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

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

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

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

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

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

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

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

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

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

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

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

GOAL 1:  ENHANCE ECONOMIC OPPORTUNITIES FOR AGRICULTURAL PRODUCERS

Analysis of Results:  This goal is related to production agriculture, adding quality and value to agricultural products, new products, biobased products, and biofuels.  Under Goal 1, 24 Indicators (in Italics) are aligned under 11 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2005.  Seventy-six 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 2005, ARS will

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

ACCOMPLISHMENTS:  About 70 percent of cotton produced worldwide (about 16 billion kg, 75 million bales) is used in woven fabrics and warp yarns are the major components therein.  These yarns are coated (sized) with expensive chemicals during preparation, and later the woven fabrics are de-sized (chemicals are removed).  Scientists at New Orleans, Louisiana, demonstrated that size-free weaving was feasible on high speed weaving machines using long fiber cotton (called Acala) rotor-spun yarn stabilized with a high torque (or twisting force). 

IMPACT/OUTCOME:  Sizing and de-sizing add to costs and environmental concerns.  Eliminating sizing and de-sizing will enhance the use and competitiveness of cotton and reduce chemicals use.   

develop new or improved methods to measure or predict quality.

ACCOMPLISHMENTS:  The global cotton market is increasingly demanding a NIST-traceable color standard for grading cotton (i.e., measurements can be referenced to unchanging absolute standards).  Calibration cottons covering a wide range of color values were compared to standard color tiles, using the Agricultural Marketing Service’s “master colorimeter” and a more precise spectrophotometer.  Spectrophotometric results were highly correlated with results of the standard method.

IMPACT/OUTCOME:  Use of a spectrophotometer for cotton color determinations will allow more accurate and precise descriptions based on absolute physical properties, rather than being referenced to a set of “calibration cottons,” which are themselves variable and unstable with time.  A NIST-traceable color standard will eventually be the uniform basis for determinations of cotton color around the world, removing variations from one location to another and allowing the marketplace to set a fair price.

ACCOMPLISHMENTS:  Short fiber content (SFC, the percentage of fibers with lengths of less than ½ inch) of cotton is increasingly recognized as an impediment to processing and textile manufacturing.  Computer programs were developed to predict SFC from data on fiber length distributions, and factors affecting the accuracy and precision of SFC measurement were identified.  In addition to natural variation, they include sampling technique, sample preparation, and presence of neps.  The origin of SFC was hypothesized to be largely from fiber breakage during processing.  Mathematical analysis of the distribution of fiber lengths revealed it to have two components, indicating the important role of fiber breakage during processing in generating SFC. 

IMPACT/OUTCOME:  Increasingly, users of cotton demand low SFC in cotton that they purchase, even though SFC is not one of the standard quality measurements.  Institutionalizing measurements of SFC and setting the schedule of price discounts or premiums requires a better method of measurement.  These studies are a first attempt to develop reliable, accurate, and precise methods to determine SFC so that buyers and sellers of cotton will have a common understanding of value and can reach a fair price.

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

ACCOMPLISHMENTS:  A soy oil-based metalworking fluid was developed by scientists at Peoria, Illinois, and tested in the private sector CRADA partner’s pilot plant.  The biobased lubricant outperformed the equivalent mineral oil lubes and is economically competitive.    

IMPACT/OUTCOME:  The CRADA partner plans to conduct trials next year in large rolling mill plants in the United States and Europe.  This development could provide a new market for soybean oil.

ACCOMPLISHMENTS:  Scientists at Peoria, Illinois, developed a commercially viable procedure to deposit thin layers of starch onto the surface of normally water repellant plastics such as polyethylene.  These starch coatings impart water receptive properties to the plastic surface, thereby facilitating the absorption of water-based dyes and inks, reducing electrostatic charging, and improving compatibility with aqueous agents and biological fluids. 

IMPACT/OUTCOME:  This technology has applications in plastic containers, biomedical devices, and wrapping materials for sensitive electronic components.  ARS’ Peoria scientists have filed two patent applications in cooperation with a private sector CRADA partner who is interested in marketing the technology.  This development could open new markets for corn starch.

ACCOMPLISHMENTS:  Using techniques initially developed by ARS scientists in Albany, California, an industrial manufacturer began the first large scale commercial production of latex from the guayule plant.  Researchers at ARS facilities in Albany, California, and Phoenix, Arizona, also developed methods for moist storage of harvested guayule that would increase latex yields. 

IMPACT/OUTCOME:  This development provides a domestic source for rubber and new opportunities for Southwest farmers.

ACCOMPLISHMENTS:  A cheaper, more efficient binder is needed for commercial production of charcoal briquettes.  A team of scientists from Albany, California, collaborated with engineers from an industrial partner to develop a corn-based binder that is much lower in cost than the currently used binder.  The corn binder also improved the strength of the briquettes. 

IMPACT/OUTCOME:  This research may save the company $5 million in material costs and could provide a new niche market for corn.

ACCOMPLISHMENTS:  Researchers at Clemson, South Carolina, in partnership with a commercial textile mill, organized a commercial scale trial to demonstrate the use of cotton/flax blend yarns developed by ARS to produce commercial quantities of fabric for shirting material and denim.  The yarn was woven on high speed weaving machines at high efficiency and resulted in fabrics with a unique appearance and improved fabric breathability without compromising the fabric strength. 

IMPACT/OUTCOME:  The success of this effort demonstrates that domestically grown flax fiber is a good alternative natural fiber source that provides enhanced fabric characteristics for domestic textile mills, will provide a competitive advantage in the global textile market, and should result in increased amounts of U.S. produced cotton sold for denim garments.   

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  Because StarLink is a genetically modified corn that produces an insecticidal protein, the U.S. Food and Drug Administration (FDA) limits the use of StarLink corn to feed-use only and has established a zero tolerance for StarLink corn in the human food supply.  Since some StarLink corn has been found in the human food supply, FDA, USDA, and corn millers now inspect shelled and milled corn destined for human consumption for the presence of StarLink.  Sampling and analytical errors associated with measuring StarLink in corn meal and flour were determined and the effects of sample size, the number of analyses on reducing testing errors, and the number of lots misclassified were demonstrated. 

IMPACT/OUTCOME:  Knowledge of the StarLink measuring errors will reduce both health risks to the consumer and economic loss to the processor.

ACCOMPLISHMENTS:  ARS engineers at Athens, Georgia, consulted with a major manufacturer of farm equipment to develop a new grain moisture sensor for its grain combines, using principles developed by the ARS engineers.  Microwave moisture sensing equipment supplied by an instrument manufacturer in Iceland also utilizes principles developed by the ARS.

IMPACT/OUTCOME:  ARS technology has helped enhance moisture measurement technology, improving cost savings and food safety.

ACCOMPLISHMENTS:  A decision support system for managing peanut curing operations was developed by researchers at Albany, Georgia, and released for use by the peanut industry.  The software includes models to accurately predict peanut drying time in response to specific drying equipment, weather conditions, and dryer control parameters.  It also includes tools to manage the flow of peanuts at the drying facility from the time they are delivered by the farmer until they are graded and marketed. 

IMPACT/OUTCOME:  Use of the decision support system will reduce labor, minimize overdrying, and document drying conditions for all peanuts cured at that facility.

ACCOMPLISHMENTS:  Researchers at Manhattan, Kansas, developed an NIR (near infrared) sorting system that automatically scans individual wheat kernels and sorts them based on specific attributes such as protein content, hardness, amylose content, and other selected quality attributes.  The technology was commercialized through a CRADA with a Swedish-based company and is being publicly marketed. 

IMPACT/OUTCOME:  The system is being used by breeders to select specific traits from early generation breeder samples.  This will significantly reduce the time and expense required to develop cultivars with specific end-use traits.

develop functional food ingredients and/or products.

ACCOMPLISHMENTS:  Researchers in Albany, California, discovered that soluble fibers reduce oxidative damage in test animal tissues.  In addition, fibers previously thought to be inactive were found to have significant beneficial activity.  The research is being done in collaboration with an industrial partner.  Two patent disclosures have been filed.

IMPACT/OUTCOME:  These results and the new fiber source will provide an alternative to pharmaceuticals to prevent dietary-related metabolic disease such as type II diabetes.   

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

ACCOMPLISHMENTS:  Researchers at Parlier, California, developed a method to enhance activity of the fungicide, imazalil, to control green mold while reducing its rate of use by 50 percent or more using sodium bicarbonate.  Also accomplished was partial control of imazalil-resistant isolates of the fungal pathogen which causes most of the postharvest losses in California.  The ARS researchers worked with commercial interests to optimize the combination treatment so that it could be incorporated into commercial use. 

IMPACT/OUTCOME:  Decreasing fungicide use is valuable to reduce industry costs and residues in the citrus fruit ingested by consumers.  Some version of the method is now used in most California packinghouses.

ACCOMPLISHMENTS:  Traditional honeydew melons (netted, orange flesh) have been linked to outbreaks of foodborne illness due to the presence of bacteria within the netting on the exterior surface of the melon.  Researchers at Weslaco, Texas, have developed a non-netted, orange flesh honeydew melon that has elevated phytonutrient content, longer shelf-life, better flavor, and greater consumer preference than the traditional honeydew melon. 

IMPACT/OUTCOME:  This development will reduce the potential health risks associated with netted melons while providing the consumer with a better tasting, more nutritious melon.   

ACCOMPLISHMENTS:  ARS researchers at Fargo, North Dakota, collaborated with researchers at North Dakota State University in the development of a high soluble fiber oat cultivar ‘HiFi’.  An organic food company will market oat flakes from the cultivar as a health food under an agreement with the University.  The company is contracting with several small organic farms to produce HiFi oats.  ARS is facilitating the smooth transfer of this technology to the marketplace.

IMPACT/OUTCOME:  This development will provide a new market for oats and offer improved nutrition for oats consumers.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  ARS identified and characterized a gene that plays an important role in cell wall biosynthesis in alfalfa plants.

IMPACT/OUTCOME:  There now is a capability to modify cell walls of alfalfa plants, thereby increasing the value of this important crop as a bioenergy feedstock.

ACCOMPLISHMENTS:  ARS identified switchgrass germplasm characteristics that are correlated with valuable traits such as biomass yield, drought tolerance, and seed production.

IMPACT/OUTCOME:  There now is a greater understanding of switchgrass genetics that will facilitate genetic modification of this plant for enhanced energy feedstock production.

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

ACCOMPLISHMENTS:  ARS developed new enzymes and fermentation organisms that are more adapted to harsh industrial environments and that more efficiently and economically convert plant biomass to ethanol. 

IMPACT/OUTCOME:  This development will result in improved process efficiency and economic competitiveness that will aid in the commercialization of the biological conversion of biomass into renewable fuels and coproducts, and in turn reduce the Nation’s dependency on imported petroleum. 

ACCOMPLISHMENTS:  ARS developed a high performance liquid chromatographic method for quantifying biodiesel blend levels of 1 to 30 percent in petrodiesel that can be completed within 20 minutes. 

IMPACT/OUTCOME:  A rapid blend level measurement procedure could become a much needed standard to help maintain quality control and remove a barrier to biodiesel use. 

ACCOMPLISHMENTS:  ARS genetically modified a strain of lactic acid bacteria which produced increased levels of ethanol from cellulosic biomass.

