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.
Performance Measure 1.1.1: Develop cost effective and functional industrial and consumer products from agricultural and forestry resources.
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.
Performance Measure 1.1.2: Provide higher quality, healthy foods that satisfy consumer needs in the United States and abroad.
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.
Performance Measure 1.1.3: Improve efficiency and reduce cost for conversion of biomass to energy.
During FY 2005, ARS will
develop improved biomass plants, sustainable biomass production systems, and efficient handling and storage technology for biomass feedstocks.
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.
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.
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.
Performance Measure 1.2.1: Provide producers with scientific information and technology that increase production efficiency, develop improved germplasm, safeguard the environment, improve animal well-being, and reduce production risks and product losses.
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.
Performance Measure 1.2.2: Develop needed information on the relationships between nutrients, reproduction, growth, and conversion to and marketability of animal products.
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.
Performance Measure 1.2.3: Identify genes responsible for economically important traits, including animal product quality, efficiency of nutrient utilization, and environmental adaptability.
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.
Performance Measure 1.2.4: Maintain, characterize, and use genetic resources to optimize and safeguard genetic diversity and promote viable, vigorous animal production systems.
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.
Performance Measure 1.2.5: Provide producers with scientific information and technology that increase production efficiency, safeguard the environment, and reduce production risks and product losses.
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.
Performance Measure 1.2.6: Improve the understanding of the biological mechanisms that influence plant growth, product quality, and marketability to enhance the competitive advantage of agricultural commodities.
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.
Performance Measure 1.2.7: Identify genes responsible for plant product quality and resistance to diseases, pests, and weather losses.
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.
Performance Measure 1.2.8: Maintain, characterize, and use genetic resources to optimize, safeguard, and enhance genetic diversity and promote viable and vigorous plant production systems.
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.