMENTS:  In research conducted at the U.S. Meat Animal Research Center (MARC), Clay Center, Nebraska, long-term genetic selection utilizing estimated breeding values has resulted in an annual increase in ovulation rate and twinning rate of 5 and 3 percent, respectively.  The 2003 twinning rate in this herd is now in excess of 55 percent with a 48 percent increase in total weaning weight per cow calving. 

IMPACT/OUTCOME:  This research clearly shows that alteration of the reproductive rate, the most limiting factor affecting efficiency of beef production, is possible.

develop technologies leading to improved marketability of animal products.

ACCOMPLISHMENTS:  ARS meat scientists at Clay Center, Nebraska, compared a system (the MARC Beef Classification System) developed in their lab to two noninvasive systems for identifying beef that could be guaranteed tender on-line in beef processing plants.

IMPACT/OUTCOME:  Profitability of the U.S. beef industry is limited by the inability to consistently produce lean, highly tender products.  The MARC Beef Classification System was identified as the only system accurate for industry use and has been subsequently recommended to companies for implementation by the National Cattlemen’s Beef Association.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  Researchers at MARC, Clay Center, Nebraska, identified two DNA markers in the u-calpain gene that are associated with differences in tenderness of beef products and have assisted in the successful validation of these markers by cattle producers in two large scale tests.

IMPACT/OUTCOME:  Tenderness of beef has consistently been identified by all sectors of the beef industry as the highest priority issue for enhancing the value of beef products.  It is estimated that approximately 25 percent of steaks are less tender than desired.  Tests for these markers are now available and are being used to select against the negative impacts of u-calpain on tenderness.   

ACCOMPLISHMENTS:  Research at MARC, Clay Center, Nebraska, has identified swine chromosomes 10 and 14 to harbor important quantitative trait loci (QTL) affecting ovulation rate, nipple number, plasma FSH, and age at puberty.  Comparative maps of these two chromosomes were developed to allow identification of positional candidate genes in these QTL regions.

IMPACT/OUTCOME:  The availability of these comparative maps with the human and mouse genomes will allow candidate genes to be sequenced to study association with phenotypic performance for these traits.

ACCOMPLISHMENTS:  Dual-energy X-ray absorptiometry (DEXA) was utilized in research at the Beltsville Agricultural Research Center, Beltsville, Maryland, to determine that an increase in lean mass was initiated between 27 and 34 days of age in genetically enhanced mice expressing the disruption of the myostatin gene.   

IMPACT/OUTCOME:  Genetic disruption in the myostatin gene interferes with myostatin function promotes muscle growth and reduction in fat in food animals.  This work further elucidated the effect of myostatin gene and how it may be used to improve lean tissue production in food animals.

ACCOMPLISHMENTS:  Researchers at Beltsville, Maryland, have successfully identified and cloned portions of the ghrelin gene in both chickens and turkeys, revealing a high degree of similarity to its mammalian counterpart with expression in stomach tissue of chickens during periods of feed deprivation and re-feeding.

IMPACT/OUTCOME:  Feed costs are the single most important cost in meat animal production, approaching 75 percent of total costs in poultry production.  These results suggest a functional role for the ghrelin gene in regulating feed intake in poultry.

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

ACCOMPLISHMENTS:  ARS scientists at Clay Center, Nebraska, and Beltsville, Maryland, have worked collaboratively with the International Bovine BAC Mapping Consortium (includes labs in the United States, Canada, United Kingdom, New Zealand, Australia, Brazil, and France) and the Michael Smith Genome Science Centre, Vancouver, British Columbia, to develop a bovine bacterial artificial chromosome (BAC) map that includes fingerprints of 300,000 BAC clones and 75,000 BAC-end sequences.

IMPACT/OUTCOME:  Development of a BAC map dramatically reduces the time and expense necessary for identifying genes affecting important traits, improves the effectiveness of marker-assisted selection, and anchors assembled genomic sequence to chromosomes.  This physical map will be used as the scaffold for the sequencing of the bovine genome at Baylor College of Medicine and by ARS scientists in linking the physical, radiation hybrid (in collaboration with Roslin Institute), and USDA linkage maps. 

ACCOMPLISHMENTS:  ARS scientists at Clay Center, Nebraska, and Beltsville, Maryland, have successfully enhanced the genetic linkage maps for swine and cattle to include over 1,000 expressed sequence tags (genetic markers within expressed genes). 

IMPACT/OUTCOME:  The availability of a “gene-based” map allows the integration of all available linkage, radiation hybrid, and physical map information into consensus maps for identification of genes and their function in previously identified important chromosomal regions.  Additionally, comparative approaches between swine, cattle, and human genome information can now be fully utilized.

ACCOMPLISHMENTS:  Statistical software was developed by researchers at Clay Center, Nebraska, to identify three genomic regions affecting ovulation and twinning rate in cattle and incorporate DNA marker genotype information into estimating breeding value for these traits. 

IMPACT/OUTCOME:  This bioinformatic tool will be instrumental in the implementation of marker-assisted selection programs in the beef and dairy industries.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists in the Animal Improvement Programs Laboratory at Beltsville, Maryland, developed a methodology to allow genetic evaluation of fertility in young females and for calving ease in cows and have recently implemented new genetic evaluations for both traits. 

IMPACT/OUTCOME:  The dairy industry has identified decreased cow fertility as a major economic concern in recent years.  This advancement will allow dairy breeders to make genetic improvements in reproductive efficiency of the Nation’s dairy herd.

ACCOMPLISHMENTS:  ARS researchers in Brooksville, Florida, completed several years of intensive data collection on tenderness in Brahman sire lines.  In cooperation with scientists at Louisiana State University, these results have been used to produce the first sire genetic evaluation for carcass traits in this economically important breed.

IMPACT/OUTCOME:  Brahman-based cattle are well suited for use in the subtropical United States because of their adaptation to adverse conditions.  However, this is at least partially negated by lower market value for these cattle due to lowered meat quality associated with decreased tenderness.  This development will allow selection for improved carcass quality in subtropically-adapted germplasm.

ACCOMPLISHMENTS:  Five sheep breeds were compared at the U.S. Meat Animal Research Center, Clay Center, Nebraska, revealing superior productivity of the Romanov breed due to greater conception rate, prolificacy, and longevity compared to Finnsheep, Dorset, Texel, and Montadale breeds.

IMPACT/OUTCOME:  Comparison of sheep breeds provides critical information to guide the appropriate use of breeds in commercial crossbreeding systems.  Broader use of crossbred ewes incorporating Romanov germplasm offers breeders a means to increase the efficiency of commercial sheep production.

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

ACCOMPLISHMENTS:  Researchers at Beltsville, Maryland, and East Lansing, Michigan, developed a novel method for removing glycerol from frozen/thawed chicken semen. 

IMPACT/OUTCOME:  Glycerol is the most effective cryoprotectant for poultry semen, but unfortunately is a contraceptive in the hen.  This development is significant for it allows the immediate banking of semen from at-risk genetically valuable and/or unique chicken lines.

ACCOMPLISHMENTS:  The National Animal Germplasm Program was formally established in 1999 to protect the U.S. livestock industry by preserving genetic diversity in food animal species.  In 2003, the total number of breeds in the repository increased to 42 (a 147 percent increase).  In addition to 40 lines of chickens, the total number of units of semen increased by 337 percent (from 16,000 to 70,000).  The number of cattle and sheep embryos stored increased to 689. 

IMPACT/OUTCOME:  Breeding populations of livestock have narrowed considerably in their genetic diversity over the past several decades prompting concern regarding adequate levels of genetic variability.   Several economically important breeds, including the Holstein, are now considered secure.  This progress provides increased security of farm animal genetic resources and long-term maintenance of animal genetic variation.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  Modern genetic methods make identification, modification, and utilization of disease resistant genes much faster than before.  ARS scientists are very active in identifying, locating, and modifying resistant genes so they can be introduced into new varieties.  Examples include the following:  resistance to bacterial angular leaf spot disease in strawberry (Beltsville, Maryland); resistance to postharvest decay organisms in peach (Kearneysville, West Virginia); resistance to late blight in potato (Madison, Wisconsin); resistance to various pathogens in papaya (Hilo, Hawaii); resistance to Sclerotinia blight in peanut (Stillwater, Oklahoma); resistance to blast in rice (Stuttgart, Arkansas); resistance to soybean cyst nematode in soybean (Beltsville, Maryland); resistance to Fusarium head blight in barley (Madison, Wisconsin and Fargo, North Dakota) and wheat (Albany, California).

IMPACT/OUTCOME:  The resistance genes, which include those introduced by both breeding and genetic engineering will protect the next generation of crop varieties to be used in American agriculture.

ACCOMPLISHMENTS:  Accurate yield estimates are critical for growers, juice processors, and wineries to make decisions on crop thinning, harvest, and the management of processing facilities.  The current standard method is based on hand sampling and provides only limited information and static estimates.  ARS scientists at the USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon (located at Prosser, Washington), in collaboration with faculty at Washington State University, have developed an automated method of measuring trellis wire tension and vibration frequencies to estimate grapevine yield.

IMPACT/OUTCOME:  This new automated method improves production efficiency by saving labor and providing nearly continuous estimates of fruit mass.  It has the potential to enhance production management strategies for hundreds of thousands of acres of vineyards in the United States.

ACCOMPLISHMENTS:  There is an increasing incidence, severity, and negative economic impact of a physiological abnormality of pecan, termed "mouse-ear."  Scientists at the USDA-ARS Southeastern Fruit and Tree Nut Research Laboratory in Byron, Georgia, investigated the problem.  The disorder was discovered to be due to a nickel (Ni) deficiency.

IMPACT/OUTCOME:  This discovery will allow for development of improved nutrient management strategies that will improve orchard profitability and likely reduce applications of nitrogen, zinc, and copper in pecan production.

ACCOMPLISHMENTS:  The single most important pollination management concern of U.S. alfalfa seed producers is a chalkbrood disease that kills immatures of the alfalfa leafcutting bee.  This bee pathogen has been notoriously difficult to culture, and existing tests for spore germination give highly variable results.  ARS scientists at the Bee Biology and Systematics Laboratory, Logan, Utah, collaborating with scientists at the Biosciences Research Laboratory, Fargo, North Dakota, recently discovered that lipids act to stimulate the germination of chalkbrood spores.  Very few fungi are known to require lipids for germination or growth, however, the alfalfa leafcutting bee has unusually large stores of lipids.