IMPACT/OUTCOME:  The researcher has demonstrated that metabolic engineering is a viable strategy for the development of new biocatalysts to convert agricultural materials to biofuels.

ACCOMPLISHMENTS:  ARS determined that contaminants of biodiesel, such as free fatty acids and monoglycerides, possess better lubricity than neat alkyl esters and are largely responsible for the lubricity of low level blends of biodiesel with petrodiesel. 

IMPACT/OUTCOME:  The research may result in new technology to design improved lubricity enhancing components of fuels that can increase biodiesel use. 

ACCOMPLISHMENTS:  ARS developed processes for dry fractionation of the field pea into enriched protein and starch streams, and for fermenting the pea starch to ethanol.  They found that ethanol yields from pea starch were comparable to that from corn starch.

IMPACT/OUTCOME:  There now is an alternate feedstock for ethanol production that can benefit both farmers and ethanol producers. 

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

ACCOMPLISHMENTS:  ARS developed a procedure to minimize noise and bearing wear encountered with the operation of wind powered helical pumps. 

IMPACT/OUTCOME:  An attractive pumping system that Farmers and ranchers have an attractive pumping system that can be used to supply water to livestock in remote locations.

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

Indicators:

During FY 2005, ARS will develop scientific information that contributes to improved efficiency and environmental stewardship of food animal production systems.

ACCOMPLISHMENTS:  Collaborative efforts of the Noble Foundation, Forage Genetics, and the ARS U.S. Dairy Forage Research Center have resulted in alfalfa transgenics that were down-regulated in enzyme C3H, a crucial step of lignin synthesis.  They have shown that such plants produced lignin with dramatic changes in composition and structure.

IMPACT/OUTCOME:  Alfalfa is widely used as a fiber and energy source for dairy cow diets.  It is limited, however, by poor digestion of the structural carbohydrates (fiber components) limiting the energy recovered from the plant by the dairy cow.  Lignin (the glue that holds fiber together) is completely indigestible itself, and as a result of how it is made and incorporated into the fiber the structural carbohydrates also become less digestible.  One approach to solving the problem of poor fiber digestibility is to alter the lignin to decrease its negative impact.  This process provides a potential approach to improving plant fiber utilization in dairy and beef cattle, sheep, and goats.

ACCOMPLISHMENTS:  ARS developed a method to reproductively rejuvenate (molt) laying hens maintained on a balanced diet.

IMPACT/OUTCOME:  The research was published in two peer reviewed journal articles, a patent application was submitted, and the results were communicated to industry.  This method of molting has potential for use by the industry to induce reproductive rejuvenation and maintain full feed of a nutritional balanced diet and avoid the negatives associated with limiting nutrient intake.

ACCOMPLISHMENTS:  Perchlorate is a goitrogenic anion that competitively inhibits the sodium iodide transporter; has been detected in forages and in commercial milk throughout the United States.  The fate of perchlorate and its effect on animal health were studied in lactating cows, ruminally infused with perchlorate for five weeks by ARS scientists at Beltsville, Maryland.  Milk perchlorate levels were highly correlated with perchlorate intake; milk iodine was unaffected and there were no demonstrated health effects. 

IMPACT/OUTCOME:  The results demonstrated that up to 80 percent of dietary perchlorate was metabolized, most likely in the rumen, which would provide cattle with a degree of refractoriness to perchlorate.  These results are important for assessing the environmental impact on perchlorate concentrations in milk and its relevance to human health, and provide important data for agencies assessing health risks of environmental perchlorate.

ACCOMPLISHMENTS:  ARS conducted research that showed the optimal stocking density in broiler houses varies with weight required at market.

IMPACT/OUTCOME:  This research provides the industry the basis for using different stocking rates to achieve maximum production efficiency of broiler chickens marketed at various weights. This technology was communicated to the broiler industry during several dialogue sessions across the region.

ACCOMPLISHMENTS:  Recirculating aquaculture systems (RAS) reduce water use and place waterborne wastes into concentrated and relatively small discharges.  When a RAS is operated at high salinities for culture of marine species, recovering the saltwater contained in the backwash effluent would allow for reuse within the RAS and reduce salt discharge to the environment. Scientists at the Conservation Fund’s Freshwater Institute, Shepherdstown, West Virginia, evaluated a pilot plant membrane biological reactor (MBR) for ease of operation and effectiveness at removing bacteria, turbidity, suspended solids, and nutrients from the biosolids backwash flow discharged from RAS’.  Results indicate the pilot scale MBR system removed in excess of 99 percent of the suspended solids, carbonaceous BOD, and bacteria, as well as more than 93 percent of total nitrogen contained within the backwash operated at salinity levels of 0 ppt, 8 ppt, 16 ppt, and 32 ppt.

IMPACT/OUTCOME:  RAS’ for marine aquaculture species will become more important for the production of fish in the future.  There are numerous commercially operating freshwater RAS’, but few if any marine systems using saline water.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland, implemented national genetic evaluations for calving ease of Brown Swiss and Holstein bulls that will be provided quarterly to the National Association of Animal Breeders for distribution to the U.S. dairy industry.

IMPACT/OUTCOME:  Calving difficulty (dystocia) has a major economic impact on productivity and profitability of dairy production.  Dairy producers are increasingly interested in crossbreeding as a tool to improve calving ease, health, fertility, and longevity.  Brown Swiss bulls appear to produce daughters that give birth more easily than those of Holstein bulls.  National genetic evaluations for calving ease provide the dairy industry with information to reduce losses from difficult births.

ACCOMPLISHMENTS:  ARS scientists at Athens, Georgia, utilized DNA microarray technology to identify 63 brain and 24 pituitary differentially regulated genes during pubertal development in swine.  The genes studied control the release of brain hormones which regulate luteinizing and growth hormone release from the pituitary gland.

IMPACT/OUTCOME:  These pituitary hormones play critical roles in determining growth and the onset of puberty.  Understanding these interactions is necessary in order to develop new methods to promote maximum growth while enhancing onset of puberty and reproductive function in the pig, critical components impacting efficiency of swine production.

ACCOMPLISHMENTS:  An experiment was conducted at the U.S. Dairy Forage Research Center, Madison, Wisconsin, with lactating dairy cows to investigate the effect of the rumen degraded protein (RDP) on milk production and microbial protein synthesis in the rumen. Diets were composed of alfalfa silage, corn silage, and high moisture corn (typical feeds used for dairy cows in the United States), and contained a range of levels of RDP added from different proportions of soybean meal (a source of true protein) and urea (a source of non-protein nitrogen NPN).  There was decreased feed intake, milk yield, and body weight gain as more and more urea replaced soybean meal.  Replacing RDP from soybean meal with that from urea NPN also resulted in increased milk urea nitrogen (N) and ammonia in the rumen, and reduced microbial protein formation in the rumen.

IMPACT/OUTCOME:  Optimizing the amount of protein formed by the rumen microbes of dairy cows is important because this source provides more than half of the protein actually used by the animal.  It is widely believed by dairy nutritionists that NPN can replace true protein to meet the nitrogen requirements of the rumen microbes.  Farmers benefit from this research by knowing that replacing true protein with NPN will reduce milk production and impair N utilization in lactating dairy cows.

ACCOMPLISHMENTS:  ARS demonstrated that feeding albuterol, a beta 2-agonist, had no negative effects on handling, but did improve growth rates and lowered carcass fat of market pigs.

IMPACT/OUTCOME:  These results will provide information allowing swine producers to select an alterative growth enhancer/carcass composition modifier that does not affect animal excitability.

ACCOMPLISHMENTS:  Understanding the genetic components of nutrient utilization in trout is critical for the U.S. aquaculture industry to remain competitive particularly with higher feed costs, limited natural protein resources, and stricter environmental standards.  Scientists at the Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, measured differential gene expression relating to growth, health, and metabolism of trout reared on a diet containing cereal grains or commercial ingredients.  Rainbow trout of distinct lineage were separated and reared on either a commercial diet or a diet containing a high level of barley (32 percent) for one year, after which tissue samples were taken and the changes in gene expression were evaluated using quantitative real time PCR for several genes and microarray hybridization.

IMPACT/OUTCOME:  This method will be imperative for selecting rainbow trout (and other fish) with improved performance traits for using nutrients from plant sources.  Fish with the capacity to use nutrients from non-fishmeal sources have a reduced cost of feeding advantage.

develop technologies leading to improved marketability of animal products.

ACCOMPLISHMENTS:  Scientists at the U.S. Meat Animal Research Center, Clay Center, Nebraska, in collaboration with the National Cattlemen’s Beef Association and five beef companies, produced a non-invasive beef tenderness prediction system on a broad sampling of cattle types that was validated in several packing plants. 

IMPACT/OUTCOME:  Previously, the only method to accurately predict whether or not a beef carcass would produce tender or tough steaks was to remove a steak from the carcass and evaluate tenderness mechanically, resulting in a high cost from product devaluation.  The beef industry has sought the development of a non-invasive method for beef tenderness prediction.  Based on the current level of interest in adoption of this technology, it is expected to have an annual multi-million dollar impact on the beef industry and its consumers.

ACCOMPLISHMENTS:  There is high potential to make milt meal from the large volumes of pollock and salmon in Alaska.  Today most of the milt is included in the production of fishmeal or discarded.  A study was conducted by a team of University of Alaska and ARS scientists at the Subarctic Agricultural Research Unit to develop an industrial scale extraction method for the production of high quality milt meal from both pollock and salmon.

IMPACT/OUTCOME:  The meals were found to have high concentrations of nucleic acids.  There are a number of potential new high value uses for these kinds of meals in diets of fish, farm animals, and pets.

ACCOMPLISHMENTS:  An ARS scientist at Newport, Oregon, in collaboration with an ARS scientist in Corvallis, Oregon, discovered significant levels of genetic variations for bioaccumulation of cadmium in Pacific oysters.  Ongoing international negotiations that could limit cadmium content in seafood may impact the marketability of Pacific oysters.  There is a possibility that selective breeding can modify this character.

IMPACT/OUTCOME:  These preliminary results suggest that the cadmium content of Pacific oysters can be modified by selective breeding to meet new market standards.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  Scientists in the ARS Bovine Functional Genomics Laboratory at Beltsville, Maryland, in collaboration with colleagues at the University of Missouri-Columbia, have identified a mutation in the osteopontin gene promoter region of dairy cattle, which is a candidate quantitative trait nucleotide underlying a previously identified quantitative trait locus for protein percentage located on bovine chromosome 6. 

IMPACT/OUTCOME:  The percentage of milk made up by the protein fraction is of critical importance to the dairy industry (e.g., for cheese production).  A provisional patent application for using this polymorphism information in marker assisted selection programs was submitted and has been licensed by a multi-national pharmaceutical company that is currently validating its effectiveness.

ACCOMPLISHMENTS:  Previously, markers for two genes associated with differences in beef tenderness (u-calpain and calpastatin) have been proposed to improve meat quality.  It was not known if the effects of these two commercially available gene markers would add together or if the effect of one gene marker would be masked by the other.  ARS researchers at Clay Center, Nebraska, tested these markers in two diverse populations of cattle (both Bos indicus and Bos taurus) and crosses between these populations.  Regardless of the population, the effects of the gene markers on tenderness were nearly independent indicating that both markers can be used to genetically improve tenderness.  Additionally, a new u-calpain marker was developed and released to industry that allows use of the test across all breed populations.

