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United States Department of Agriculture

Agricultural Research Service

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2004 Annual Performance Report
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1 - Introduction
2 - Table of Contents
3 - Goals 1 and 2
4 - Goal 3
5 - Goal 4
6 - Goal 5
7 - Goal 6
Goals 1 and 2



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 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 2004.  Ninety-three 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 2004, ARS will


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


ACCOMPLISHMENTS:  To meet the needs of the military for wool fabrics that will not burn, scientists at Wyndmoor, Pennsylvania, processed wool with a heat-resistant synthetic polymer which exhibited burning behavior similar to blended wool and Nomex (synthetic fiber known to resist burning). 


IMPACT/OUTCOME:  Participating wool mills are anticipated to include this new technology in their existing product lines, thereby increasing the demand for domestic wool fiber and apparel for traditional and new uses.


ACCOMPLISHMENTS:  Industry is searching for a biobased process to produce mannitol (a low-calorie sugar alcohol widely used in foods, pharmaceuticals, medicines, and chemical industries) to replace the problematic low yield chemical process currently used.  Researchers at Peoria, Illinois, developed a fermentation process for production of mannitol from sugars using a lactic acid bacterium obtained from the ARS Culture Collection.  The process has been scaled up to 30 liters and the purity of the product has been established.


IMPACT/OUTCOME:  The private sector partner in this project has applied for FDA approval of the process and the product.  The new process offers an attractive alternative to the chemical production process and utilizes inexpensive corn-derived sugars.


develop new or improved methods to measure or predict quality.


ACCOMPLISHMENTS:  Moisture is typically added back to cotton during ginning and spinning, but too much moisture can adversely affect fiber quality and processing.  In trials on a commercial gin with a commercially available moisture restoration system, researchers in Clemson, South Carolina, in partnership with researchers at Lubbock, Texas, found that restored moisture above 8 percent resulted in deteriorating fiber quality and poor yarn properties.  In related work, engineers at Lubbock, Texas, developed a novel low cost microwave-based cotton bale moisture sensor with high accuracy and precision. 


IMPACT/OUTCOME:  Based on the work at Clemson, the National Cotton Council established a level of 7.5 percent moisture as the highest level of restored moisture acceptable at ginning.  Based on the work at Lubbock, a U.S. patent application has been initiated.  Reliable moisture measurement will limit excessive moisture application to the bale, which results in lint deterioration and lower grades for the end user.


ACCOMPLISHMENTS:  Non-destructive sensing of fruit quality attributes, such as firmness and soluble solids content (SSC), will allow the fruit industry to deliver superior, consistent quality fruit to the marketplace and better meet consumer demands for high quality fruit.  Researchers at East Lansing, Michigan, developed a light-based multispectral imaging prototype which was able to inspect individual apples for firmness and SSC in real time for up to two fruit per second. 


IMPACT/OUTCOME:  Initial evaluation demonstrated that the prototype is promising for sorting and grading individual apples and other fruit for firmness and SSC.   


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


ACCOMPLISHMENTS:  A soy oil-based elevator hydraulic fluid technology was developed by scientists at Peoria, Illinois, in response to a request from the National Park Service (for the Statue of Liberty).  The fluid was independently evaluated by an industrial partner and scaled up and retrofitted in the Statue of Liberty elevator; it has been successfully operating for nearly two years. 


IMPACT/OUTCOME:  A leading lubrication company has applied for a product license for commercial production of the fluid.  This work resulted in a 2004 “Excellence in Technology Transfer” award from the Federal Laboratory Consortium.  Potential exists for expanded utilization of this biobased, biodegradable fluid in place of petroleum-based fluids.


ACCOMPLISHMENTS:  Scientists at New Orleans, Louisiana, developed products from cottonseed and its derivatives to control fire ants and termites.  A patent has been approved by the U.S. Trade Mark and Patent Office.  Field tests with the cottonseed-containing baits in Mississippi have been conducted for almost three years with good results. 


IMPACT/OUTCOME:  A Japanese company is interested in the technology and is currently evaluating the bait system.  This development offers a possible new market for cottonseed and a biobased biocontrol technology.


Performance Measure 1.1.2:    Provide higher quality, healthy foods that satisfy consumer needs in the United States and abroad.