IMPACT/OUTCOME:  These results will be used to develop a reliable and standardized chalkbrood spore viability test that will form the basis of investigations leading to management options for beekeepers designed to disrupt the disease cycle in commercial scale populations of the alfalfa leafcutting bee.

ACCOMPLISHMENTS:  Honeybee colonies are threatened by an assortment of parasites, pathogens, and pests that affect their well-being.  Research was conducted to evaluate the role of parasitic mites in transmitting honeybee viruses.  Scientists at the Bee Research Laboratory in Beltsville, Maryland, demonstrated conclusively that parasitic mites of honeybees are capable of transmitting viruses from infected bees to uninfected bees.  Using molecular techniques, researchers were able to calculate the transmission efficiency from mites to bees and demonstrate that non-infected mites can acquire virus by sharing the same cell with one or more infected mites.

IMPACT/OUTCOME:  The immediate impact of this research is a better understanding of how bee viruses are spread between bees and the importance of mite control.

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

ACCOMPLISHMENTS:  ARS scientists at Columbia, Missouri, and researchers at Iowa State University have developed a central web interface for maize (corn) research called MaizeGDB (maize genetics and genomics database).  Up-to-date genetic and genomic data are delivered from the site, along with software tools, literature references, and instructions about how to access the data.

IMPACT/OUTCOME:  This “one-stop” site for maize researchers ensures that the most recent genetics and genomics discoveries are widely accessible to maize crop improvement and genetics programs worldwide.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at Phoenix, Arizona, showed that a photosynthetic rate at high temperatures is controlled by heat sensitivity of the enzyme, Rubisco activase, which is necessary for plants to take up and incorporate carbon dioxide.  Plants with different temperature tolerances have Rubisco activase sensitivities to temperature that mirror those of the plants.  In related research at Urbana, Illinois, ARS scientists have tested other potential sites of heat damage to photosynthesis and found that those sites do not account for heat sensitivity.  At Lubbock, Texas, ARS scientists are describing molecular processes in plants that restore cell functions after heat damage.  They have also identified mutations that reduce the plant’s ability to protect itself against heat damage.

IMPACT/OUTCOME:  The identification of the primary “subcellular” sites of heat injury is a major scientific advance that should enable breeders to improve crop productivity at high temperatures more rapidly.

ACCOMPLISHMENTS:  Ethanol production, providing more than 1 percent of automotive fuel needs in the United States, still represents only a very small fraction of the demand for renewable energy.  Cornstarch is a relatively high value “starting material” for ethanol production.  Utilization of low value cellulosic sources, such as corn stalks, is hindered by the presence of lignin, which complicates ethanol production.  ARS scientists at Albany, California, have now demonstrated that a regulatory gene in corn controls the amount of lignin deposited in the stalk.  Plants with reduced levels of this gene make more lignin and plants with increased levels make less lignin.

IMPACT/OUTCOME:  Manipulation of lignin offers the first chance to control the amount of this gene in stems or branches, thereby possibly providing a mechanism for efficiently using waste cellulosic materials for ethanol production. 

ACCOMPLISHMENTS:  Fruits and vegetables contain many minerals, vitamins, and other compounds that are needed for health.  ARS is pursuing several ways to improve the nutritional quality of these foods.  At Ithaca, New York, ARS scientists have focused on several natural mutations that increase concentrations of lycopene and other carotenoids in tomato and on a gene that stimulates ripening and development of flavor and nutrient compounds.  In Houston, Texas, ARS scientists found that a broad spectrum of genetic lines of pea have a 10-fold range of essential mineral concentrations, in some cases considerably higher than the standard garden pea.  In both cases, these discoveries can form the starting point for breeding more nutritious vegetables.  In Beltsville, Maryland, ARS scientists have genetically engineered a calcium-binding protein into potatoes and have shown that it can be useful in increasing the calcium content of this widely consumed food which is deficient in calcium.  In Oxford, Mississippi, ARS scientists, in cooperation with University of Idaho scientists, genetically engineered blueberries to contain high amounts of resveratrol believed to be a dietary cancer preventative.

IMPACT/OUTCOME:  The next steps in improving these fruits and vegetables are to test for bioavailability of the nutrients and to breed for higher nutrient levels using those genetic lines with increased bioavailable nutrients.

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

ACCOMPLISHMENTS:  Many consumers demand measures to promote the biosafety of genetic engineering; ARS is responding in several ways.  One important goal is the confinement of genetically engineered gene products, when appropriate, to specific tissues of the plant or to specific times in the plant’s development, rather than in the whole plant throughout its life.  This specificity is provided by specialized gene promoters that respond to specific stimuli.  At Beltsville, Maryland, research has identified promoters that respond to viral diseases.  At Albany, California, ARS scientists have identified promoters that are specific for various tissues.  At Kearneysville, West Virginia, ARS scientists have demonstrated that a leaf specific promoter in apple trees does not allow expression of transgenes in fruits.  At Madison, Wisconsin, a promoter has been developed that is specific for the “hull” (seed covering tissues) in barley.  At Lubbock, Texas, ARS scientists have “taken apart” the process by which viruses take over plant gene expression and have identified characteristics that make promoters effective.

IMPACT/OUTCOME:  These studies are leading to the development of highly specific, effective gene promoters which will limit genetically engineered products to only those sites within the plant and times when they are needed.

ACCOMPLISHMENTS:  In Albany, California, ARS scientists have tested a novel recombination system that enhanced the specificity of gene incorporation into the host genome.  The system provides precise integration in a model test system, that minimizes disruption of the DNA, and in which the gene is heritable.  This provides the basis for research to apply this novel system to crop plants.  Also at Albany, California, ARS scientists have successfully tested a new system to “stack” separate genes end-on-end in the host genome, so that they can be incorporated and passed on to the next generation together.

IMPACT/OUTCOME:  This stacking technology is expected to be broadly used in creating plants with several desirable characteristics, including having all the genes respond to the same genetic controls.

ACCOMPLISHMENTS:  The European Union has adopted regulations that will prohibit genetically engineered materials that are resistant to an antibiotic. At Lubbock, Texas, ARS scientists have developed a simple procedure to replace the use of antibiotic resistant genes during genetic engineering.

IMPACT/OUTCOME:  This new procedure will enable creation of transgenic plants without antibiotic resistance which will help maintain exports of agricultural products to Europe.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  Corn varieties differ genetically, but until genetic variation in the genes for starch quality and protein are identified at the molecular level, it will be difficult to improve corn for specific cooking purposes and nutritional value.  ARS scientists at Raleigh, North Carolina, have characterized the molecular variation for seven genes controlling starch quality and protein content.  These genes are associated with pasting quality, starch to protein ratio, and environmental effects on grain quality.

IMPACT/OUTCOME:  These new findings can help design new corn varieties for specialized cooking purposes and improved nutritional value.

ACCOMPLISHMENTS:  ARS scientists at Beaumont, Texas, in cooperation with the U.S. Rice Foundation have developed molecular markers for rice cooking quality, grain aroma, and disease resistance.  These markers, which are more accurate than standard breeding methods, may enable breeders to select simultaneously for several economically important traits.

IMPACT/OUTCOME:  Providing these molecular markers to U.S. rice breeders will help bridge the technology gap for many conventional breeding programs and result in new specialty rice desired by consumers.

ACCOMPLISHMENTS:  Drought is the greatest single limitation to soybean yield in the United States. No drought tolerant cultivars, however, are available for commercial production.  ARS scientists at Raleigh, North Carolina, coordinated a national program to develop drought tolerant soybean varieties and, through DNA marker analysis, discovered genes that partially control drought resistance in new drought tolerant soybean lines.

IMPACT/OUTCOME:  Incorporation of genes that mediate drought tolerance in commercial soybean cultivars will provide significant protection against U.S. production losses due to inadequate rainfall.

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

ACCOMPLISHMENTS:  Highly detailed genomic maps may accelerate the genetic improvement of soybeans and help better position U.S. producers in competitive global oilseed markets.  ARS scientists at Beltsville, Maryland, and Ames, Iowa, in collaboration with the Universities of Nebraska, Utah, and the Monsanto Company, developed and used nearly 2,000 DNA markers to create a new soybean genome map that encompasses all 20 soybean chromosomes.

IMPACT/OUTCOME:  The newly constructed map is an essential tool for discovering genes affecting important soybean traits, for marker assisted selection to identify superior breeding lines and for basic studies aimed at the cloning of genes.

ACCOMPLISHMENTS:  Vegetable pigments may enhance human health as well as consumer appeal, which may increase vegetable consumption.  Manipulating pigment content through breeding requires an understanding of the genetic control for such content.  Until now, the genes that control orange color in carrot roots had not been placed on the carrot genetic map.  ARS scientists at Madison, Wisconsin, mapped 19 genes on the carrot genome for orange, red, yellow and white color.  Most genes were clustered in three groups along the carrot chromosomes so apparently a few key genetic regions control root color.

IMPACT/OUTCOME:  This information is critical for improving color and health promoting properties of carrots through plant breeding.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  Genetic stocks, specialized germplasm lines with specific genetically-characterized traits (often mutants), comprise a vitally important tool for plant genetic and genomic research.  The USDA/ARS Maize Genetics Cooperation-Stock Center (the world’s largest and highest quality collection of maize genetic stocks) in Urbana, Illinois, distributed a record number of stocks (15,000+) to fill a number of requests (more than 300).

IMPACT/OUTCOME:  These stocks have enabled research worldwide that will enhance understanding of maize as a biological organism which could ultimately lead to maize crop improvement.

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

ACCOMPLISHMENTS:  Rust diseases pose serious challenges for dry bean production.  Merlot, a small red dry bean, developed by the USDA-ARS Sugarbeet and Bean Research Unit, East Lansing, Michigan, in cooperation with Michigan State University and Washington State University, is an upright, short-vine (Type IIA), full season cultivar with consistent and desirable canning quality.  It is the first small red commercial cultivar with resistance to bean rust disease.  Merlot improves the seed characteristics, canning quality, and disease resistance of the small red market class.

IMPACT/OUTCOME:  Grower interest in Merlot is considerable as determined by the quantity of foundation seed ordered through commercial channels.