IMPACT/OUTCOME:  Inadequate beef tenderness is the principal cause of consumer dissatisfaction. These DNA marker tests have been transferred to industry and are being offered commercially by several companies for genetic screening and improvement programs for seedstock breeders and their customers.

ACCOMPLISHMENT:  AMP-activated protein kinase (AMPK) is an enzyme complex that plays a key role in sensing cellular energy (AMP/ATP) levels, maintaining intracellular energy homeostasis and, on the whole animal level, in regulating energy balance and food intake.  Scientists in the ARS Growth Biology Laboratory at Beltsville, Maryland, have identified seven distinct chicken AMPK gene homologues and have studied their expression in different tissues.

IMPACT/OUTCOME:  Regulation of feed intake and energy balance is critical to profitable poultry production.  The expression of these genes confirmed, for the first time, the existence of a functional AMPK pathway in chickens and indicated that AMPK is likely to be a master cellular energy sensor/regulator.  These findings provide new information related to the regulation of feed intake, energy balance, and body weight in chickens at the molecular level.

ACCOMPLISHMENT:  The Inhibitor of DNA Binding/Differentiation (ID) proteins play a role in determining the number of muscle cells that develop in an organism.  ARS scientists at the National Center for Cool and Cold Water Aquaculture characterized the ID genes in rainbow trout.  Two additional ID genes were identified and all six known ID genes were characterized with respect to their expression throughout embryonic development and adult tissues.

IMPACT/OUTCOME:  These proteins’ impact on growth is of great interest to the aquaculture community for understanding growth efficiency.

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:  A major international project has been underway since 2003 to sequence and analyze the bovine genome.  This project has been led by the research team at Baylor College of Medicine’s Human Genome Sequencing Center (Houston, Texas).  An international consortium of researchers has been working alongside the Baylor team to develop and carry out this project.  Key ARS contributions include the development of a:  1) Scaffold onto which to assemble the bovine genomic sequence.  This scaffold will allow the fine mapping of genes and their function in the genome.  2) Multi-breed DNA panel for building the bovine haplotype map.  One of the major thrusts of the bovine genome project is to develop a large pool of single nucleotide polymorphisms (SNP) for use in evaluating genetic diversity and in developing gene-based genetic improvement programs.  3) Large panel of full length complementary DNAs (cDNAs).  ARS scientists at Miles City, Montana, collected tissues from animals related to L1 Dominette 01449, the base DNA source for the bovine genome sequence.  A wide range of tissues were collected and are being used for construction and sequencing of a large number of cDNA libraries in collaboration with Genome Canada and others.  These tools will allow the determination of the function of genes in different tissues. 

IMPACT/OUTCOME:  The annotated bovine genome sequence and associated tools will enable the full scale development of genetic diagnostics for the improvement of dairy and beef cattle for traits related to production efficiency, efficiency of nutrient utilization, genetic resistance to disease, and animal adaptation to production environments.

ACCOMPLISHMENTS:  A control panel of sheep DNA was created to increase the accuracy of prion genotyping by research and commercial laboratories. Variation in the prion gene is associated with susceptibility and resistance to scrapie, a neurological disease of sheep that is similar to bovine spongiform encephalopathy (BSE) in cattle. ARS scientists at Clay Center, Nebraska, created a control DNA panel from sheep representing each of 15 prion genotypes associated with susceptibility and resistance to scrapie.

IMPACT/OUTCOME:  This DNA panel is used to detect genotyping errors and to improve the quality of genetic information.  This valuable resource is helping producers in the United States and other countries to correctly select for genetic resistance to scrapie and to achieve the industry goal of eradicating the disease from its flocks.

ACCOMPLISHMENTS:  ARS scientists at Clay Center, Nebraska, identified a panel of 40 suitable single nucleotide polymorphism (SNP) DNA markers for individual identification in swine.  This information has been released to 39 different investigators representing scientific and commercial genotyping laboratories around the world.

IMPACT/OUTCOME:  Individual animal identification is critically important for livestock biosecurity.  Until recently, DNA genotyping laboratories did not have access to a set of the most robust swine DNA markers to uniquely identify animals or accurately determine parentage.  SNP markers are easily typed with automated techniques that do not rely on human interpretation.  These markers will likely develop the framework of markers used by most commercial genotyping companies to determine individual animal identification in swine.

ACCOMPLISHMENTS:  An ARS scientist at Newport, Oregon, demonstrated that pedigrees of Pacific oysters can be reconstructed using a number of microsatellite DNA markers.  This is important because current selective breeding protocols require that genetic families be reared separately to maintain pedigree information, and experiments be highly replicated in order to account for small scale environmental variation, making oyster breeding costly.

IMPACT/OUTCOME:  The ability to mix oyster families and construct pedigrees will streamline protocols, reduce costs, and increase selection intensity, all contributing toward shortening the time to develop improved lines of Pacific oysters.

ACCOMPLISHMENTS:  ARS scientists at Leetown, West Virginia, in collaboration with researchers at West Virginia University and the University of California at Davis, applied a recently introduced DNA fingerprinting technique previously used for plant species to rainbow trout.  To complement the ongoing construction of a genetic map for rainbow trout, a project was initiated to develop a physical map of the rainbow trout genome using the Swanson 10X bacterial artificial chromosome library.

IMPACT/OUTCOME:  The integration of a physical chromosome map with the genetic map will greatly facilitate the identification of genes that affect aquaculture production traits. 

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  The security of U.S. animal genetic resources was significantly enhanced in the past year.  Samples in the ARS National Animal Germplasm collection at Fort Collins, Colorado, increased 52 percent and the number of breeds or lines increased 63 percent. In addition, a total of 19 livestock, poultry, and fish populations met minimum collection requirements considered to be secure.

IMPACT/OUTCOME:  These achievements were made possible by the contributions of 170 different livestock producers, public institutions, and companies.  Conservation of germplasm resources will allow continued ability to maintain important levels of genetic variability in the Nation’s livestock, poultry, and fish populations.

ACCOMPLISHMENTS:  Progress is being made with an additional year-class (2004) of Atlantic salmon from 5 different sources obtained from collaborators to continue the breeding program at the ARS National Cold Water Marine Aquaculture Center, Franklin, Maine.  Eyed eggs were disinfected, incubated, hatched, and fish reared as parr (juveniles) in indoor (greenhouse) tanks. Early growth evaluation of different genetic stocks during the parr stage was completed and data are being analyzed.  Parr from the 2003 year-class were pit tagged, vaccinated, and stocked into replicated communal tanks for evaluation of growth to smolts.  Smolts from the 2003 year-class were transferred into sea cages at an aquaculture lease site operated by industry collaborators.

IMPACT/OUTCOME:  Fish will be reared through 2006 to market size, data collected on harvest weight, and analyzed to determine broodstock to be spawn as a selected line.

ACCOMPLISHMENTS:  First generation tetraploid male and female rainbow trout matured this year and produced a number of tetraploid and triploid crosses for further evaluation.  The tetraploid fish generated in this project by ARS scientists at the NCCCWA, Leetown, West Virginia, offer opportunity to produce 100 percent triploid offspring, which are desirable because they are sterile and potentially faster growing than typical diploid production animals.  Initial studies suggest that the triploid fish have the expected growth advantage at a very early age.

IMPACT/OUTCOME:  The trout industry is anticipating this technology to reduce production costs.

ACCOMPLISHMENTS:  ARS scientists at Leetown, West Virginia, exposed 75 full-sib families to a challenge with a pathogen, Flavobacterium psyhrophilum, the causative agent of bacterial coldwater disease.  This disease is of major concern to the trout industry.  The objective of the research was to determine genetic variation for resistance to this bacteria.  A standardized challenge was applied to 45 replicated and 30 unreplicated family groups.  Mortality ranged from 28 to 99 percent and was similar in replicates.  Genetic relationships among multiple families with low mortality indicate that there is a genetic component of resistance to this pathogen.

IMPACT/OUTCOME:  This research demonstrates that rainbow trout can be selectively bred for enhanced disease resistance.

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:  ARS scientists at Beltsville, Maryland, have found that long-term storage and freeze-thawing did not prematurely increase capacitation or decrease acrosome integrity in viable swine sperm as previously suggested.  However, compared to fresh semen, the ability of sperm to undergo capacitation after specific lab treatment was greatly decreased by storage and freeze-thawing, and responses varied among individual boars.

IMPACT/OUTCOME:  Boar sperm that have been subjected to long-term low temperature liquid storage or freeze-thawing are less fertile after artificial insemination than freshly collected sperm. Two key physiological processes must occur in order for the sperm cell to be functionally fertile:  capacitation and release of enzymes from the acrosome.  However, low temperature liquid storage and cryopreservation are thought to prematurely increase lipid fluidity in the plasma membrane (an early sign of capacitation) and decrease the integrity of the acrosome rendering sperm less capable to survive in the reproductive tract of the female, making them less capable of fertilizing eggs.  Future work is addressing the differences among boars to determine if these differences are correlated with fertility.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  Although there is market demand for fresh strawberries in the fall and winter, most current strawberry production methods produce fruit only in the spring.  ARS scientists at the Appalachian Fruit Research Station, Kearneysville, West Virginia, have developed a new transplant propagation technique that causes strawberry plants to flower within four weeks after field establishment, and that can be used to grow strawberries that fruit in both the fall and the spring. 

IMPACT/OUTCOME:  This propagation technique stretches the picking season to late fall when the price is greatest and also lessens the risk of weather-related crop loss. 

ACCOMPLISHMENTS:  Annotation is the process of taking raw DNA sequence and adding analysis and interpretation to determine the biological significance of the DNA code, i.e., what do the DNA sequences mean?  ARS scientists at Beltsville, Maryland, and Weslaco, Texas, in cooperation with a large international effort, have annotated much of honey bee genome which had been sequenced by the Baylor College of Medicine’s Human Genome Sequencing Center.  The honey bee is the first agricultural and beneficial insect to be sequenced.

IMPACT/OUTCOME:  The annotated genome will be used to improve bee health and pollination efficiency.  This effort is crucial since it comes at a time when the honey bee is being devastated by a variety of invasive parasitic mites (particularly varroa and tracheal mites) and diseases.  With further annotation, the honey bee genome project will enable scientists to effectively deal with the problems faced by beekeepers.

ACCOMPLISHMENTS:  Previously, ARS scientists at the Donald Danforth Center in St. Louis, Missouri, demonstrated how to remove the major human allergen in soybean (P34/Gly m Bd 30k) by genetic engineering.  The same scientists, in collaboration with the University of Illinois, have now discovered two accessions of conventional soybean in the USDA soybean germplasm collection in which nature has accomplished the same feat by a natural deletion of the gene that encodes the allergen. 

IMPACT/OUTCOME:  This finding provides a basis for producing conventional soybeans with greatly reduced allergenicity and improved digestibility and nutritional value, especially for uses where genetically enhanced soybeans are not accepted. 

ACCOMPLISHMENTS:  ARS, in conjunction with its partner, Cotton Incorporated, released three improved lines of upland cotton to the public for use in breeding new varieties.  For the first time, these lines combine some of the excellent fiber quality of Acala-type cottons with the heat tolerance of Delta-type cottons. 