During FY 2004, ARS will


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


ACCOMPLISHMENTS:  Aflatoxin and fumonisin are carcinogens found in corn.  Rapid detection means are needed to ensure a safe food and feed supply.  Researchers at Manhattan, Kansas, in cooperation with scientists at Peoria, Illinois, developed a high speed sorting machine to remove corn kernels that are contaminated with aflatoxin- or fumonisin-producing fungi.  The sorter, which uses near-infrared detectors, removes as much as 80 percent of these toxins in a single pass. 


IMPACT/OUTCOME:  This technology will help ensure the safety of the U.S. food and feed supply and could save the corn industry millions of dollars.


ACCOMPLISHMENTS:  The mechanical harvesting of billeted (9-15cm long) sugarcane is now more predominant than the harvesting of whole stalk cane in Louisiana, but the billeted cane deteriorates faster so there is now a more urgent need to have a reliable test of the extent of cane deterioration at the factory.  Deteriorated cane contributes to sugar losses and processing problems in the factory.  Researchers in New Orleans, Louisiana, demonstrated that mannitol (a sugar alcohol) is an excellent predictor of sugarcane deterioration, and they developed a quick, easy, reliable, cheap enzymatic method to measure it in cane press juices from individual loads of sugarcane. 


IMPACT/OUTCOME:  This new method will allow factory staff to determine if a shipment load of cane can be economically processed or not.   


develop functional food ingredients and/or products.


ACCOMPLISHMENTS:  New fruit and vegetable products and processes and their consumption can help to combat the rising obesity epidemic in the United States.  Researchers at Albany, California, in cooperation with an industrial partner developed and tested novel fruit- and vegetable-based films for use in wrapping food products. 


IMPACT/OUTCOME:  A patent was filed on the final products and processes.  The cooperator is building a food manufacturing plant in a rural area of California and expects to begin commercial production in 2005.  As a result of ARS; research new jobs will be created in an area of high unemployment, and new healthy food products for consumers and novel value-added outlets for fruits and vegetables will be provided.


ACCOMPLISHMENTS:  Scientists at WRRC in Albany, California, in collaboration with a large commercial food manufacturer, found that food processing can improve the ability of legume proteins to lower blood-serum cholesterol in lab animals, ostensibly due to certain peptide fractions in the processed products. 


IMPACT/OUTCOME:  This discovery provides the legume industry with critical scientific knowledge necessary for the development of more heart-friendly foods.


ACCOMPLISHMENTS:  Fantesk(TM) is a patented technology developed at the NCAUR in Peoria, Illinois, which uses cornstarch and soybean oil, surplus products of U.S. agricultural production, or other crop-based materials, which has both food and non-food applications.  A starch-based Fantesk gel was developed that has many of the desirable properties of a solid fat.  This gel is blended into low fat ground beef produced hamburger patties with improved flavor, texture, and juiciness. 


IMPACT/OUTCOME:  The licensee of the technology is currently working with food processors to produce and market Fantesk containing low fat meat products.  Improving the sensory properties of low fat foods, to make them more closely resemble their full fat analogues, will encourage consumers to purchase these low fat, healthier alternatives.     


ACCOMPLISHMENTS:  Current rice starch processing requires extensive soaking of rice in dilute caustic solutions prior to separation of its starch and protein.  These processes involve water and energy, and are time intensive and require costly wastewater treatment.  The process uses high pressure supplied by a microfluidizer (homogenizer) to separate the starch from the protein.  Scientists at New Orleans, Louisiana, working through a Cooperative Research and Development Agreement with a private sector partner and partially supported by a Small Business Innovative Research grant, developed and successfully scaled up a process for commercial production of rice starch.   


IMPACT/OUTCOME:  This technology has the potential of reducing imports of rice starch and increasing profits for the U.S. rice industry.    


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


ACCOMPLISHMENTS:  Scientists at Fargo, North Dakota, in cooperation with the Wheat Quality Council and Federal, State, and commercial bakers, evaluated quality traits of spring wheat experimental lines, resulting in the identification of the most promising lines and the release of four new commercial varieties with superior agronomic, disease resistance, and end use quality traits. 


IMPACT/OUTCOME:  This research could result in a higher net income for producers, and a greater marketing potential of higher quality wheat to domestic and overseas buyers.