ACCOMPLISHMENTS:  Existing and emerging plant pathogens pose serious economic threats to U.S. oilseed production and profitability.  ARS scientists at Fargo, North Dakota, developed an efficient and effective molecular marker technique, termed TRAP (targeted region amplified polymorphism) that takes advantage of the 60,000+ ESTs (expressed sequence tag) available for sunflower.  This technique was used to assess the genetic variability of 16 perennial sunflower species, and hybrids between wild perennial sunflower and cultivated sunflower lines.  New resistant lines are not strongly susceptible to the new broomrape race F in Spain and are resistant to a new broomrape race G in Turkey.  Virus resistance also was transferred from three wild annual sunflower lines into cultivated sunflower.  ARS scientists at Stoneville, Mississippi, deployed similar genomic approaches to develop soybeans resistant to charcoal rot (one of the most important pathogens attacking southern soybean), and to identify genes for resistance to that disease.  ARS scientists at Tifton, Georgia, developed more effective methods for evaluating and using peanut germplasm collections.  By characterizing peanuts’ genetic variability, they developed a small group of peanut lines that collectively encompassed much of the genetic diversity of the entire U.S. peanut germplasm collection, thereby enabling more rapid discovery of novel valuable genes and traits.

IMPACT/OUTCOME:  This research will help advance and expand the capacity of U.S. oilseed breeders to breed disease resistant lines in several different crop species.

GOAL 2:  SUPPORT INCREASED ECONOMIC OPPORTUNITIES AND IMPROVED QUALITY OF LIFE IN RURAL AMERICA

The major thrusts of ARS’ mission are to conduct research that ensures high quality, safe food and other agricultural products; assess the nutritional needs of Americans; sustain a competitive agricultural economy; and enhance the natural resource base and the environment.  In performing these activities, ARS helps provide economic opportunities for rural citizens, communities, and society as a whole.  While ARS research has a large and very positive impact on rural America, the agency has chosen to organize its research program around the other four programmatic USDA/REE/ARS Strategic Plan goals.

GOAL 3:  ENHANCE PROTECTION AND SAFETY OF THE NATION’S AGRICULTURE AND FOOD SUPPLY

Analysis of Results:  This is the focus of ARS’ research related to food safety and the security of the U.S. agricultural production system (crop and livestock protection).  Under Goal 3, 20 Indicators are aligned under 8 Performance Measures.  Because of the adoption of a new ARS Strategic Plan 2003-2007, the Performance Measures and Indicators have changed dramatically from those last reported in the FY 2002 Annual Performance Report and FY 2003 to 2005 Annual Performance Plan.  In addition, the agency made a policy decision to have fewer and broader Indicators then in past Plans and Reports.  As the National Programs become more internally coherent, the agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in all 20 Indicators was completed or substantially completed during FY 2003.  Seventy-one significant accomplishments are reported below.

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

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland, developed genetic-based detection and differentiation methods for Trichinella and Toxoplasma in pigs and evaluated methods for the inspection of pigs and horses for Trichinella at slaughter.

IMPACT/OUTCOME:  The methods that have been developed are critical to: (1) establishing and maintaining, in cooperation with the Agricultural Marketing Service (AMS), an export market inspection program for horses, (2) maintaining a certification program for these parasites in pork (modeled on the National Trichinae Certification Program), and (3) achieving an extremely low incidence of Trichinella and Toxoplasma parasites in swine, which has significantly increased consumer acceptance of pork products.

ACCOMPLISHMENTS:  ARS scientists at Clay Center, Nebraska, generated monoclonal antibodies as accurate diagnostic reagents for the detection and characterization of shiga toxin producing E. coli (STEC) and Salmonella.  Other ARS scientists at Ames, Iowa, developed a rapid, sensitive, and specific fluorescent-based (TaqMan) polymerase chain reaction (PCR) test for detecting E. coli O157:H7 and other STEC in bovine feces and tissues.

IMPACT/OUTCOME:  Several of these antibodies have been formatted for diagnostic tests, including one currently sold by Meridian BioSciences, are widely used in the U.S. meat industry and in human clinical tests to identify the presence of STEC.  The PCR tests will provide the basis for rapid and specific detection of E. coli O157:H7 and related pathogens at various stages of pre- and postharvest operations.  Since these tests can be completed within 8 to 12 hours, potentially contaminated bovine food products can be identified before they are shipped to retailers and consumers.

ACCOMPLISHMENTS:  ARS scientists at Clay Center, Nebraska, demonstrated that STEC O157 is endemic in U.S. cattle herds and occurs at high fecal prevalence rates in summer months.  The scientists also isolated STEC O157 from multiple pest fly species trapped on livestock farms and confirmed the clonality of livestock and pest fly bacterial isolates from a given farm, that is, they came from the same source.  They documented that high pest fly and livestock fecal prevalence of STEC O157, O111, and O26 and Salmonella at agricultural fairs are similar to that found in commercially reared livestock.  They also demonstrated that finished beef cattle have a high prevalence of STEC O157 in both their oral cavity and their hide.

IMPACT/OUTCOME:  These findings demonstrate that because of the ubiquitous nature of STEC O157, eliminating exposure will be almost impossible.  They also establish the need for a live animal treatment to kill the pathogens prior to slaughter, and the need to target non-fecal sources as important for both within herd livestock transmission and in-plant carcass contamination.

ACCOMPLISHMENTS:  Through the National Antibiotic Resistance Monitoring System (NARMS), which is located in the ARS facility at Athens, Georgia, scientists determined the antibiotic resistance of over 35,000 Salmonella isolates and lesser numbers of Campylobacter, Enterococcus, and E. coli.  Other ARS scientists at College Station, Texas, showed that ionophore antibiotics in cattle had no effect on foodborne pathogens or their antimicrobial susceptibility, and that certain antibiotic growth promoters do not select for particular species of Enterococcus (commensal bacteria) and do not alter normal bacterial populations in animals.

IMPACT/OUTCOME:  As the only national program for surveillance of resistant bacteria in animals in the United States, NARMS provides critical information regarding the prevalence and distribution of anti-microbial resistant bacteria in support of the Public Health Action Plan to Combat Antimicrobial Resistance of HHS/CDC and FDA.  The NARMS information is also essential to both animal producers and developers of animal drugs to help assure continued drug availability.  The finding that certain growth promoting drugs for livestock production do not increase antibiotic resistance in common pathogens helps identify basic mechanisms and selective pressures involved in the evolution and transfer of antibiotic resistance genes, thus helping to maintain both the availability of these drugs to producers and safe meat for consumers.

ACCOMPLISHMENTS:  ARS scientists in Athens, Georgia, described a variety of environmental sources of Campylobacter spp. during epidemiological studies conducted in the United States and Iceland. In laboratory studies they analyzed levels of Campylobacter translocation to different lymphoid and reproductive organs in inoculated breeder hens and roosters utilizing molecular detection techniques.

IMPACT/OUTCOME:  This research has demonstrated that just one method will never be sufficient to control Campylobacter in poultry, and multiple target interventions will be needed to reduce the incidence of contamination in production flocks.  Campylobacter may be stable in rooster semen and the bacteria may be carried to lymphoid organs.  This is a source of potential transmission among poultry flocks in addition to environmental sources.  Producers of hatching eggs can now work to eliminate this source of contamination.

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

ACCOMPLISHMENTS:  ARS scientists in Peoria, Illinois, developed rapid, easy to perform, and quickly learned fluorescence polarization immunoassays for measuring the mycotoxin, fumonisin, and zearalonone in maize and deoxynivalenol in wheat.

IMPACT/OUTCOME:  These assays offer environmentally friendly alternatives to traditional instrumental methods and ELISAs.  They will be useful screening tools for both State and Federal government agencies and industry to determine mycotoxin contamination.

ACCOMPLISHMENTS:  ARS scientists in Athens, Georgia, determined that Fusarium verticillioides is transmitted from seed to corn plant to seed as an endophyte, and the fungus grows more readily on reproductive and immature tissues than old vegetative tissue.  No deleterious effects on corn yield were found in a 3-year study and there were only infrequent negative effects on plant growth under ideal field conditions.  However, under stress fumonisin accumulation is accelerated.

IMPACT/OUTCOME:  This information on fungal transmission provides a basic understanding of the very complex fungal endophyte/crop interaction which is necessary to develop effective strategies to prevent mycotoxin accumulation in crop plants.  This knowledge will also help reduce investment and utilization of ineffective control strategies for fumonisin mycotoxins produced by Fusarium verticillioides.

ACCOMPLISHMENTS:  ARS scientists in Peoria, Illinois, developed the data and formulated a computer program that will give useful predictions for fumonisin and aflatoxin occurrence in most corn hybrids in most years.  They demonstrated that Bt corn often had significantly reduced levels of mycotoxins compared to non-Bt corn, but that the degree of benefit was dependent on the timing and makeup of the insect pest complex in the particular crop year.

IMPACT/OUTCOME:  This computer program provides farmers with a valuable tool for creating a comprehensive mycotoxin management program.  It has been made available to producers in an easy to use format.  This information is critical in predicting the usefulness of genetically engineered corn and in providing corn producers with information on the specific benefits that they can expect from planting.

ACCOMPLISHMENTS:  ARS scientists at New Orleans, Louisiana, developed a cloned DNA library of A. flavus which was prepared and sequenced for The Institute for Genomic Research (TIGR) using expressed sequence tag (EST) technology to identify unique genes that the fungus uses to accomplish all its biological and physiological functions.

IMPACT/OUTCOME:  This gene library will allow deciphering of how environmental factors affect the fungus, which genes are turned on during the plant-fungus interaction and aflatoxin production, as well as fungal survival in the field environment.  It will provide identification/characterization of a complex set of genes involved in fungal virulence, aflatoxin formation signaling pathways between the fungus and the environment, and fungal reproduction/survival, and processes which need to be understood if fungal infection and aflatoxin production in crops is to be prevented.

ACCOMPLISHMENTS:  ARS scientists at New Orleans, Louisiana, developed atoxigenic strain technology to reduce aflatoxin contamination in cottonseed and the associated costs to industry.  Working in Phoenix, Arizona, they established baseline levels of the atoxigenic biological control fungus AF36 which provides a basis for determining the influence of AF36 on natural mycoflora and fungal communities when applied over large expanses.  They compiled all of the information and interpreted the data which was used to obtain EPA approval of AF36, and developed a commercial scale production system for this fungal biological control agent.  Specific technologies were transferred to industry and the Arizona Cotton Research and Protection Council, including simple strain identification, starter culture procedures, scale-up procedures, quality control procedures, and methods to assess efficacy.