IMPACT/OUTCOME:  The new germplasm will be used as a resource for breeders attempting to improve fiber quality of Mid-South and Southeast cottons, as well as for breeders attempting to improve heat tolerance of Acala cottons for the Western United States.  The outcome will be better yields and quality of cotton fiber in the United States.

ACCOMPLISHMENTS:  ARS scientists at Dawson, Georgia, in collaboration with the University of Florida, developed an innovative strategy for developing peanut germplasm resistant to the devastating impact of tomato spotted wilt virus (TSWV) infection.  Physiological and genetic responses under heavy TSWV pressure showed that the physiological gas exchange and drought responses of TSWV-infected plants were correlated with specific gene expression products throughout the growing season.

IMPACT/OUTCOME:  This finding will facilitate the improvement of production methods and breeding programs that increase the resistance of peanut to TSWV.

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

ACCOMPLISHMENTS:  New computer tools for corn researchers have been developed by ARS researchers at the Maize Genetics Stock Center, Urbana, Illinois, in cooperation with the ARS Maize Genetics/Genomics Database, Ames, Iowa.  This new curational software enables data about corn genetic stocks to be entered directly into the ARS Maize Genetics/Genomics Database.

IMPACT/OUTCOME:  Corn breeders and other researchers now have faster and better access to all the data for corn genetic stocks at one easy-to-use website.

ACCOMPLISHMENTS:  ARS scientists at Ames, Iowa, constructed genetic maps of soybean and common bean from public databases and used CMap, a program that allows for the side-by-side comparisons of chromosomal maps of any species.

IMPACT/OUTCOME:  These new maps support the direct transfer of genetic progress in one species to another, without the time and expense required for additional research.  For example, genes for Asian soybean rust resistance in common bean may now be mapped, and the information can be immediately translated to soybean.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at Columbia, Missouri, discovered that three genes control the level of linolenic acid in soybeans.  The scientists have now developed molecular markers specific for the beneficial genetic mutations in two of these fatty acid desaturase genes (GmFAD3A and GmFAD3C). 

IMPACT/OUTCOME:  The use of these mutation-specific molecular markers to identify breeding lines homozygous for these alleles will expedite the development of elite soybean varieties with superior oil quality.  Commercial production of soybeans with genetically reduced linolenic acid concentration provides the oil supply that fuels an industry led drive to improve the nutritional quality of food products with low-trans isomer formulations and lower the use of hydrogenated soybean oil. 

ACCOMPLISHMENTS:  Plant architecture genes control plant structure and effect important traits such as number of flowers, fruit size, and tree shape.  ARS researchers at Albany, California, have cloned the Ultrapetala genes, which affect bloom formation and determined that these genes are key players in determining plant architecture. 

IMPACT/OUTCOME:  The results can be applied to improve agriculturally important plants for many valuable traits from fruit size to developing fruit trees that are ideal for mechanical harvesting.

ACCOMPLISHMENTS: ARS researchers and collaborators at the University of Wisconsin have demonstrated that feeding an oat antioxidant, called avenanthramide, reduced exercise-induced inflammation in rats. 

IMPACT/OUTCOME:  Antioxidant compounds found in oats may have healthful benefits for specific cellular mechanisms.  Further research to characterize these oat antioxidants will provide consumers with new knowledge about the nutritional value of whole grains and enhance the use and value of oats.

ACCOMPLISHMENTS:  The functional role of genes that encode invertase, a sugar-metabolizing enzyme found in corn cell walls, has been determined by ARS researchers at Gainesville, Florida, in collaboration with researchers at the University of Florida.  The scientists used biotechnology to examine the effects of eliminating genes for invertase.  Results showed a pivotal role for these genes that can be exploited to enhance the use and competitiveness of corn. 

IMPACT/OUTCOME:  Enzymes that metabolize sugar affect the value of corn for food and non-food uses.  Identifying the functions of invertase in the plant is the essential first step in learning how to improve carbohydrate metabolism in corn. 

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:  New genetic technology is needed that allows the removal of unwanted transgenes after their usefulness is ended (for example, antibiotic resistance genes used as selectable markers).  ARS scientists in Albany, California, have shown that recombination systems capable of accomplishing this removal, and previously demonstrated in yeast, also function efficiently in higher plants.  This technology is intended to be put in the public domain and made available for general use, so that access to this advance in genetic engineering methods is available to all.

IMPACT/OUTCOME:  Technology for removing unwanted genes will be available to all practitioners.  Some of the concerns of the public about safety of genetically engineered foods will be eliminated.  Consumers will have more confidence in their food supply and in the efficacy of science to improve foods.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  ARS researchers characterized the first pea Bacterial Artificial Chromosome (BAC) library, a valuable genetic tool for genomic and gene function analyses in this crop. 

IMPACT/OUTCOME:  This new genetic tool will facilitate the discovery and cloning of genes governing economically important pea traits such as yield, disease resistance, plant architecture, and mineral content. 

ACCOMPLISHMENTS:  ARS researchers in Beaumont, Texas, have identified DNA markers associated with resistance to rice blast for blast biotypes that occur in the United States.  The markers were then used in cooperation with other ARS researchers at Stuttgart, Arkansas, to identify accessions in the USDA rice collection that have blast resistance. 

IMPACT/OUTCOME:  Rice blast is a fungal disease that causes significant crop losses for rice growers worldwide.  Use of these DNA markers will improve the speed and efficiency of breeding new varieties for U.S. rice growers with improved rice blast resistance.

ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland, developed the only pinto beans in the world with four genes for resistance to the hyper variable bean rust pathogen, Uromyces appendiculatus, and two genes for resistance to the bean common mosaic (BCMV) and bean necrosis (BCMNV) potyviruses.  They have released six high yielding germplasm lines with rust disease resistance.

IMPACT/OUTCOME: In the United States, bean rust occurs frequently on snap beans in Florida, Tennessee, and other Southern States, and on dry beans east of the Rocky Mountains.  This new germplasm will benefit public and private breeders in commercial seed companies, as well as bean producers and consumers.

ACCOMPLISHMENT:  ARS scientists at Lubbock, Texas, established a desiccation tolerance EST (expressed sequence tag) collection and the bioinformatics tools required for the accompanying EST database.  A comprehensive profile of gene expression associated with desiccation tolerance revealed new insights into the role of late embryogenesis abundant proteins in cellular protection.

IMPACT/OUTCOME:  The ESTs and database have greatly enhanced our understanding of the genetic components associated with desiccation tolerance in plants.  They have provided numerous new candidates for dehydration tolerance genes that may enhance the drought tolerance capacity of U.S. crops.

ACCOMPLISHMENTS:  In cooperation with the company, SePRO, ARS scientists at Oxford, Mississippi, determined the genetic basis for resistance of hydrilla (an aquatic invasive plant) to the herbicides flurideon, norflurazon, diflufenican, picolinafen, flurochloridone, beflubutamid, and flurtamone.  The inheritance gene mutations governing the activity of phytoene desaturase (PDS) enzymes conferred cross resistance to norflurazon and overall negative cross resistance (hypersensitivity) to these PDS-inhibitor herbicides.  Arabidopsis thaliana plants transformed with these mutated PDS genes from hydrilla had similar patterns of cross resistance to the herbicides.  These plants exhibited normal growth and development even after long-term exposure to herbicide.

IMPACT/OUTCOME:  This work has identified the basis for herbicide resistance in a noxious aquatic weed, one of the most serious pests of waterways in the United States.  The results provide a basis for research to overcome resistance and re-establish control of this invasive species. 

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

ACCOMPLISHMENTS:  ARS researchers at College Station, Texas, in collaboration with Texas A&M University researchers, have completed the cytogenetic map of sorghum.  The 10 chromosomes of sorghum were digitally imaged, revealing the architecture of each sorghum chromosome. 

IMPACT/OUTCOME:  Mapping the sorghum genome provides a foundation for identifying the gene rich regions of the sorghum genome.  Results will advance the identification of valuable agronomic genes that can contribute to more environmentally adapted and disease resistant sorghum.

ACCOMPLISHMENTS:  ARS researchers established the first genetic map for the important spice crop garlic.  In doing so, they demonstrated that garlic gamete and progeny formation was strictly sexual, not asexual, and that diversity stemming from sexual reproduction could be exploited with classical crop breeding approaches.

IMPACT/OUTCOME:  Garlic breeding will be accelerated.  Before this, only random mutagenesis could be used to generate novel genetic variability and traits in two parental lines could not be combined via crossing and recombination

.

ACCOMPLISHMENTS:  ARS scientists at Fargo, North Dakota, in cooperation with researchers at North Dakota State University, have made advances in mapping the sunflower genome by developing a set of sunflower trisomic lines which each have one extra chromosome.

IMPACT/OUTCOME:  The large size of the sunflower genome makes it difficult to develop physical maps.  Sunflowers breeders will use this information to better understand the structure of the sunflower genome.

Indicators:

During FY 2005, ARS will    

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

ACCOMPLISHMENTS:  During FY 2005, the 20-plus genebanks in the USDA/ARS National Plant Germplasm System (NPGS) added about 9,000 separate samples of more than 1,000 plant species to its collections, bringing to a total of 465,000 samples from more than 11,300 plant species conserved by NPGS genebanks.  Scientific interest in this germplasm has increased significantly during the last few years, with the average number of samples distributed per year totaling about 120,000, 20,000 more than the average several years ago.

IMPACT/OUTCOME:  Crop genetic diversity is conserved and distributed to researchers.  These materials are keys for continued progress in crop genetics and breeding requisite for future food security.

ACCOMPLISHMENTS:  ARS scientists at Fargo, North Dakota, conducted an exploration to collect a rare and endemic wild sunflower, Helianthus niveus, subspecies tephrodes (Algodones, dune sunflower) in California and Arizona.  Five populations were collected and added to the Sunflower Germplasm Collection in the National Plant Germplasm System.

IMPACT/OUTCOME:  More accessions of this rare, wild sunflower species are now available to search for novel genes for resistance to a multitude of insects and diseases that can be used to improve cultivated sunflowers.

ACCOMPLISHMENTS:  The U.S. corn germplasm base is narrow and only a small percent of U.S. maize germplasm is derived from exotic corns of tropical origin.  ARS researchers at Ames, Iowa; Raleigh, North Carolina; and both private and public cooperators in the ARS Germplasm Enhancement of Maize (GEM) project have developed new corn lines from exotic germplasm.

IMPACT/OUTCOME:  Corn breeders can exploit these new lines with high protein levels, unique starch properties, and increased disease resistance for developing new germplasm with a more diverse base and enhanced traits.

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

ACCOMPLISHMENTS:  ARS researchers developed and/or applied powerful new genetic markers to a broad spectrum of “specialty crops,” such as apples, pears, garlic, hops, beet, rye, wild rice, blueberries, hydrangeas, grapes, plums, apricots, pecans, walnuts, figs, and olives.

IMPACT/OUTCOME:  These valuable new genetic markers will enable rapid, inexpensive, and accurate assays of genetic variability which are key for accelerating progress in crop genetic resource conservation and breeding.  Some of the markers can be used for more rapid and accurate selection of specific high value traits, e.g., disease resistance in hops.