IMPACT/OUTCOME:  Over 30,000 acres of crops will be treated in collaboration with ARS in Arizona in 2004, and 5,000 acres will be treated in Texas where some areas have severe problems with aflatoxin.  Up to $18 million in annual cottonseed losses by Arizona industries alone could be prevented by use of atoxigenic strain technology as a biocontrol for aflatoxin.  Prevention of the losses throughout the million plus acres of cotton and corn in affected parts of south Texas would have an even greater effect.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland, and Athens, Georgia, working with industry and university scientists have developed and are now validating a low cost, nonhuman intervention, computer controlled, on-line automated system for broiler carcass inspection that operates in the slaughter plant at typical processing speeds.  The system operates at greater than 98 percent accuracy and can identify diseased or damaged broilers and surface contamination (feces), critical to protecting the consumer from a potential source of inedible food.  The work is consistent with ARS research in Ames, Iowa, utilizing similar technology to detect surface contamination on beef carcasses.

IMPACT/OUTCOME:  By implementing this technology, FSIS could redeploy thousands of inspectors to HACCP inspection tasks.  The broiler industry would financially gain billions of dollars in discounted value.  A hand held version of the technology, approved by FSIS, is already in use by the beef industry.

ACCOMPLISHMENTS:   ARS scientists at Albany, California; Athens Georgia; Beltsville, Maryland; Peoria, Illinois; and Wyndmoor, Pennsylvania, working in collaboration with various universities have developed several rapid, high throughput methods to enumerate bacteria and toxins in foods and other types of samples.  The new procedures allow high throughput processing of samples, minimize space utilization, streamline processing time/labor, incur very low expenses, and have excellent accuracy and precision.  The technologies can be further modified and incorporated into an automated (robotics) sample processing scheme to increase efficiency.

IMPACT/OUTCOME:  Development of this technology can have significant impact on the ability of FSIS and the Food and FDA’s ability to increase sampling of locally produced and imported foods.

ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, developed a rapid and simple, quantitative and confirmatory method of analysis for beta-lactam antibiotics.  The new approach can also be expanded to include other antibiotic drugs of concern eventually allowing ARS to devise the most effective and efficient overall analytical scheme to monitor chemical residues in foods. 

IMPACT/OUTCOME:  Development of this technology will have a significant and immediate impact for FSIS and FDA, which have a critical problem with the differentiation between the beta-lactam antibiotics, ceftiofur, and penicillin in their current regulatory monitoring program.

ACCOMPLISHMENTS:  ARS scientists at Albany, California and Athens, Georgia, are part of a European Union funded (EU) international consortium, bringing together nine participants from six EU countries, South Africa, and the United States to develop international “gold standard” procedures for the routine isolation and detection of emerging Campylobacter bacteria from food, water, environmental, and clinical samples.  The bacterium is a significant national and international public health risk.  It is the cause of human bacterial associated gastroenteritis worldwide, responsible for 500 million cases of diarrhea each year.  The bacteria can also cause reactive arthritis and the neurological disease Guillain-Barre which can result in paralysis and death.

IMPACT/OUTCOME:  The procedures which will be developed will have application both in epidemiological and inoculation studies in determining the prevalence and assessing the survival of these pathogens throughout the food chain.  Factors that affect pathogenicity will be determined, practical control strategies will be developed, and data will be produced which will allow development of a risk assessment model.

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

ACCOMPLISHMENTS:  ARS scientists in Clay Center, Nebraska, in association with industry and universities in the National Alliance for Food Safety and Security, investigated the problem of seasonal variations in the prevalence of E. coli O157:H7, Salmonella, and non-O157 Shiga toxin-producing E. coli (STEC) during beef production and processing.  The studies indicated a marked seasonal effect on the prevalence of these pathogens, emphasized the efficacy of antimicrobial interventions used by the industry, and implicated hides as a major source of pathogens on beef carcasses.

IMPACT/OUTCOME:  Regulatory action agencies, in particular FSIS, and industry will use this information to develop risk assessments based on seasonal prevalence, and to support the development of new antimicrobial strategies for preventing hide-to-carcass transfer of pathogens.

ACCOMPLISHMENTS:  ARS scientists at Athens, Georgia, in association with industry and university researchers, determined that soiled transportation coops, and carcass defeathering with subsequent airborne contamination are not critical control points in HACCP plans for broiler slaughter and processing.

IMPACT/OUTCOME:  Although cage costs and space requirements make routine storage of transportation coops between uses impractical for industry, these data justify the storage of soiled cages during periods of non-use.  That airborne contamination is not a significant issue will allow future studies to focus on other potentially critical sources of pathogens, such as feces and ingesta.  Sources of contamination of poultry are a critical issue for both FSIS and industry.

ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland, in cooperation with industry, have developed and are now validating the use of bacteriophages (highly specific bacterial viruses) to kill bacterial pathogens in packaged fruits, vegetables, and meats.

IMPACT/OUTCOME:  Implementing the use of bacteriophages as an intervention strategy in certain pre-packaged food products has the potential to significantly reduce the number of outbreaks of foodborne disease, thus decreasing the public health risk.  Use of bacteriophage as an intervention strategy has the support of industry and regulatory agencies.  A national and international patent has been filed for its use.

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

ACCOMPLISHMENTS:  ARS, in association with The Institute for Genomic Research (TIGR), sequenced, annotated, and compared the genome of four L. monocytogenes strains.  In association with university collaborators, the National Alliance for Food Safety and Security, and the Institute of Food Research, Norwich, United Kingdom, ARS scientists also developed genomic microarrays for L. monocytogenes and E. coli O157:H7.

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

ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, in association with national and international advisors from other Federal agencies (FSIS/FDA), industry, and various universities, have developed the next generation of the Pathogen Modeling Program (PMP) software.  The data behind the models and other predictive microbiology records are now available through an on-line relational database, called ComBase, developed in association with the Institute of Food Research in Norwich, United Kingdom, and the United Kingdom Food Standards Agency.  The ComBase web site (http://wyndmoor.arserrc.gov/combase/ currently contains more than 30,000 data sets.

IMPACT/OUTCOME:  The PMP software is utilized by national and international regulatory agencies and various food industries to control the presence and levels of bacterial pathogens in food.  Microbial models assist in identifying specific food processing steps that can serve as critical control points in HACCP systems.  At the international level, predictive models are an integral part of microbial risk assessment used to support food safety measures adopted by member countries of the World Trade Organization.  ComBase is a unique database and on-line resource, impacting the development and validation of new microbial models, providing the food industry with an efficient location of specific food microbiology data, and allowing access to improved models that consider the complex nature of pathogen-food interactions.  The Chief Executive of the United Kingdom Food Standards Agency described ComBase as “an exemplar of the way that governments and the research community can successfully work together to help improve the safety of food products” while the Co-Director of the Australian Food Safety Center stated “the ComBase initiative will be a watershed in the evolution of predictive modeling and its widespread application.”

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

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS has taken the lead in coordinating an international effort (involving researchers worldwide) to sequence the tick genome (more than one billion nucleotides) and organizing the sequencing of Boophilus microplus.  In 2003, the first library of 20,000 clones of expressed genes was produced.  It is now being analyzed.

IMPACT/OUTCOME:  No tick or related arthropod has yet been sequenced.  The economic and health significance of ticks makes this a priority project.  By the end of 2004, it is estimated that 60,000 clones of expressed genes will have been isolated.

ACCOMPLISHMENTS:  Seven regions of the DNA of Mycobacterium paratuberculosis (Johne’s disease) that stimulate protective responses and one that exacerbates infection were identified. Sequencing was completed on two of the putative protective regions; a microarray system of gene pooling was developed and is ready for testing. 

IMPACT/OUTCOME:  The identification of M. paratuberculosis genes that are associated with host protection is an important milestone in the development of an effective molecular vaccine to control Johne’s disease.

ACCOMPLISHMENTS:  The Brucella abortus (Brucellosis) genome sequencing project was used to identify variable regions in the genome in an effort to differentiate Brucella abortus strains resulting in the development of a polymerase chain reaction (PCR) assay.

IMPACT/OUTCOME:  The Brucella abortus PCR assay developed by ARS will allow Federal (APHIS) and State action and regulatory agencies to determine the source of a brucellosis infection in a cattle herd (including wildlife or other cattle) and help determine if a brucellosis outbreak is from single or multiple sources.

investigate the pathogenesis of two important animal pathogens to better understand tissue tropism, disease transmission, virulence, and the identification of phenotypic markers.

ACCOMPLISHMENTS:  ARS scientists conducted and published the first pathogenesis studies of high and low virulence Bovine Viral Diarrhea Virus (BVDV) and generated tag sequence libraries for sequential analysis of gene expression (SAGE libraries) in infected cells in vitro.

IMPACT/OUTCOME:  The BVDV SAGE libraries, developed by ARS, provide a tool to study the interaction of high and low virulence viruses with host cells and identify the factors that control virulence which will enable the development of intervention strategies to limit the effects of viral infection.

ACCOMPLISHMENTS:  ARS obtained 18 different Porcine Reproductive and Respiratory Syndrome (PRRS) virus isolates from disease outbreaks in the Midwest and sequenced the NSP2 genes of these viruses to examine variations that may correlate with disease expression.  Recombinant antigens have been developed and immunity to individual PRRS virus proteins evaluated from naturally infected swine from around the country.  Researchers conducted kenetic analysis studies of host-cell gene expression in response to PRRS virus infection using cDNA microarrays.  Studies to date indicate a number of responsive genes that increase in expression while others decrease in expression as a result of PRRS virus infection. 

IMPACT/OUTCOME:  The sequence analysis of a number of PRRS virus isolates will lead to an understanding of the host-virus interactions in the field and identification of viral genes responsible for induction of a protective immune response.

ACCOMPLISHMENTS:  ARS conducted functional genomics studies of selected Marek's disease viral genes to better understand the mechanism by which the virus causes changes in infected chickens.  Several virus preparations with specific deletions or changes in selected genes were developed and the effects compared to unaltered viruses.  Results to date indicate that the 132 base pair nucleic acid repeats are non-essential for Marek’s Disease Virus (MDV) replication in cell culture, and chickens and viruses lacking these repeat sequences are still pathogenic.  Furthermore, the putative MDV oncogene called “meq” could be deleted but was found to be essential for the transformation of lymphocytes in infected chickens.  It was also found that the pp38 gene in the vaccine virus, Rispens, functions identically to the pp38 gene in the very virulent Md5 virus.

IMPACT/OUTCOME:  The functional genomics studies of selected Marek's disease viral genes are enhancing our knowledge of the mechanisms of virus replication and virulence, which is an important milestone for developing a new class of vaccines against this very important poultry disease.

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

ACCOMPLISHMENTS:  ARS collected swabs from the species of wild birds previously found to have Avian Pneumovirus (APV) antibodies.  Avian Pneumovirus was identified from 12 of the sampled wild birds and it was determined through sequence analysis of the glycoprotein, matrix, and fusion genes that the wild bird viruses are closely related to viruses found in domestic poultry.

IMPACT/OUTCOME:  The identification of APV in wild birds and its relationship to viruses found in domestic poultry indicate the potential for wild birds to spread APV infections in areas of the United States where the virus is currently not found in poultry.

ACCOMPLISHMENTS:  ARS identified the viral shedding patterns of Malignant Catarrhal Fever (MCF) in both adolescent and adult sheep.  The data indicate that nasal shedding is the major mode of sheep-associated MCF virus transmission among domestic sheep and that the adolescents are by far the heaviest shedders of virus for other species.

IMPACT/OUTCOME:  The kinetics of the shedding patterns of MCF in adolescent sheep appear to be a unique biological phenomenon without precedent, and definition of the virus-host mechanisms underlying this behavior should lead to new knowledge on the potential ways viruses can interact with hosts.

ACCOMPLISHMENTS:  ARS scientists established that the tonsils of deer are a reliable early indicator of infection and established a valid method for detecting Chronic Wasting Disease (CWD) in live deer.  This test is suitable for use in surveillance of deer in highly populated areas, where hunting is not allowed but artificial feeding may increase disease prevalence.  In addition, scientists have established that the dorsal motor nucleus of the vagus nerve is the earliest site of PrP-CWD accumulation in mule deer.  This research identifies the tissue to be selected for diagnostic testing in hunter harvest surveys.

IMPACT/OUTCOME:  The CWD pathogenesis studies conducted by ARS in deer and mule deer have resulted in the identification of tissue samples that has enabled the development of effective diagnostic procedures for live animals.

Indicators:

During FY 2003, ARS will identify one genetic marker and one gene from food animals that can be used to identify animals with disease resistant traits.

ACCOMPLISHMENTS:  ARS developed a DNA-based test for the Avian Leukosis Virus (ALV) receptor gene known as TVB (a tumor necrosis factor receptor-related protein).  This genetic test can distinguish if a chicken carries TVB alleles that confer resistant to ALV subgroups B or E, which are some of the most prevalent ALV types in the field.

IMPACT/OUTCOME:  The TVB DNA-based assay developed by ARS allows poultry breeders to accurately select for chickens for resistance to specific ALVs, which will enhance egg production and decrease mortality losses.

Indicators:

During FY 2003, ARS will

discover and develop two novel diagnostic technologies to detect and control diseases that impact animal health, animal production, and trade.

ACCOMPLISHMENTS:  ARS scientists developed serotyping polymerase chain reaction (PCR) primers designed from variable regions of the Listeria monocytogenes genome.  Three primer sets were used in conjunction with a previously described Division III primer set in order to classify 122 Listeria monocytogenes strains into five serotype groups.

IMPACT/OUTCOME:  The Listeria monocytogenes serotyping PCR primers developed by ARS will enhance the ease and accessibility of the “gold standard” serological classification system that permits differentiation between important food-borne strains.

ACCOMPLISHMENTS:  Poult Enteritis Mortality Syndrome (PEMS) is a highly infectious disease of young turkeys.  Currently, no rapid or sensitive laboratory tests are available to identify the viruses involved in PEMS production.  A rapid and sensitive real time reverse transcriptase polymerase chain reaction test (RRT-PCR – a biotechnology test to detect genes) was developed to detect turkey astrovirus type-2, one of the major viruses involved in production of PEMS in turkeys.

IMPACT/OUTCOME:  The development of a real time RT-PCR diagnostic test for PEMS offers substantial advantages over the older standard RT-PCR technology, including improved accuracy, speed, and sensitivity.

develop and evaluate one new delivery system that will enhance the value of disease prevention.

ACCOMPLISHMENTS:  ARS scientists developed a self propelled vaccinator capable of vaccinating 75,000 chickens in 7½ minutes.  The research has resulted in a machine that is capable of uniformly and consistently delivering Mycoplasma gallisepticum (MG) vaccine to 75,000 chickens in less than 8 minutes as compared to 50 minutes for conventional methods.

IMPACT/OUTCOME:  The impact of the MG vaccinator developed by ARS is that producers using the available commercial vaccines can administer MG vaccines quicker and more consistently and uniformly to pullets reducing labor by 60 percent.

ACCOMPLISHMENTS:  Lyme disease is transmitted by ticks that multiply on whitetail deer.  ARS scientists have patented and licensed to the National Lyme Disease Foundation the “4-Poster,” a novel device shown to control ticks on wild deer.

IMPACT/OUTCOME:  Because of its feral epidemiology, Lyme disease is especially difficult to control.  The “4-Poster” will reduce Lyme disease in the Northeast by controlling the vector in the forest before it has contact with humans.

discover two immunological reagents and one novel vaccine formulation to control a high priority infectious disease.

ACCOMPLISHMENTS:  ARS scientists discovered an adenovirus-vectored H3N2 Swine Influenza Virus (SIV) vaccine with novel characteristics:  it prevents shedding and it is efficacious in the presence of maternal antibodies.

IMPACT/OUTCOME:  With H3N2 SIV, the first time an efficacious vaccine can be developed for the period when pigs are the most vulnerable.  Unfortunately, because of potential intellectual property/patent infringement associated with the adenovirus vector selected for this research, this novel vaccine technology cannot be transferred to a commercial partner for full development.

ACCOMPLISHMENTS:  ARS discovered and produced three monoclonal antibodies to study host immune responses in chickens and have transferred them to diagnostic firms for further development.  Several of these monoclonal antibodies can now be used to assess the immune status of chickens vaccinated with different infectious agents.  The results to date indicate that these monoclonal antibodies are useful in the identification of lymphocyte subpopulations and macrophages in the tissues and the peripheral blood from chickens infected with microbial agents or vaccinated with the viral vaccines.

IMPACT/OUTCOME:  The discovery of immunological reagents is paramount to understanding the mechanisms of protective immunity and is a critical milestone in diagnostic and vaccine discovery.

ACCOMPLISHMENTS:  ARS has discovered and characterized the gene for soluble CD14 which binds and neutralizes endotoxins responsible for mastitis.  The gene was cloned and recombinant bovine (rbo)-CD14 protein was successfully produced and evaluated.  Intraperitoneal injection of rboCD14 together with endotoxin reduced the fatality rate in mice.  Preliminary studies indicate that intramammary injection of soluble rboCD14 is 100 percent effective in preventing mastitis by Escherichia coli in lactating dairy cows.

IMPACT/OUTCOME:  The discovery of CD14 will potentially lead to a product that for the first time can be used effectively to treat and prevent mastitis caused by E. coli.

ACCOMPLISHMENTS:  Solanum glaucophyllum is a plant that contains the active form of vitamin D.  ARS scientists have investigated the utility of this plant in the prevention of subclinical hypocalcemia (milk fever) in periparturient dairy cows and discovered that when used in combination with diets high in anions (chloride), the incidence of subclinical hypocalcemia in dairy cows can be reduced.

IMPACT/OUTCOME:  Identifying the medical benefits of using Solanum glaucophyllum in feed will offer further opportunities to dairy farmers in avoiding complications due to hypocalcemia, such as displaced abomasum, retained placenta, and mastitis.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists have generated greenbug resistant wheat.  Greenbug resistance, bred into a new, hard red winter wheat germplasm line, is now available for use in developing new varieties of the crop.  Greenbug is a major pest of wheat and plagues cereal crops in both the northern and southern Great Plains.  Attacks by the tiny, sap-sucking pest cost wheat farmers $250 million annually in crop losses and pesticide expenses.  Resistant wheat is a cornerstone of integrated approaches to fighting the greenbug.  But new cultivars are always needed because new biotypes of the pest can emerge to overcome them.  The new line which is designated N96L9970, was developed by ARS scientists in Stillwater, Oklahoma.

IMPACT/OUTCOME:  The new greenbug-resistant wheat germplasm line, N96L9970, should provide wheat breeders with a source of genes conferring resistance to five greenbug biotypes:  B, C, E, G, and I. ARS scientists are taking seed requests at the ARS’ Wheat, Sorghum and Forage Research Unit in Lincoln, Nebraska.

ACCOMPLISHMENTS:  ARS is developing new root weevil and disease resistant citrus rootstocks.  The three new citrus rootstocks developed by ARS scientists in Fort Pierce, Florida, have emerged as strong candidates to help the U.S. citrus industry combat key diseases, such as Phytophthora and the citrus root weevil.  The new rootstocks are called US-897, US-942 and US-802.  Collaborators are an important part of ARS’ research effort, helping to test new rootstocks for resistance to diseases and pests.  A quality rootstock can defend itself against these diseases and pests while producing a high yield of quality fruit sustained over a long period of time that is up to 50 years.

IMPACT/OUTCOME:  The three citrus rootstocks developed by ARS and resistant to citrus root weevil and Phytophthora diseases are at least three to four years away from commercialization, but they have performed well in initial tests in damp coastal soil for combating the Diaprepes citrus root weevil and Phytophthora.

ACCOMPLISHMENTS:  The sunflower stem weevil, a pest of cultivated sunflower, causes severe crop losses in the Central Plains sunflower production areas of Colorado and Kansas.  ARS scientists in Fargo, North Dakota, in cooperation with scientists at the University of Colorado and Kansas State University, have evaluated sunflower hybrids and other accessions for resistance to the sunflower stem weevil using field nurseries located in both western Colorado and eastern Kansas.  The impact of altered planting dates to reduce weevil damage was also a part of the research.

IMPACT/OUTCOME:  Sunflower accessions evaluated for resistance to the sunflower stem weevil had as high as 70 percent less weevil larvae in the stalks.  Populations of larvae in the stalks were reduced as planting was delayed.  Integrated pest management schemes that incorporate resistant sunflower hybrids and delayed planting dates can effectively reduce weevil damage, thus preventing yield losses to growers.