ACCOMPLISHMENTS:  ARS researchers developed superior new varieties and breeding stocks for an extremely broad spectrum of “specialty crops,” such as prize-winning ornamental peppers, table grape varieties, hardy winter peas, white mold resistant pinto beans, thornless blackberries, high yielding and rapidly maturing potatoes, disease resistant pecans, high-quality blueberries, high yielding sugarcane cultivars, novel southern pea varieties, disease resistant sweet potatoes, superior subtropical ornamental shrubs, and disease tolerant elm trees.

IMPACT/OUTCOME:  Development of superior varieties and valuable breeding stocks provides valuable new genetic resources for the U.S. “specialty crops” industry.

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

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

Analysis of Results:  This goal is related to food safety and the security of the U.S. agricultural production system (crop and livestock protection).  Under Goal 3, 17 Indicators (in Italics) are aligned under 8 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2005.  Forty-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 2005, ARS will

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

ACCOMPLISHMENTS:  Shiga toxin producing E. coli O157:H7 were isolated from various fair environments following human outbreaks of E. coli O157:H7.  Scientists at Clay Center, Nebraska, collaborated with two State Departments of Agriculture and the Center for Disease Control (CDC) in the investigation of these human outbreaks of E. coli O157:H7 at fairs and petting zoos in Raleigh, North Carolina, and Tampa, Orlando, and Plant City, Florida.  These scientists developed methodology to isolate E. coli O157:H7 from the various fair environments and thus helped determine the likely outbreak vehicle and sources.  In collaboration with State officials working at a contaminated fair site, these scientists determined that E. coli O157:H7 can survive for many months in agricultural soils and that environmental decontamination techniques against E. coli O157:H7 will probably not be 100 percent effective or may even worsen contamination.

IMPACT/OUTCOME:  This information developed by ARS was used for CDC recommendations to help keep petting zoo and fair sites safe for visitors, and particularly for very young children.

ACCOMPLISHMENTS:  Engulfment of bacterial pathogens, such as Salmonella typhinurium DT104, by rumen protozoa in cattle, increases their virulence.  Easily available and effective substances are needed to kill the protozoa in order to increase both animal productivity and food safety.  Scientists in Ames, Iowa, developed an antiprotozoal screening assay to screen test compounds, particularly non-drug substances, for their ability to kill rumen protozoa.  These scientists found some natural plant extracts, i.e., yucca and rosemary, which effectively control protozoa in the rumen without harming the general fermentation. 

IMPACT/OUTCOME:  Use of these plant extracts which kill protozoa could greatly reduce the incidence and shedding of Salmonella and other pathogens at critical time points in the production of both beef and dairy cattle.

ACCOMPLISHMENTS:  Campylobacter contamination is a serious food safety issue and optimum production practices are needed to reduce the incidence in live poultry.  Scientists at Athens, Georgia, placed day-of-hatch chicks on wood shavings in high (approximately 80 percent) and low (approximately 30 percent) humidity controlled pens and challenged the chicks with C. jejuni (the most commonly found species of Campylobacter).  Significantly higher Campylobacter colonization rates were observed in chickens raised under the high humidity conditions.  Thus, the influence of relative humidity on transmission rates is an important factor influencing transmission of this poultry food safety pathogen.

IMPACT/OUTCOME:  This information demonstrating that high humidity enhances the transmission of Campylobacter jejuni could lead to practical applications in production practices to help reduce Campylobacter colonization in broilers.

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

ACCOMPLISHMENTS:  New sources of genes that bring about aflatoxin resistance in corn are needed.  Insect damage and their associated ear mold toxins cause hundreds of millions of dollars in losses each year.  Thus, incorporation of new insect resistance genes into corn could reduce mycotoxins.  Scientists in Peoria, Illinois, found that plant derived genes that either killed insects or enhanced resistance to insects is in direct correlation to expression of the genes.  The corn plants that expressed both genes had significantly less damage by caterpillar and beetle pests.  

IMPACT/OUTCOME:  Incorporation of these genes into corn through multigenic transgenic means could result in reduced levels of mycotoxins, thus increasing both the safety and the exportability of U.S. corn.

ACCOMPLISHMENTS:  Genes encoding many different aspects of corn physiology must be identified and introduced for use in selective breeding of aflatoxin resistant corn.  Scientists in New Orleans, Louisiana, and their cooperators used proteomics, the study of proteins, to identify fungal resistance related and stress responsive proteins/genes in corn.  Genes encoding many of these resistance associated proteins (RAPs) have been cloned, and two have been further characterized.  Corn lines selected for superior agronomic traits, ear rot resistance, and aflatoxin resistance (in either temperate or tropical backgrounds) for 7 to 8 generations are now undergoing final testing for aflatoxin resistance.

IMPACT/OUTCOME:  This progress could lead to an official release in the next 2 to 5 years of these resistant lines which also will have superior agronomic performance.

Indicators:

During FY 2005, 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.  ARS will also ensure that the technologies are transferred to the Food Safety Inspection Service (FSIS) and the Food and Drug Administration (FDA); the Department of Homeland Security; and industry for implementation into Hazard Analysis Critical Control Point (HACCP) programs, and Good Manufacturing Practice (GMP) protocols for both large and small producers and processors.

ACCOMPLISHMENTS:  At the request of the FSIS, ARS scientists at Beltsville, Maryland, evaluated the accuracy and reliability of temperature indicator devices used by consumers.  The thermometers selected were: digital probe, bimetal probe, forks/tongs, remote wireless, as well as disposable indicators that change color at specified temperatures.  None of the thermometers tested consistently reached the end point temperature within the manufacturer's recommended time and several models did not reach the end point temperature even after an extended time period.  At the manufacturer's recommended time, the remote wireless thermometers were the least accurate.  The accuracy of the other thermometers was dependent on the meat product and the cooking method.  Because the thermometers indicated that the temperature was lower than the actual temperature, consumers using these thermometers when cooking meat products would actually cook the product to higher temperatures ensuring food safety but reducing the quality of the product.

IMPACT/OUTCOME:  FSIS is concerned that consumers cook meat products to safe end point temperatures before consumption.  As a result of this research, FSIS will revise their food safety information on consumer use of instant-read-thermometers to further reduce the potential for foodborne illnesses.

ACCOMPLISHMENTS:  Efficient methods are needed by regulatory agencies to detect pesticide residues in foods to ensure their safety for the consumer.  However, a serious issue is the cost of maintaining the testing equipment to ensure it is in optimal condition for use.  Such costs are often prohibitive for routine testing laboratories.  Scientists at Wyndmoor, Pennsylvania, developed a different approach called automated direct sample introduction.  It reduces the need for frequent instrument maintenance by eliminating many contaminants before final analysis.  This step also improves the detection of the pesticides.

IMPACT/OUTCOME:  Regulatory agencies, such as FSIS, that implement this approach will benefit considerably through significant cost savings and ease of use, and by improved detection efficiency.

ACCOMPLISHMENTS:  ARS scientists at various locations took the lead in developing new and better technologies that have regulatory, industry, and research use.  A variety of new, improved and innovative methods were developed to detect, differentiate, type, and quantify numerous foodborne pathogens.  For example: scientists at Wyndmoor, Pennsylvania, developed a portable fiber optic biosensor that can detect very low levels of E. coli O157:H7 bacteria in ground beef within five hours.  Higher levels of contamination can be detected in even less time.  The biosensor and battery pack can be carried in a briefcase, allowing assays to be performed at the farm, processing plant, distribution center, and retail store.  ARS scientists at Dover, Delaware, developed a real-time molecular method to quickly and easily detect a broad spectrum of Noroviruses (NV), and hepatitis A and E viruses in the stools of infected individuals.  This method involves the detection of viral genes through the polymerase chain reaction.  The assay allows over 90 percent of the strains of NVs circulating in the world today to be detected within three hours.  ARS scientists at Albany, California, characterized over 300 Campylobacter strains through the identification of very specific proteins which are particular to certain species and sub-species.  The technology which can be used for any pathogen of concern, including E. coli O157:H7 and Salmonella, provides a fast, high throughput method for identifying and differentiating specific species and strains.

IMPACT/OUTCOME:  Technologies were transferred to the end users, mainly FSIS, FDA, CDC, and DHS who work with ARS to refine them for (automated) day-to-day use.  Methods for virus detection will find extended use since they are a problem in water and foods such as shellfish, and are commonly associated with outbreaks on cruise ships and Navy vessels, and among troops particularly in Operation Desert Storm.

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. ARS will also ensure that these technologies can be implemented into HACCP and GMP protocols and have efficacy for approval by FSIS and FDA.

ACCOMPLISHMENTS:  Shell eggs are required to be cleaned/washed before packaging and marketing.  The current Federal guideline in the U.S. requires that the wash water be at least 90º F or 20º F warmer than the warmest egg entering the processing facility.  In the hot summer months using wash water at high temperatures can cause the egg to become too hot leading to conditions that allow bacteria in and on the eggs to grow.  ARS scientists at Athens, Georgia, in collaboration with scientists at Auburn University, examined the effects of using cool water washing of shell eggs on the microbial and physical quality of the final product. The research indicated to the regulatory agencies and industry that shell eggs can be commercially processed using cooler water without any reduction in their safety.

IMPACT/OUTCOME:  The research indicated that washing with cooler water enhanced the product quality. It also was more cost effective for the typical shell egg washing company to maintain the cooler wash water temperature during processing.  A commercial transfer study was conducted in two separate shell egg processing facilities showing the efficacy of the processing change.

ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, developed new washing procedures and sanitizer treatments for whole and fresh cut cantaloupe.  Hot water surface pasteurization with water at 170º F for three minutes using commercial scale equipment resulted in reductions of E. coli and Salmonella populations in excess of 99.999 percent. Experimental and simulation data on thermal penetration profiles indicated that the internal temperature of melons treated with hot water did not increase rapidly compared to the rind temperature.  Edible flesh 10 millimeters from the surface of the rind remained cool regardless of the process temperature.  The data clearly demonstrate the efficacy and utility of this treatment for reducing the risk of foodborne illness from consumption, while maintaining sensory qualities and extending the shelf life of fresh-cut cantaloupes.  Cut melon pieces could also be directly treated with nisin plus sodium lactate or sodium lactate plus potassium sorbate to effectively reduce pathogen populations without adverse effects on quality attributes.

IMPACT/OUTCOME:  Outbreaks of foodborne illness due to consumption of fresh and fresh-cut produce, especially cantaloupe, contaminated with bacterial pathogens continues to be a concern to regulatory agencies and industry.  This research will directly assist the FDA in developing good agricultural practices and good manufacturing practices, and developing a Guide to Minimize Microbial Safety Hazards for Fruit and Vegetables for industry. 

undertake genomic and proteomic analyses of pathogens affecting food safety.  ARS will also develop bioinformatic databases and tools, and predictive user-friendly models to understand pathogen behavior and acquisition of virulence characteristics under various stress conditions.  In addition, the Agency will 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:  Genetic sequencing and annotation of microbial genomes yields fundamental information about the organism and is critical for definitive knowledge about pathogens.  ARS scientists from Albany, California, in collaboration with The Institute for Genomics Research (TIGR), sequenced the genomes of four different species of foodborne Campylobacter.  The sequence data revealed new information regarding the population structure, virulence factors, lateral transfer of DNA, gene regulation, and metabolism of Campylobacter species.  The Albany scientists subsequently developed a new genotyping system used to genotype about 500 strains of Campylobacter isolated from a variety of sources including humans, animals, and food.  A strong association between animal host and sequence type was identified that indicated potential biological fitness differences among Campylobacter strains.