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

ACCOMPLISHMENTS:  Losses due to stripe rust have been severe for U.S. wheat producers.  ARS scientists at Pullman, Washington, have identified new, emerging races of the stripe rust pathogen.  Also, they have evaluated over 12,000 wheat and barley accessions from the ARS National Small Grain Collection for rust resistance. 

IMPACT/OUTCOME:  Wheat and barley accessions with stripe rust resistance can now be used as breeding sources to develop more stripe rust resistant wheat and barley varieties.

ACCOMPLISHMENTS:  ARS scientists at Madison, Wisconsin, have been working to locate a disease resistant gene in order to permit studies on fine mapping of the wild potato (Solanum bulbocastanum), which has resistance to late blight disease.  Using molecular markers, ARS scientists in collaboration with the University of Wisconsin, were able to determine the location of the resistant gene in the potato genome.  The gene was located and cloned. 

IMPACT/OUTCOME:  The impact of identifying disease resistant genes in wild potato will be a plant resistant to late blight, thus eliminating the need for fungicide spraying.

ACCOMPLISHMENTS:  Wheat is vulnerable to diseases and insect damage.  Researchers at West Lafayette, Indiana; Purdue University; and the CuraGen Corporation have discovered over 3,000 new wheat genes that respond to disease pathogens and pests.  These genes are differentially regulated when wheat is attacked by scab, viruses, or Hessian flies. 

IMPACT/OUTCOME:  The new wheat disease resistant gene information can be used to develop wheat with improved resistance to disease or insect threats.

ACCOMPLISHMENTS:  ARS scientists at Ames, Iowa, working with national and international barley researchers, and Affymetrix, have developed a microarray chip that contains over 400,000 ESTs (expressed sequence tags) for barley genes.  The project received funding from a USDA-CSREES initiative for Future Agriculture and Food Systems. 

IMPACT/OUTCOME:  The barley genome GeneChip enables cereal researchers to assess the effects of drought, pests, and diseases on most barley genes simultaneously, which will result in improvements to barley.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists can now predict Asian Longhorned Beetles’ (ALB) roaming habits.  If the ALB continues its advance, this invasive pest may potentially alter the makeup of North American hardwood forests.  Losses to lumber, maple syrup, and tourism industries could reach $670 billion.  ARS scientists in Newark, Delaware, have generated new dispersal data that predicts how far the beetle might spread once it begins to invade an area.  Determining ALB presence has depended solely upon visual surveys.  Locating these subtle signs of ALB infestation is time-consuming and costly.  The scientists conducted the first ALB dispersal research in the beetle’s home territory of Gansu Province, China.  They found that the beetles, even females carrying eggs, fly much longer distances than originally thought.

IMPACT/OUTCOME:  The new ALB dispersal data could be used by APHIS and officials in infested States to establish more reliable survey and quarantine boundaries, increasing the chances of successful control or eradication.

ACCOMPLISHMENTS:  New caterpillar attractants from flowers show promise for pest control in potato crops.  Alfalfa loopers, cabbage loopers, cutworms, and armyworms damage potato foliage through their feeding, reduce yields, and require multiple applications of chemical pesticides.  ARS scientists at Wapato, Washington, have identified a novel combination of natural product chemicals in flower odors that are highly attractive to both sexes of alfalfa looper moths.  These chemicals were evaluated in pesticide-treated bait stations to lure and kill female moths before they lay eggs.

IMPACT/OUTCOME:  In five-acre potato plots, the number of pest moths was reduced by 75 percent using new caterpillar attractants from flowers.  Commercial production of this technology can provide a way to bait these moths in order to reduce reproduction and prevent damage to potato and other susceptible crops, while minimizing pesticide use.

ACCOMPLISHMENTS:  Squash bugs and cucurbit yellow vine disease can be thwarted by kaolin particle film applications.  Cucurbit Yellow Vine Disease (CYVD) transmitted by the squash bug, is an emerging and serious disease of watermelon, muskmelon, squash, and pumpkin from Texas to Massachusetts.  It is caused by a bacterium that inhabits the plant’s vascular system.  ARS scientists in Lane, Oklahoma, in cooperation with scientists at Texas A&M University and Oklahoma State University, have found a way to reduce losses to CYVD and its insect vector.  Over a two-year period, weekly applications of a non-toxic kaolin particle film, which is commercially available, significantly reduced both squash bug populations and incidence of CYVD in summer squash.

IMPACT/OUTCOME:  Adoption of kaolin particle film technology by watermelon, muskmelon, squash, and pumpkin growers could substantially reduce squash bug feeding and CYVD incidence in cucurbit crops.

ACCOMPLISHMENTS:  ARS participation in the IR-4 program consisted of 77 field trials for food crops and 31 field trials for ornamentals which contributed to EPA registrations on 23 food crops for 10 insecticides and on 25 ornamental crops for 4 insecticides.

IMPACT/OUTCOME:  Availability of these insecticides has enhanced the pest management options for minor crop producers.

ACCOMPLISHMENTS:  The Systematic Entomology Laboratory, Beltsville, Maryland, provided over 19,418 identifications of insect port specimens, including 7,270 of urgent priority.  Fourteen species were discovered to be new invasives into the continental United States, Hawaii, or Puerto Rico.  Additionally, the laboratory identified the emerald ash borer, a destructive pest of ash trees in the Great Lakes region.  Scalenet, containing information on over 1,000 scale insects, has now been made accessible at http://www.sel.barc.usda.gov/scalenet/scalenet.htm.  A fossil fly from the South Pole was identified.  This identification questions theories of fly dispersal, and documents a significant warming period on the Antarctic continent 3-17 million years ago.

IMPACT/OUTCOME:  Systematics is essential for all work research on combating invasive and native pest insects.  Accurate identification is needed to determine pest management strategies, including finding natural enemies for pest control. 

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

ACCOMPLISHMENTS:  ARS participation in the IR-4 program with 31 field trials for food crops and 46 field trials for ornamentals contributed to EPA registrations on 10 food crops for 5 herbicides and on 33 ornamental crops for 6 herbicides.

IMPACT/OUTCOME:  Availability of these herbicides enhanced the pest management options for minor crop producers.

ACCOMPLISHMENTS:  Saltcedar, Tamarix spp., is a destructive invasive shrub/small tree that has invaded riparian areas all across the western United States where it extensively consumes valuable water.  There are currently no sustainable methods available for its management.  ARS scientists in Albany, California, in cooperation with ARS scientists in Temple, Texas, and several State and local collaborators, conducted studies on a beneficial biological control agent, a leaf beetle (Diorhabda elongata), from China, Greece, North Africa, and other locations in Eurasia.  After regulatory approval, these beetles were released into the open environment in several Western States where they have begun to defoliate saltcedar. 

IMPACT/OUTCOME:  The saltcedar leaf beetle is rapidly spreading.  At locations in Nevada, the beetles have spread several hundred meters and have caused extensive defoliation to saltcedar for two seasons in a row.  As the impact by this biological control agent continues, management of saltcedar is expected to occur over vast areas, reducing water loss, lowering the use of herbicides, and returning the land to productivity.

ACCOMPLISHMENTS:  Roundup-Ready crops have proliferated in the United States, Canada, and Argentina, but little is known about the effects of this new cropping system on the environment, specifically on biodiversity.  ARS scientists at Pullman, Washington, in conjunction with land grant universities in Minnesota, Iowa, Missouri, Arkansas, and Louisiana, as well as the University of Buenos Aires, Argentina, examined the effects of Roundup-Ready soybean on biodiversity (as characterized by number and quantities of weeds) and soybean yield along a transect from Minnesota to Louisiana.  Roundup-Ready crops promoted biological diversity compared to traditional crop management techniques and weed treatments.  This occurred only if the crops are treated with a single application of glyphosate (the active ingredient in Roundup). 

IMPACT/OUTCOME:  The research demonstrated that the European perception of reduced biological diversity with adoption of Roundup-Ready technology may not be valid, at least under U.S. conditions, if the technology is used judiciously. 

ACCOMPLISHMENTS:  Russian thistle (tumbleweed), Salsola kali, is an invasive weed across many Western States, where it competes with better forage plants for water and resources, and becomes a safety hazard when it blows across expressways and blocks the vision of drivers.  Fall application of a persistent, soil-active herbicide may be an effective way to control Russian knapweed growth the following year; however, current-year.  An ARS scientist in Burns, Oregon, the Oregon Department of Agriculture, Harney County Extension Service, and a private landowner cooperatively researched a new technology that mows and applies herbicide in a single pass, removing standing dead plants, and allowing more herbicide to reach the soil where it is taken up by plant roots. 

IMPACT/OUTCOME:  Russian knapweed control in the two years following application was improved by using this new technology.  This method increases profits to hay and forage growers by reducing herbicide costs and providing better control of Russian knapweed.

ACCOMPLISHMENTS:  Plant pathogens are needed as biological control agents for management of yellow starthistle (YST), Centaurea solstitialis, a serious invasive weed in the Western United States that currently infests over 12 million acres in California alone.  Puccinia jaceae, a rust fungus biological control agent from Eurasia that causes severe disease on YST rosettes and bolting stems, was released in California by ARS scientists from Frederick, Maryland, in cooperation with the California Department of Food and Agriculture.  P. jaceae is the first fungus to be released for weed biological control in the continental United States in over 25 years.

IMPACT/OUTCOME:  P. jaceae established quickly, and is expected to spread long distances without human intervention, attack YST throughout the Western United States, complement insect biological control agent species already in place, and play a key role in the ultimate management of YST, California’s worst weed.  Approval of a rust fungus as a biological control agent is a breakthrough for weed management in the continental United States and is expected to facilitate approval of other fungal agents in the future.

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

ACCOMPLISHMENTS:  ARS participation in the IR-4 program consisted of 31 field trials for food crops and 24 field trials for ornamentals which contributed to EPA registrations on 11 food crops for eight fungicides and on 11 ornamental crops for four fungicides.

IMPACT/OUTCOME:  Availability of these fungicides enhanced the pest management options for minor crop producers.

ACCOMPLISHMENTS:  Little is known about the genetic variability on maize chlorotic dwarf virus, a corn virus that causes significant disease problems in the Southeastern United States.  ARS scientists at Wooster, Ohio, sequenced both severe and mild isolates of the virus.  The severe strain shared about 60 percent sequence identity with the mild type. 

IMPACT/OUTCOME:  Wide variability among the corn chlorotic dwarf viruses suggest that the disease may be caused by a complex of more than one virus, a finding that will likely impact the design of disease control strategies.