IMPACT/OUTCOME:  The availability of new genetic information increases our understanding of why a bacterium can make you sick (pathogenicity and virulence), and how it can survive and grow in foods even under stressed conditions.  The information facilitates the development of better and more rapid detection technologies so that the human illnesses can be attributed to a particular food source.  Such research also increases our understanding of the epidemiology of outbreaks of foodborne illness, and furthers the development of data for risk assessment, which is used by FSIS, FDA, and other regulatory agencies worldwide to reduce foodborne diseases.

ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, produced robust models that now enable risk assessors and food safety managers to predict the activity of Listeria monocytogenes in ready-to-eat delicatessen salads at different storage temperatures and product formulations, and in commercially prepared cheeses.

IMPACT/OUTCOME:  Predicting L. monocytogenes in ready-to-eat foods is a high priority for FDA/FSIS. The models developed by ARS directly assist Federal regulatory agencies in developing risk assessment information for consumers, and food companies in designing salad formulations that present lower health risks.  In addition, ARS’ research also helps U.S. food companies meet new Federal regulations.

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 2005, ARS will

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

ACCOMPLISHMENTS:  ARS scientists at the National Animal Disease Center in Ames, Iowa, have successfully sequenced the full genome of the RB51 vaccine strain of Brucella abortus.  This sequence is currently being compared to its parent strain and other B. abortus strains to identify genetic differences which may influence protection, immunologic responses, and virulence.  Preliminary work has identified genetic differences when RB51 is compared to its parent strain or a sequenced field strain.  It is anticipated that this sequence will be valuable for identifying genes that mediate protection and assisting in development of new vaccines for wildlife or domestic livestock that induce greater protection.

IMPACT/OUTCOME:  Comparative microbial genomics, studies to identify genetic variations associated with differences in phenotypic or biological traits, is a powerful way to identify genes and gene products that may be important in protection and may be useful in developing improved vaccines and diagnostic tests.

ACCOMPLISHMENTS:  Bovine babesiosis is a tick borne, hemoparasitic protozoal disease.  The United States is currently free of the disease, but there is a significant threat of re-introduction into the United States from Mexico.  An effective vaccine would provide an important tool to alleviate this threat.  Babesial parasites have a complex life cycle, including sexual stages in tick vectors and asexual reproduction during the erythrocytic stage in the mammalian host.  Ideally, an effective anti-babesial vaccine will include parasite antigens of known function that will induce immune responses that prevent disease in the mammalian host and block transmission from tick vectors.  ARS scientists in Pullman, Washington, have successfully constructed 45,000 expressed sequence tags (ESTs) covering 35 to 60 percent of the genes (and 13,000 coding regions) of Babesia bigemina and Babesia bovis.

IMPACT/OUTCOME:  The lack of a vaccine for control of babesiosis leaves U.S. cattle vulnerable to this disease if it was re-introduced from Mexico.  Various estimates of the cost associated with a re-introduction have been made; a conservative estimate would be $500 million per year.  Babesia vaccine development requires the characterization of the protective immune mechanisms, the identification of protective antigens from the parasites, and the development of effective delivery systems.

ACCOMPLISHMENTS:  Bordetella bronchiseptica is an important respiratory pathogen of pigs associated with the porcine respiratory disease complex.  When pathogenic bacteria encounter their host, they react by turning on specific genes which enable them to establish an infection and cause disease.  ARS scientists at the National Animal Disease Center in Ames, Iowa, successfully created a microarray of B. bronchiseptica genes.  Using the B. bronchiseptica genome sequence, a DNA microarray was designed on which each gene of the bacteria was represented.  As an initial experiment, this microarray was used to monitor which genes of B. bronchiseptica were expressed when the bacteria were grown at 37 degrees C and 23 degrees C, representing body temperature and room temperature, respectively.

IMPACT/OUTCOME:  Until recently, monitoring what genes are turned on or off in response to infection has been difficult.  With the advent of microarray technology and whole genome sequencing, ARS has been able to identify proteins that are produced during infection that are potential vaccine candidates.

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

ACCOMPLISHMENTS:  Intensive genetic selection for fast growing high yield birds has led to tremendous improvements in production efficiency.  However, selection pressure for rapid growth has negatively affected the normal development of the musculoskeletal system.  ARS scientists have been investigating the molecular mechanisms of tibial dyschondroplasia (TD), a common poultry skeletal problem, using a disease model that employs thiram (a fungicide) to disrupt chondrocyte growth and differentiation with the goal of finding whether this important skeletal problem can be prevented using nutritional means.  ARS scientists examined the changes in gene expression and the cellular and metabolic alterations in the growth plate during early periods of the onset of TD.  These studies revealed that TD was not induced by an aberrant pattern of gene expression in the growth plate, but was due to the death of endothelial cells that cause capillary vessel degeneration that leads to subsequent chondrocyte death. 

IMPACT/OUTCOME:  These studies provide insight into the pathogenesis of TD.  They will be useful in identifying the nutritional factors that may help prevent blood vessel death and TD. 

ACCOMPLISHMENTS:  ARS scientists have determined critical innate immune markers required for effective immune responses against porcine reproductive and respiratory syndrome (PRRS).  Ongoing genetic studies with University Nebraska-Lincoln scientists indicate that there may be correlations between levels of certain innate cytokines and resistance to PRRS associated pathologies.  ARS scientists have demonstrated that PRRS virus infection does not result in the induction of type I interferons in MARC 145 cells as would be expected with most ribonucleic acid viruses. 

IMPACT/OUTCOME:  These results are significant because both IFNA and IFNB (type I interferons) are members of the innate immune system, which is typically viewed as the first responder of the immune system.  Activation of this response signals other branches of the immune system to become activated and mount a protective immune response.  The fact that PRRS virus is capable of suppressing the activation of this response may explain the general delayed immune response to PRRS virus infection.  Elucidation of the mechanism of PRRS virus suppression of the type I interferon response may provide targets for novel vaccination approaches to control this important disease.

ACCOMPLISHMENTS:  Vesicular Stomatitis Virus (VSV) causes a disease in horses, cattle, swine, and occasionally sheep and goats that resembles foot-and-mouth disease.  Although generally self-limiting, it can have severe economic consequences by reducing production through recrudescence and secondary bacterial infection. Transmitted by a number of biting flies, the common biting midge of the Northern Plains is one of the important vectors in the United States.  ARS explored the physiology of the transmission of VSV by this biting midge vector, Culicoides sonorensis, by creating cDNA libraries of the insect’s midgut cells and salivary glands during the process of infection.

IMPACT/OUTCOME:  The creation of cDNA libraries provides a tool for determining which biting midge genes are involved in the infection process of the fly.  Beyond biological interest, an understanding of the physiological mechanisms of vector infection will provide additional targets for suppression of VSV transmission.  Potential mechanisms to disrupt transmission include genetic alteration of the biting midges to make them non-susceptible to VSV, creation of transmission blocking vaccines (administered to livestock) that disrupt the vector infection process, or the use of antiviral preparation administered to flies.

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

ACCOMPLISHMENTS:  ARS scientists have discovered an avian rotavirus in specimens from turkeys with poult enteritis and broiler chickens with runting-stunting syndrome.  Rotaviruses are well known enteric pathogens that have been minimally characterized in poultry.  Initial pathogenesis studies were performed with clinical specimens containing rotavirus.  Identification of the viral agents associated with poult enteritis and the new similar condition in chickens, broiler runting-stunting syndrome, is critical to controlling the disease. 

IMPACT/OUTCOME:  Poult enteritis mortality syndrome (PEMS) is a highly infectious disease of young turkeys. PEMS was first reported in North Carolina in 1991.  Since then, PEMS and similar disease conditions have been reported in most regions where turkeys are commercially produced and are costing the poultry industry millions of dollars annually.  The major impact of PEMS is due to mortality and decreased production as turkeys are stunted and grow poorly when affected by the disease.  Currently the agent or agents that cause PEMS are unknown. 

ACCOMPLISHMENTS:  New methods were developed and validated by ARS scientists for geographically extensive and site intensive surveys and inventories of parasites in ungulate hosts based on the application of molecular sequence data.  Protostrongyle nematodes include pathogenic parasites that reside in the pulmonary system, skeletal musculature, or the central nervous system of their ruminant hosts.  Identification based on either adults in tissue and tissue spaces, or larval parasites in feces has remained problematic, and has hampered a detailed understanding of host distribution and geographic range.  Such information is critical in defining the potential for disease, and the degree to which parasites may be shared among a number of different ungulates.  A combination of comparative morphology and molecular analyses were applied to define the host and geographic range for Parelaphostrongylus odocoilei in North America.  Molecular identification of larvae indicates that the protostrongylid parasite occupies a broader geographic range in western North America than previously reported.  A total of 2,124 fecal samples from 29 locations from thinhorn sheep, bighorn sheep, mountain goats, woodland caribou, mule deer, and black-tailed deer were tested. 

IMPACT/OUTCOME:  This research provided significant molecular epidemiological data and represents the first study to combine extensive fecal surveys, comparative morphology, and molecular diagnostic techniques to comprehensively describe the host associations and geographic distribution of a parasitic helminth.  The development of such “epidemiological probes” will have significant applications in veterinary and conservation medicine.

ACCOMPLISHMENTS:  Vesicular Stomatitis Virus (VSV) infects animals worldwide, with constant transmission in the tropics and seasonal, sometimes epizootic, transmission in temperate regions.  A variety of biting flies (black flies, sand flies, biting midges) are known to transmit the virus.  ARS has shown that in addition to the biting midge, Culicoides sonorensis, the sand fly, Lutzomyia apache, and grasshoppers (through ingestion by livestock) are important in the transmission of VSV.

IMPACT/OUTCOME:  The addition of Lutzomyia apache to the list of vectors is of interest because this sand fly is not generally targeted for vector control and also because it could become a vector of invasive pathogens like Rift Valley Fever virus.  The discovery that it is a vector of VSV should lead to additional studies of its basic bionomics so that entomologists can develop the means for its management. Infection with VSV from the ingestion of grasshoppers is a surprising finding.  It remains to be discovered whether or not this occurs over a broad enough area that it justifies control.

ACCOMPLISHMENTS:  West Nile virus (WNV) was suddenly introduced into the New York City area in 1999 and has since spread throughout the United States and most of the Western Hemisphere.  The virus is harbored in the wild bird population and is transmitted to horses and people by a number of different mosquitoes.  Most infected horses have to be euthanized and about 20 percent of infected people have the disease with mild to fatal complications.  Older and immunocompromised people are particularly at risk of neuroinvasive disease that can cause long term disability or death.  In 2005, there were 2,819 cases and 105 deaths, making a total of 19,525 cases and 771 deaths since 1999.  In 2002 alone, there were 14,571 equine cases.  ARS discovered that WNV transmission in Wyoming is associated with the production of methane from coal fields, a process that creates abundant larval habitats for the major vector species, Culex tarsalis.

IMPACT/OUTCOME:  WNV transmission in Wyoming has been surprising intense, considering its high elevation and northern location.  Poorly drained prairie and flood plains of seasonal rivers create abundant sites for mosquitoes in the summer, so that identification of the vector of WNV in the State was not obvious.  ARS research definitely implicates Culex tarsalis as the major vector.  A major source for this species was found to be the water accumulated in an industrial process to extract methane from coal fields.  This knowledge will enable entomologists the means to design integrated control programs to suppress the populations of Culex tarsalis thereby reducing the risk of WNV transmission.

Indicators:

During FY 2005, ARS will continue to identify genetic markers and genes (target one marker, gene, or gene cluster) from food animals that can be used to identify animals with disease resistant traits.

ACCOMPLISHMENTS:  ARS scientists in Pullman, Washington, in collaboration with Colorado State University and the Canadian Food Inspection Agency, have described the distribution of the chronic wasting disease (CWD) prion protein in elk and the genotypes in elk susceptible to disease.  Their research also demonstrated the first confirmed case of CWD in an elk of the relatively rare genotype 132LL, thereby ruling out this genotype as conferring resistance to disease under field conditions.

IMPACT/OUTCOME:  Current control measures for transmissible spongiform encephalopathies in livestock depend on identification of the most appropriate tissue for diagnostic testing and identification of candidate resistant genotypes.  The genetic analysis performed by ARS scientists provides the scientific basis for selecting the brain as the most reliable indicator of disease in elk, in contrast to the tests for deer, which rely on lymphoid tissue. 

Indicators:

During FY 2005, ARS will continue to discover and develop novel technologies (target two high priority diseases) to detect and control diseases of food animal pests that impact animal and human health, animal production, and trade.

ACCOMPLISHMENTS:  Research into live Mycoplasma gallisepticum (MG) vaccine administration to layer chickens has shown that the pressure (psi) utilized for spray administration is extremely important in impacting subsequent seroconversion (positive blood tests).  A survey of the layer chicken industry showed that pressure settings used for the administration of live MG vaccine varied from 35-70 psi.  Research conducted by ARS scientists using the CPJ Vaccinator to determine the optimum pressure setting to dispense live MG vaccine demonstrated dramatic increases in MG colony counts resulting from using the lower (40 psi) setting as compared to the higher 60 psi setting. 

IMPACT/OUTCOME:  This information is important as it explains one factor (pressure setting of the vaccinator) that can impact the administration of live MG vaccines that may, in turn, result in poor vaccination results.  As a result of poor vaccine test results, re-vaccination must take place, which entails costs of additional vaccine (approximately $1,500 for a 75,000 bird house) and labor. 

ACCOMPLISHMENTS:  ARS scientists, in collaboration with scientists at Mount Sinai School of Medicine and St. Jude's Children's Hospital, successfully used reverse genetics to develop a novel cross-protective vaccine for swine flu.  Preliminary studies indicate this vaccine may have a broader level of cross protection when compared to currently available swine influenza virus (SIV) vaccines that are inactivated or killed.  These studies have also demonstrated a virulence mechanism that will impact the design of future commercially available SIV vaccines. 

IMPACT/OUTCOME:  Swine influenza is a re-emerging disease around the world as a result of several genetic changes in the viral populations being isolated from swine.  This has resulted in a reduced efficacy of current commercially available vaccines.  The availability of a highly effective vaccine for control and eradication may be the first line of defense against emerging swine flu outbreaks.

ACCOMPLISHMENTS:  ARS scientists in Beltsville, Maryland, have discovered a conserved protein named SZ-1 that is highly conserved in Eimeria tenella and two other important protozoans:  Toxoplasma gondii and Neospora caninum. The full length gene from T. gondii was characterized, expressed in a bacterial system, and the cloned protein was used to make antibodies to T. gondii SZ1.  These antibodies are providing important functional genomics research tools that can be used to determine the function of the SZ1 protein, and determine whether this protein might confer cross-protective immunity across Eimeria strains.

IMPACT/OUTCOME:  Coccidiosis is a ubiquitous intestinal protozoan infection of poultry that seriously impairs the growth and feed utilization of infected birds.  This enteric disease is caused by several distinct apicomplexan species of obligate intracellular parasites of the genus Eimeria.  The use of anti-coccidial drugs is the primary control method, but the worldwide emergence of drug-resistant coccidia strains are limiting the effectiveness of existing therapeutics.  This problem is compounded by our lack of understanding of the mechanism(s) that confer(s) drug resistance and the host-parasite and environmental factors that influence coccidiosis susceptibility.  The discovery of highly effective vaccines may provide an important alternative to drug therapy.  Current vaccines, which are comprised of one or more live coccidian species do not provide cross-protection against all seven species of Eimeria.

Indicators:

During FY 2005, ARS will continue to identify and characterize genes of insect resistance in crop plants, closely related non-crop species, and other species, to enhance opportunities for developing host plant resistance, and to incorporate such genes into commercially acceptable varieties.

ACCOMPLISHMENTS:  Researchers at St. Paul, Minnesota; Aberdeen, Idaho; and other ARS locations have assessed the vulnerability of U.S. wheat lines to a new virulent wheat stem rust mutant that has spread across East Africa.

IMPACT/OUTCOME:  The results of greenhouse evaluations conducted under controlled conditions at St. Paul, Minnesota, indicated that many hard red spring wheat and soft red winter wheat lines from the United States are susceptible to the African race.  The results of these evaluations are being distributed to all U.S. wheat breeders so they can promptly begin to incorporate resistance into their breeding lines, thus reducing the vulnerability to this potentially threatening stem rust mutant.

ACCOMPLISHMENTS:  ARS scientists in Frederick, Maryland, and Urbana, Illinois, evaluated nearly 20,000 soybean accessions from the USDA soybean germplasm collection for resistance to soybean rust.  Approximately 300 to 400 soybean lines showed some resistance and will be tested further with individual rust isolates. 

IMPACT/OUTCOME:  Identifying sources of resistance is a key step in the development of rust-resistant commercial soybean cultivars that can be planted by growers thereby reducing potential losses due to rust.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  Most U.S. pests have been introduced from other parts of the world and cause billions of dollars in damage annually.  Scientists in Beltsville, Maryland, provided 11,145 insect identifications (5,083 of urgent priority) to a broad array of organizations.  In addition, a new species of fruit fly was described from Columbia.  Response to scale pests will now be facilitated by development of an online expert system, which has tools for accommodating a large amount of morphological variation in specimens.  In addition, a comprehensive analysis was completed that describes and illustrates all members of the genus Diuraphis, including the destructive Russian wheat aphid. 

IMPACT/OUTCOME:  The vast majority of identifications are provided to the Animal and Plant Health Inspection Service’s (APHIS) Plant Protection and Quarantine division.  APHIS reports that nine species identified by ARS scientists were new immigrants to the United States.  The new identification of the fruit fly from Columbia will facilitate trade in mangos and other fruit between Columbia and the United States. 

ACCOMPLISHMENTS:  The red flour beetle is the first agronomic pest species to be sequenced.  It represents the joint efforts of the ARS Grain Marketing and Production Center, Biological Research Unit, Manhattan, Kansas; Kansas State University; and the Baylor College of Medicine’s Human Genome Sequencing Center.  The genome sequence scaffolds were merged with genetic and physical maps, resulting in map position assignment for 75 percent of the genome.  Planning and coordination of the genome analysis and annotation efforts were initiated at the International Tribolium Genomics Meeting in Gottingen, Germany, in August 2005. 

IMPACT/OUTCOME:  The analysis of this sequence will have far reaching impacts on understanding physiological adaptations of pest and beneficial beetle species, and the identification of novel targets for pest control exploitation.

ACCOMPLISHMENTS:  Radio transmitters have been used to track everything from antelope to zebra, but not insects.  Scientists from the ARS Northern Plains Area, University of North Carolina-Chapel Hill, and University of Toronto-Mississauga, placed miniature radio transmitters on Mormon Crickets to study their behavior and movement.  Mormon Crickets are notorious for their huge and devastating swarms (or bands), and their ability to migrate hundreds of miles in the Western States.  Why and how these swarms are formed and maintained has been a mystery until now.  The researchers demonstrated that Mormon crickets form migratory swarms to avoid being eaten by their predators.  Once the swarms are formed, the movement of individual crickets within these groups is induced simply by contact with other crickets, thereby providing a mechanism to explain the constant long-term movement of these insect groups across the landscape.

IMPACT/OUTCOME:  This research helps explain why insects around the world, such as the infamous desert locust in Africa, form migratory bands and provides important information on the movement of individuals within these groups.  This knowledge will form the basis for predictive movement models that will aid in managing Mormon crickets and desert locusts.

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

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

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

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

ACCOMPLISHMENTS:  Scientists at Corvallis, Oregon, developed methods for trapping and identification of aerial borne spores of hop and grape powdery mildew pathogens that are suitable for PCR analysis.

IMPACT/OUTCOME:  These methods allow for highly accurate assessments of when an epidemic begins in a specific field and the timing of fungicide applications.  More accurate determinations of the environmental conditions favorable for spore movement can be determined leading to more accurate assessments of disease outbreaks.

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

IMPACT/OUTCOME:  ARS has provided this assay to diagnosticians across the United States and Canada as part of a national surveillance system.  The detection assay was used by regulatory officials to accurately determine and identify a new outbreak of soybean rust in the Southern United States. 

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  The Russian wheat aphid is a serious pest of wheat and barley in the Western States.  Resistant wheat varieties served as the cornerstone for managing Russian wheat aphid until 2003, when a biotype (AKA strain) of the aphid appeared that was able to feed on, injure, and kill the resistant wheat.  The aphid-resistance in these wheat varieties was based on the same wheat gene.  In 2005, ARS scientists at the Wheat, Peanut and Other Field Crops Research Unit in Stillwater, Oklahoma, discovered three new Russian wheat aphid biotypes differing in their ability to injure wheat with unique resistance genes.  One of the new biotypes is especially troublesome because it damages all commercially available sources of plant resistance.  While the new biotypes still occur in low numbers in the field, they may become numerous in the near future.  This information was quickly disseminated to wheat breeding programs in the United States. 

IMPACT/OUTCOME:  Due to these population monitoring activities by the ARS, scientists in the United States have a head start in finding and developing new sources of Russian wheat aphid resistance before the new biotypes become abundant.

ACCOMPLISHMENTS:  The tarnished plant bug is a serious pest of cotton that is becoming more resistant to insecticides, requiring growers to use higher and higher levels of chemicals to achieve the same level of control.  Within a few years, insecticides may no longer be effective against this pest.  The tarnished plant bug is being thwarted thanks to a program that includes use of alternative host destruction, host-plant resistance, fungal pathogens, and remote sensing technology by ARS scientists based in Stoneville, Mississippi, in cooperation with cotton growers and university scientists in Mississippi, Louisiana, Tennessee, and Arkansas.  Grower adoption of the technology is 86 percent in the Mississippi Delta and 33 percent in Arkansas, a State where the technology was demonstrated for the first time in 2004.  Adoption of the technology is approximately 33 percent in Louisiana and Tennessee.  Across the four states, the technology is applied to approximately 1.47 million acres of cotton. 

IMPACT/OUTCOME:  A cost/benefit analysis of the program on over 21,000 acres demonstrated benefits of $10.28 for every $1 applied to using the technology.  Economists have determined the technology produced a $5.48 savings per acre in reduced insecticide costs.  The savings in reduced insecticide costs for the technology was $8.1 million.