ACCOMPLISHMENTS:  Citrus Tristeza Virus (CTV) is the most important virus disease of citrus.  Evaluation of the rate of spread and virulence of CTV in the San Joaquin Valley of California remains critical to the local citrus industry and the fate of the CTV eradication program.  ARS scientists at Parlier, California, found that CTV spread continues at a high rate despite extensive eradication efforts.  Isolates from different infected trees in a 4 square mile area yielded the same highly transmissible virus strain by the cotton aphid, but the virulence was benign in commercial varieties grown in this area.

IMPACT/OUTCOME:  Findings from the characterization and epidemiology of citrus tristeza virus suggests that the eradication program in its present state may no longer be useful or cost effective.

ACCOMPLISHMENTS:  Tomato Spotted Wilt Virus (TSWV) is a significant viral pathogen on peanut in the southwest United States.  The ability of this virus to infect plants and the host range of the virus is controlled by a critical gene (NsM).  ARS scientists at Stillwater, Oklahoma, cloned and sequenced the NsM gene and determined the molecular origin of the genotypic differences that exist among the collection of TSWV isolates taken from peanut. 

IMPACT/OUTCOME:  The NsM gene of TSWV will aid in the identification of stable sources of resistance for the peanut germplasm.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  The boll weevil has wreaked havoc on the American cotton industry, with yield losses and control costs totaling more than $22 billion since its 1892 arrival in the United States.  As boll weevils spread, they forced radical economic and social changes in areas that had been almost completely dependent on cotton production.  Hope for stopping the boll weevil had been bleak until the 1970’s, when ARS research began to create needed tools.  ARS developed an essential pheromone lure and trap, along with basic biological information about the pest.  Then ARS helped assemble the research − from ARS and from universities, state experiment stations, extension agents, and many others − into an areawide pest eradication model.

IMPACT/OUTCOME:  Eradication of the boll weevil is now a major success, thanks in large part to ARS research.  The success story of boll weevil eradication was built on cooperation between government research and regulatory agencies, especially ARS and USDA’s Animal and Plant Health Inspection Service, which has regulatory responsibility for the eradication program – along with universities, industry, states, and growers.

ACCOMPLISHMENTS:  The ARS partnership Hawaiian fruit fly areawide pest management project has resulted in the first successful program to control fruit flies that have been devastating Hawaiian agriculture for almost 100 years.  The control system is based on a combination of techniques, such as field sanitation, male fruit fly annihilation, and protein bait sprays, developed primarily by ARS, which have been adapted and coordinated into an IPM initiative specifically designed to work in Hawaii’s environment.  The target fruit flies -- melon, Oriental, Mediterranean, and Malaysian -- attack more than 400 different fruits and vegetables.  A hallmark of the program has been a network of partnerships involving ARS, the Hawaii Department of Agriculture, the University of Hawaii Cooperative Extension Service and local communities, with the support of APHIS and other research, regulatory, and government agencies.

IMPACT/OUTCOME:  ARS’ Hawaiian fruit fly areawide pest management program has found wide-spread acceptance by Hawaiian growers.  The 285 signed cooperating growers in this program, representing 6,200 acres, across the major islands of Hawaii have already been able to cut conventional pesticide use by 75 to 90 percent.  Small farms are now growing crops they had previously abandoned due to fruit fly damage.  The impact of the program is expanding in Hawaii and throughout the Pacific Basin (e.g., French Polynesia, Fiji, Vanuatu, Guam, and the Northern Mariana Islands).

ACCOMPLISHMENTS:  ARS scientists at Peoria, Illinois, have developed a new fermentation procedure for mass producing a fungus to fight whiteflies, thrips, spider mites, and other invasive insect plant pests.  Whiteflies are prime target pests because the sap sucking insects are pests of some 600 different kinds of plants, including cotton, tomato, and poinsettia.  Infestations in these and other U.S. crops have caused multimillion dollar losses through transmission of viruses, and by gumming up farm equipment with their sticky wastes.  The fungus, Paecilomyces, kills whiteflies by penetrating the pest’s body to feed and grow; new spores emerge to infect other whiteflies, sparing non-host insects as they spread. 

IMPACT/OUTCOME:  Attempts to commercialize the fungus had previously stumbled on high production costs, quality control problems, and other setbacks.  The researchers have overcome these obstacles through their innovations on how the fungus’ spores are cultured, formulated, and made stable for long-term cold storage.

ACCOMPLISHMENTS:  ARS overseas biological control laboratories in Australia, China, Argentina, France, Greece, and Italy combat invasive insect pests and weeds by identifying, collecting, testing, and shipping natural biological control agents to the U.S.  This year, natural enemies of the olive fruit fly were explored in Europe, South Africa, Kenya, and Tunisia by a team from the European Biological Control Laboratory and the South American Biological Control Laboratory, in conjunction with ARS researchers at Weslaco, Texas.  They also found potentially useful parasites of the glassy-winged sharpshooter.  In addition, the Australian Biological Control Laboratory found effective psyllids that attack the paperbark tree (Melaleuca) in Florida.

IMPACT/OUTCOME:  Invasive weeds and insect pests of foreign origin cause major economic losses (greater than $100 billion each year) and ecological problems in the United States.  The use of natural enemies derived from a pest’s point of origin in biological control programs offers the possibility for permanent, cost effective suppression of such weeds and insect pests. 

ACCOMPLISHMENTS:  ARS scientists in Gainesville, Florida, with collaboration from ARS scientists in Manhattan, Kansas, have developed an automated system to detect hidden insect infestations in stored grain and other stored commodities.  This product, called Electronic Grain Probe Insect Counter (EGPIC) was patented by ARS in 1997, provides real time information about insect numbers in stored grain.  It can even determine the species of the infesting insect pest.  EGPIC has been integrated into commercial grain management system that is currently being marketed to the grain storage market.

IMPACT/OUTCOME:  The easy-to-use system allows grain storage and milling companies to use insecticides and fumigants as well as non-toxic alternatives only when needed, based on monitoring, rather than routinely scheduling preventive treatments.  This system will provide early warning of insect infestations giving grain managers more options for handling the situation, whether immediate milling of the grain or applying an insecticidal treatment.  This will provide a cost saving to the industry and a better quality product to the public.

develop and demonstrate technologies for excluding, detecting, and mitigating native and invasive weed pests, including integrated pest management (IPM) and areawide approaches, and deliver IPM components and systems to the ARS customer base.

ACCOMPLISHMENTS:  Metham-sodium has been identified as a possible replacement for methyl bromide fumigation in vegetable crops, although questions persist regarding the optimum rate, timing, and need for polyethylene tarping for control of yellow nutsedge, Cyperus esculentus.  Field studies conducted by ARS scientists in Tifton, Georgia, identified the application guidelines for controlling yellow nutsedge in transplanted cucurbit crops with metham-sodium.  These trials demonstrated that thin film polyethylene mulch added consistency to metham-sodium efficacy and provided significant suppression of yellow nutsedge, even without a fumigant. 

IMPACT/OUTCOME:  The research suggests that the production practices for cantaloupe and other cucurbit crops can be easily altered to accommodate metham-sodium as a replacement for methyl bromide.

ACCOMPLISHMENTS:  Medusahead, Taeniatherum caput-medusae, is an invasive annual grass that has spread over millions of acres in the semi-arid West, reducing forage production for wildlife and livestock and displacing native plant species.  ARS scientists in Burns, Oregon, in collaboration with Oregon State University and Bureau of Land Management personnel, investigated second year effects of the herbicides Oust® (sulfometuron methyl) and Plateau® (imazapic) on medusahead and associated native plant species.  Medusahead may be controlled using herbicides, but the effects on associated native species are site specific. 

IMPACT/OUTCOME:  Public land managers and private landowners can use Oust® and Plateau® to improve the effectiveness of medusahead control while maintaining native biodiversity and forage production.

ACCOMPLISHMENTS:  Giant salvinia, Salvinia molesta, is one of the world's worst weeds, threatening the integrity of fresh water ecosystems in 12 Southern and Western States (and Hawaii) where it has invaded.  ARS scientists in Ft. Lauderdale, Florida, working in collaboration with the Texas Parks and Wildlife Department, U.S. Geological Survey, Texas A&M University, and Florida A&M University, released the salvinia weevil, Cyrtobagous salviniae, a proven biological control agent, on giant salvinia in Texas and Louisiana during October 2001.  The weevil successfully over wintered in Texas and Louisiana, and by spring 2003 reduced plant densities in release plots to 10 percent of the densities in control plots, and by mid-summer caused the complete elimination of giant salvinia from some study sites. 

IMPACT/OUTCOME:  The salvinia weevil is poised to eliminate or reduce the threat of giant salvinia, thereby restoring or preserving freshwater ecosystems, reducing the use of herbicides or mechanical control, and providing affordable, sustainable management throughout the southeastern continental United States and Hawaii.

ACCOMPLISHMENTS:  Little information is available on the control of common waterhemp, Amaranthus rudis, which has emerged recently as one of the most problematic weed species in soybean in the Midwest.  ARS scientists in Urbana, Illinois, conducted a three-year study to determine the critical interference period following soybean and common waterhemp emergence to enable removal practices to be implemented before soybean seed yield loss occurs.  Removal of common waterhemp interference two weeks after soybean unifoliolate expansion resulted in soybean seed yield equivalent to a season-long weed free control.  Delaying common waterhemp removal until four weeks decreased yield by 31 percent. 

IMPACT/OUTCOME:  These results will assist producers in improving the timing of management practices for common waterhemp in soybean production, resulting in increased yield at decreased cost.

ACCOMPLISHMENTS:  The effectiveness of thin film polyethylene mulches in suppressing nutsedge growth was evaluated in the wake of the impending elimination of methyl bromide.  In greenhouse studies by ARS scientists in Tifton, Georgia, purple and yellow nutsedge (Cyperus rotundus and C. esculentus, respectively) growth was monitored in pots covered with black polyethylene mulch, clear polyethylene mulch, or not covered.  Relative to the non-mulched treatments, mulches reduced yellow nutsedge tuber production 50 percent and shoot populations 96 percent; there were no differences among the treatments for purple nutsedge. 

IMPACT/OUTCOME:  Polyethylene mulch can be an important component of a yellow nutsedge management system, while other factors will need to be explored for successful management of purple nutsedge.

develop and demonstrate technologies for excluding, detecting, and mitigating native and invasive plant disease pests, including integrated pest management (IPM) and areawide approaches, and deliver IPM components and systems to the ARS customer base.

ACCOMPLISHMENTS:  Phytophthora infestans, the causal agent of potato late blight is considered to be the most significant pathogen of potatoes worldwide.  An increase in severity and aggressiveness of the pathogen has stimulated interest in developing new biological control alternatives.  ARS scientists at Peoria, Illinois, produced and formulated several bacterial strains patented for biological control of Fusarium dry rot which previously suppressed late blight in laboratory potato bioassays.

IMPACT/OUTCOME:  Late blight reduction provided by the biological control treatments ranged from 20 to 90 percent depending on strain and formulation composition.  These results demonstrate the potential of combinations of these bacteria to simultaneously control both late blight and Fusarium dry rot.

ACCOMPLISHMENTS:  White mold caused by Sclerotinia sclerotiorum is an economically devastating disease of numerous broad leaf crops throughout the United States.  ARS scientists at Fargo, North Dakota, coordinate cooperative research to manage this disease in 5 commodity crops (canola, dry bean, pea and lentil, soybean, and sunflower).  Research was conducted at 11 land-grant universities, the National Sunflower Association of Canada and 6 ARS research locations.  Genetic resistance to white mold was developed in canola germplasm at North Dakota State University.  In addition, white mold resistance was discovered in dry bean germplasm at Michigan State University.  This resulted in release of the navy bean cultivar, ”Seahawk.”  Progress also was made toward the development of plant resistance to Sclerotinia stem rot at the University of Wisconsin.  A simple, inexpensive, and reliable greenhouse method was developed for initial screens of canola to differentiate response to the disease in development of resistant cultivars.  Other research on Sclerotinia stem rot at the University of Illinois was initiated to map resistance genes from plant introductions and initiate the incorporation of these genes into elite soybean germplasm.  Progress was made in mapping quantitative trait loci in three populations developed from crosses between partially resistant soybean plant introductions and partially resistant or susceptible varieties.

IMPACT/OUTCOME:  Highlighted findings include an improved ability to forecast white mold incidence for various crops.  A risk map for canola is currently in use and is being expanded into other crops.  The map has the potential to reduce fungicide costs while maintaining use of fungicides in high risk areas, thus avoiding unacceptable white mold losses.

GOAL 4:  IMPROVE THE NATION’S NUTRITION AND HEALTH

Analysis of Results:  This goal is the focus of ARS’ research related to human nutrition and health.  Under Goal 4, 6 Indicators are aligned under 3 Performance Measures.  Because of the adoption of a new ARS Strategic Plan 2003-2007, the Performance Measures and Indicators have changed dramatically from those last reported in the FY 2002 Annual Performance Report and FY 2003 to 2005 Annual Performance Plan.  In addition, the agency made a policy decision to have fewer and broader Indicators then in past Plans and Reports.  As the National Programs become more internally coherent, the agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in all 6 Indicators were completed or substantially completed during FY 2003.  Twelve significant accomplishments are reported below.

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

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS researchers identified eating in the absence of hunger as a behavioral predictor of obesity in Hispanic children.

IMPACT/OUTCOME:  Eating habits are often not linked to hunger.  Identifying this as a factor for Hispanic children affords the opportunity to develop specific interventional strategies for obesity prevention.

ACCOMPLISHMENTS:  Researchers found that frequently “eating out” is a particularly strong predictor of excess body fat in adults.

IMPACT/OUTCOME:  The relationship of “eating out” to adult obesity underscores the central role of diet in the development of body weight problems.

conduct research to enhance the nutritive value of the food supply.

ACCOMPLISHMENTS:  ARS showed that dairy foods, as part of a weight loss diet, increased body weight and fat loss.

IMPACT/OUTCOME:  The addition of dairy foods to a weight loss regime improves body weight and fat loss.  This information was used by the 2005 USDA/HHS Dietary Guidelines Advisory Committee in concluding that three servings of dairy foods daily would provide needed calcium for osteoporosis prevention while not contributing to excess body weight gain. 

ACCOMPLISHMENTS:  ARS researchers demonstrated that eating breakfast favorably affects cognition.

IMPACT/OUTCOME:  Studies linking breakfast eating with better cognition help justify USDA’s school breakfast programs and the general recommendation not to skip the first meal of the day. 

ACCOMPLISHMENTS:  ARS scientists determined the iron bioavailability from plant foods.

IMPACT/OUTCOME:  Iron from plants is less well absorbed than from meats.  This increases the risk of iron deficiency anemia for vegetarians in the United States and worldwide.  Research on iron bioavailability and methods to compensate for lower absorption helps to alleviate this nutritional problem.

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS researchers found that antioxidants in berries and tea are bioavailable to humans. Also, it improves oxidative stress, glucose homeostasis, and cognitive function.

IMPACT/OUTCOME:  Showing that berries and tea have several beneficial health effects has expanded consumer demand for these products that are low in calories and high in nutrients.

ACCOMPLISHMENTS:  ARS scientists showed that a high protein diet does not adversely affect body calcium retention.

IMPACT/OUTCOME:  Given the popularity of several high protein diets, it is important to know if the long-held view that high protein diets elevate calcium excretion from the body is true.  ARS research demonstrates this is not the case.

ACCOMPLISHMENTS:  ARS researchers examined the role of vitamin K in bone health in a three-year clinical trial.

IMPACT/OUTCOME:  Although calcium and vitamin D are essential for proper bone health, other nutrients are required.  Vitamin K is the least studied; ARS research fills this critical void.

ACCOMPLISHMENTS:  ARS scientists determined the macronutrient needs of very low birth weight infants.

IMPACT/OUTCOME:  Very low birth weight infants have nutritional needs different from other babies and treating them properly is a medical challenge.  ARS research on their macronutrient needs helps pediatricians in caring for these infants.

develop new methods, conduct food composition analyses, and compile databases for known and new nutrients and health promoting food components.

ACCOMPLISHMENTS:  ARS released version 16 of the Standard Reference Nutrient Database including 9 new components, a supplemental database on flavonoids, and nutrient database versions for use on personal computers and PDAs.

IMPACT/OUTCOME:  Annual updates to the National Nutrient Database for Standard Reference allow professionals and the public to plan better diets.  Releasing the database in personal computer and PDA formats increases the number of potential users.  The Secretary of Agriculture recognized the value of this latter accomplishment with a USDA Superior Service Award.

Indicators:

During FY 2003, ARS will

survey and analyze national food consumption patterns of Americans.

ACCOMPLISHMENTS:  ARS scientists completed the data collection phase of an extensive, biomarker- based validation study of the new USDA Automated Multiple Pass Method, the quantitative food intake instrument used in the national food consumption survey.  

IMPACT/OUTCOME:  In this era of escalating U.S. obesity, understanding eating behaviors is essential to reducing the incidence of childhood obesity.

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

ACCOMPLISHMENTS:  ARS scientists identified that a high intake of fast foods by children was associated with poorer nutritional status and increased weight gain.

IMPACT/OUTCOME:  Underreporting of foods consumed by participants in dietary surveys is a common problem. Validation of the new USDA dietary assessment tool is critical to ensuring complete and accurate national food consumption information. 

GOAL 5:  PROTECT AND ENHANCE THE NATION’S NATURAL RESOURCE BASE AND ENVIRONMENT

Analysis of Results:  This goal is the focus of ARS’ research on a wide range of environmental issues related to agriculture.  Under Goal 5, 14 Indicators are aligned under 7 Performance Measures.  Because of the adoption of a new ARS Strategic Plan 2003-2007, the Performance Measures and Indicators have changed dramatically from those last reported in the FY 2002 Annual Performance Report and FY 2003 to 2005 Annual Performance Plan.  In addition, the agency made a policy decision to have fewer and broader Indicators then in past Plans and Reports.  As the National Programs become more internally coherent, the agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in all 14 Indicators was completed or substantially completed during FY 2003.  Thirty-one significant accomplishments are reported below.

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

Indicators:

During FY 2003, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at Logan, Utah, used molecular techniques to identify genes associated with important characteristics including biodiversity in native and introduced species.  Using this research they released Star Lake Indian ricegrass germplasm for rangeland rehabilitation and Cashe Meadow bromegrass for forage production under limited irrigation.

IMPACT/OUTCOME:  This research provides land managers with additional germplasm options that are affordable and ecologically appropriate for maintaining sustainable livestock production and ecosystem restoration.

ACCOMPLISHMENTS:  ARS scientists at Lincoln, Nebraska, in cooperation with scientists at the Universities of Nebraska and Kansas State, the Natural Resources Conservation Service (NRCS) and other ARS locations, released two new intermediate wheatgrass cultivars, Beefmaker and Haymaker. 

IMPACT/OUTCOME:  This research provides producers in the Northern Great Plains with higher quality livestock forages for better animal performance.

ACCOMPLISHMENTS:  ARS scientists at Logan, Utah, have completed work on adapting two important legumes, kura clover and sainfoin, for use on dry range sites.  

IMPACT/OUTCOME:  The research results in new affordable and appropriate germplasm options for rehabilitating and conserving rangelands, providing nitrogen for companion grasses which stay green through much of the dry season thus providing high quality forage and reducing fire hazard.  

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

ACCOMPLISHMENTS:  ARS researchers at Brooksville, Florida, demonstrated that dredge materials from lake bottoms can be applied to bahiagrass pastures to enhance pasture establishment.  Lake-dredged materials’ concentrations of heavy metals and human pathogens are well below levels approved by EPA.  The dredged materials increased bahiagrass production by around 170 percent.  

IMPACT/OUTCOME:  Bahiagrass is an important pasture grass across the Gulf Coast region but it can be difficult to establish in the region’s dry, low-fertility sandy soils.  Improving establishment of an excellent, uniform stand of bahiagrass increases the economic returns on pasture establishment costs while protecting the soil and water resources from erosion.  Using the dredge materials on pastureland also reduces the need for their disposal in landfills. 

ACCOMPLISHMENTS:  ARS scientists from St. Paul, Minnesota and the University of Minnesota found that after planting alfalfa seeds the emerging seedlings were 15 percent smaller in old alfalfa fields than in fields where other crops had been grown.  They also found the age and the cultivar of the alfalfa in the previous crop had no apparent impact.  However, the later the reseeding took place in the growing season the more significant the impact on the alfalfa seedlings.