ACCOMPLISHMENTS: Accurate and inexpensive methods are needed for monitoring wheat fields to determine the presence of Russian wheat aphid or greenbug infestations.  Wheat farmers and scientist cannot always easily detect aphid infestations or do not have the time to closely monitor their fields.  ARS scientists from the Wheat, Peanut and Other Field Crops Research Unit, Stillwater, Oklahoma, in collaboration with the cooperators at the Texas Agricultural Experiment Station, developed remote sensing technology for identifying greenbug and Russian wheat aphid-infested fields.  Images obtained from aircraft enable the detection of Russian wheat aphid and greenbug infestations.  Fields with high aphid infestations can be differentiated from fields with low infestations by unique "spatial signatures".  

IMPACT/OUTCOME: Ultimately, this technology could be applied for broad scale monitoring of wheat fields for greenbug and Russian wheat aphid infestations using existing satellites in the earth’s orbit.

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

ACCOMPLISHMENTS:  In-crop herbicidal options, especially herbicides that can be applied to control a broad-spectrum of grass and broadleaf weeds at the start of a growing season when weeds have their greatest impact on sugar yields, are limited.  Scientists at the Sugarcane Research Unit in New Orleans, Louisiana, evaluated herbicides alone and in mixtures for control of Bermuda grass, itchgrass, morning glory, and seedling johnsongrass when applied as single and sequential applications.  They found that morning glory in particular could be controlled under sugarcane crop canopy. 

IMPACT/OUTCOME:  Results of this research were used to support manufacturer petitions to the Environmental Protection Agency for two herbicides, which were received in time for the 2004 growing season.

ACCOMPLISHMENTS:  The Australian melaleuca tree (Melaleuca quinquenervia) is an extremely aggressive invasive plant that alters the drainage of South Florida, and affects natural areas, outcompeting valuable native species.  Restricting the invasiveness of melaleuca requires reducing its ability to produce massive amounts of seeds.  ARS scientists at the Invasive Plant Research Laboratory, Fort Lauderdale, Florida, in collaboration with Florida Department of Environmental Protection, U.S. Army Corps of Engineers, South Florida Water Management District personnel, and other partners, released two biological control agents:  a tip-feeding weevil (Oxyops vitiosa; 1997) and a sap-sucking psyllid bug (Boreioglycaspis melaleucae, 2002). 

IMPACT/OUTCOME:  Both species are contributing to the successful biological control of melaleuca.  In particular, the psyllid has spread throughout the infestation of melaleuca, and is significantly affecting growth and survival of the weed.  In fact, melaleuca is almost gone from public lands.

ACCOMPLISHMENTS:  Invasive saltcedar (Tamarix spp.) shrubs from Eurasia infest many Western U.S. waterways where they cause significant economic and environmental losses.  Detailed studies on foreign exploration and host specificity testing for natural enemies of saltcedar were conducted by ARS scientists at the European Biological Control Laboratory, Montpellier, France; the Western Regional Research Center, Albany, California; the Grassland Protection Research Unit, Temple, Texas; and the Crop Bioprotection Research Unit, Peoria, Illinois.  The first biological control agent for saltcedar, the beetle Diorhabda elongata, was released in 1999 at 10 sites in six States.  The beetle continues to cause widespread defoliation and death of saltcedar.  A pheromone trap was developed this year that enables detection of the leading edge of the spread of the beetle.  Additional populations of the beetle are being sought in their native range that are better adapted to areas where the beetle is not performing as well due to a climatic mismatch.  Impacts of the beetle continued on saltcedar and on native plant communities (cottonwoods and willows). 

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

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

ACCOMPLISHMENTS:  Scientists from the Molecular and Plant Pathology Laboratory at Beltsville, Maryland, identified candidate biomarkers that can distinguish strains and species of plant pathogenic phytoplasmas and spiroplasmas.  The biomarkers are potentially significant for survival of the pathogens in their hosts and in disease development. 

IMPACT/OUTCOME:  This accomplishment provides new knowledge important for understanding the mechanisms involved in pathogenicity and transmission of these pathogens by insect vectors.

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 (in Italics) are aligned under 3 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2005.  Seventeen significant accomplishments are reported below.

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

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  ARS discovered that common mutations of a gene called “perilipin” modulate body weight in humans -- and more so in women.  This genetic predisposition to obesity has been demonstrated in white Americans randomly selected from the general population as well as in Indians and Malays residing in Singapore.

IMPACT/OUTCOME:  Identifying people with a predisposition to obesity will help in tailoring appropriate strategies for obesity prevention.

ACCOMPLISHMENTS:  ARS found that low fruit and vegetable consumption and high sweetened beverage intake are independently associated with the prevalence of metabolic syndrome in young adults who participated in the Bogalusa Heart Study.

IMPACT/OUTCOME:  Metabolic syndrome, which is characterized by abdominal obesity, hypertension and the inability to use insulin efficiently, is considered a precursor to type II diabetes that predisposes individuals to heart disease.

ACCOMPLISHMENTS:  ARS found that short-term consumption of a diet containing whole grains in contrast to one with refined cereals and grains produced in women a blood lipoprotein profile associated with a lower risk for heart disease.

IMPACT/OUTCOME:  If substantiated by a long-term feeding trial, this kind of diet, which is consistent with the Dietary Guidelines for Americans, could provide an important food-based strategy for reducing cardiovascular risk.

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

ACCOMPLISHMENTS:  ARS reported that consumption of barley rich in soluble fiber results in similar cholesterol, blood sugar, and insulin-lowering effects in people as when oats are eaten.

IMPACT/OUTCOME:  The FDA approved an unqualified health claim for barley, that its consumption as part of a diet low in saturated fat and cholesterol, may reduce the risk of heart disease.

ACCOMPLISHMENTS:  ARS found that cooking elevates absorption of some, but not all, of the red-purple pigments that function as antioxidants in specialty carrots and that the body is limited in its ability to absorb these healthful compounds.

IMPACT/OUTCOME:  These findings will help consumers and health professionals plan healthful diets to reduce the risk of chronic disease and avoid unneeded supplementation.

ACCOMPLISHMENTS:  ARS demonstrated that inulin, a type of dietary fiber, enhances the absorption of iron from the intestine when fed to young pigs.

IMPACT/OUTCOME:  Inulin, already added to some brands of yogurt to increase absorption of calcium, may now be added to other food products fortified with iron, such as enriched bread or cereals, to enhance iron absorption.  Iron deficiency is the most prevalent nutritional problem world-wide, principally affecting children and women of child-bearing age.

Indicators:

During FY 2005, ARS will

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

ACCOMPLISHMENTS:  ARS demonstrated that calcium and vitamin D supplementation, in frequently recommended amounts, lowers the risk of falls and resulting fractures for the elderly population.

IMPACT/OUTCOME:  Broad-based increases in consumption of vitamin D and calcium could help lower health care costs as well as improve the quality of life for older Americans.

ACCOMPLISHMENTS:  ARS found that men and women with higher dietary and blood levels of vitamin K have fewer osteoarthritic joints and less abnormal calcification in their joints compared to people with lower dietary and blood levels. 

IMPACT/OUTCOME:  Ensuring adequate vitamin K intake may potentially reduce this age related form of arthritis in older men and women.

ACCOMPLISHMENTS:  ARS reported that rats fed marginally deficient levels of copper for a long time developed cardiovascular damage similar to that seen in animals fed severely deficient diets for a short period.

IMPACT/OUTCOME:  Not meeting dietary recommendations for copper by relatively small amounts for long periods of time may be more harmful than previously believed.

ACCOMPLISHMENTS:  ARS showed that a higher intake of total fat appears to increase cataract risk but more frequent consumption of long chain omega-3 fatty acids and fish can reduce the risk.

IMPACT/OUTCOME:  Dietary prevention of commonly occurring health concerns is a cost effective and essential way of reducing health care costs in the United States.

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

ACCOMPLISHMENTS:  ARS released National Nutrient Databank for Standard Reference, Release 18.    Information on up to 136 nutrients in over 7,100 food items is included.

IMPACT/OUTCOME:  This is the “gold standard” of nutrient composition databases for foods consumed in the United States.  It is widely used by USDA’s Research, Education and Economics, and Food and Nutrition Service agencies for research, evaluating food assistance programs, and policy formulation.  It is also used and by many other Federal agencies, such as for FDA’s food labeling and EPA’s pesticide monitoring programs.

ACCOMPLISHMENT:  ARS released the “What’s in the Foods You Eat Search Tool” on the ARS World Wide Web site.

IMPACT/OUTCOME:  In contrast to other nutrient databases, this one contains nutritional information for foods most frequently eaten by Americans, as reported in the “What We Eat in America NHANES” survey.  Such information aids the consumer in making healthful food choices.

ACCOMPLISHMENTS:  ARS developed a method for determining of the vitamin nicotinic acid and nicotinamide (the form used to fortify food) in wheat flour and cereal products.

IMPACT/OUTCOME:  Academia, government, and the food industry will use this new methodology for measuring the niacin content of foods and dietary supplements.

ACCOMPLISHMENTS:  The USDA Beef Calculator was released. This software program enables users to select among multiple types of ground beef and cooking methods for a report on nutrients per serving of ground beef.

IMPACT/OUTCOME:  This calculator, while useful to consumers, also provides the beef industry with a means to calculate ground beef nutrient values, a requirement of the proposed Food Safety and Inspection Service labeling regulation on single-ingredient meat products.

Indicators:

During FY 2005, ARS will

survey and analyze national food consumption patterns of Americans. 

ACCOMPLISHMENTS:  ARS released on the Web, nutrient intakes of the U.S. population from the “What We Eat in America, NHANES 2001-2002” dietary survey.

IMPACT/OUTCOME:  This information, from the only nationally representative dietary survey, is widely used by government, academia, and private industry to monitor American food consumption trends and dietary nutritional adequacy.

ACCOMPLISHMENTS:  ARS published on the Web, tables of Food Pyramid serving intakes in the United States as well as a search tool for this analysis.

IMPACT/OUTCOME:  Information on the adherence by Americans to the dietary recommendations set forth in the Dietary Guidelines for Americans provides crucial information to USDA’s Center for Nutrition Policy and Promotion and is essential for the development of sound nutrition education and food assistance programs by USDA’s Food and Nutrition Service. 

develop and modify dietary assessment and nutritional status methods.

ACCOMPLISHMENTS:  ARS showed that a correction method based on measured energy expenditure and body weight can reduce measurement errors inherent in food frequency questionnaires, the dietary assessment method of choice for large scale nutrition studies.

IMPACT/OUTCOME:  Reducing the error associated with this method provides higher quality epidemiological research on the relationship of diet to health.  

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

Analysis of Results:  This goal focuses on a wide range of environmental issues related to agriculture.  Under Goal 5, 14 Indicators (in Italics) are aligned under 7 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2005.  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 2005, 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:  Gulf Coast cattle producers depend heavily on tropical grasses for forage, but the nutritional value of these grasses drops during the late summer and fall.  ARS scientists at Brooksville, Florida, have shown that the tropical forage legume, rhizoma peanut, can produce high cattle gains throughout the late summer and fall.  However, use of current cultivars is limited to the warmer, well drained sites in the Gulf Coast region.  Material better adapted to cold and wet conditions was needed to expand the impact of this forage species.  As the result of two plant collection trips (in 2003 and 2004) to Paraguay, 65 new accessions of perennial peanut have been identified and made available for cultivar development.