ACCOMPLISHMENTS:  Engineers at Manhattan, Kansas, found that little co-mingling of different corn varieties occurred in elevators. 


IMPACT/OUTCOME:  The results of this study, the first of its kind, will be used by elevator operators to better segregate grain with desirable characteristics into separate channels for delivery to end users.  This information is also useful to grain processors for improving their handling of specialty grains.


ACCOMPLISHMENTS:  Researchers at Beltsville, Maryland, demonstrated that ‘Goldrush’ apples possessed better quality attributes for fresh cutting than traditional cultivars. 


IMPACT/OUTCOME:  This finding is important since repeat sales of fresh cut apple products is driven by consumer satisfaction with product taste, including texture, sweetness, acidity, and aroma.  ‘Goldrush’ apples can be refrigerated for 12 months in air before processing and for three weeks as the cut product.  Once “Goldrush” becomes more commercially available, these findings will enable fresh cut processors to provide a better testing product and enhance fresh cut apple sales.


ACCOMPLISHMENTS:  Fruity fermented off flavor is a significant economic problem for producers in areas where peanuts are exposed to high temperature during initial curing.  Scientists at Raleigh, North Carolina, discovered that sandwich windrow construction (plants placed in windrows with one up and one down providing shade for the peanuts) and a sprayed coating of white kaolin powder on normal inverted windrows reduced peanut pod temperatures and decreased intensity of fruity fermented off flavor. 


IMPACT/OUTCOME:  Because these findings occurred in one of the worst years (2003) for the off flavor, this information has been instrumental in changes by producers toward use of sandwich diggers as standard practice.


Performance Measure 1.1.3:    Improve efficiency and reduce cost for conversion of biomass to energy.




During FY 2004, ARS will


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


ACCOMPLISHMENTS:  Sustainable management technology was developed for growing switchgrass as an energy crop on marginal cropland in the western Corn Belt and was demonstrated to produce biomass amounts with the potential to yield more ethanol per acre than corn while providing environmental benefits similar to that of the Conservation Reserve Program.


IMPACT/OUTCOME:  Provides the technology for and demonstrates the potential for large quantities of ethanol producing crops to be grown while avoiding soil erosion and protecting soil quality.


ACCOMPLISHMENTS:  Genetically modified switchgrass, an herbaceous energy crop, by Agrobacterium mediated transformation to successfully provide plant material that is more readily converted to ethanol by existing technologies.


IMPACT/OUTCOME:  Provides the technology to improve the characteristics of crops grown for liquid transportation fuel production.


ACCOMPLISHMENTS:  Developed hybrid cultivars of switchgrass and demonstrated their potential to increase yields of biomass for use as bioenergy feedstock.


IMPACT/OUTCOME:  Increased potential of switchgrass as an energy crop.


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


ACCOMPLISHMENTS:  Enzymatic wet milling, a process previously demonstrated to avoid the need to use hazardous sulfur dioxide, was optimized to reduce by a factor of ten the amount of enzyme needed.  These findings reduce the cost while maintaining a production level similar to that of conventional wet milling.


IMPACT/OUTCOME:  Improved commercial potential for this environmentally favorable bioprocessing technology.


ACCOMPLISHMENTS:  Enzymes were selected and processes developed to efficiently convert beta-glucan, a material in barley that limits its suitability for fuel ethanol production, into fermentable sugars.


IMPACT/OUTCOME:  These developments increase ethanol production from barley, improve the economics of the process, and provide an additional market for farmers where barley can be grown.


ACCOMPLISHMENTS:  Developed an aqueous enzymatic process that avoids the need to use the flammable, toxic solvent hexane to extract corn oil from oven dried corn germ produced during wet milling. 


IMPACT/OUTCOME:  Development of an environmentally friendly process for extracting valuable oil from corn.


ACCOMPLISHMENTS:  Described an adaptive response of yeasts to fermentation inhibitors that are byproducts of dilute acid hydrolysis of lignocellulosic biomass, and developed adapted strains that were shown to be able to convert these inhibitors into forms that are less toxic.


IMPACT/OUTCOME:  Provided fundamental guidelines for further development of industrial yeasts to alleviate the stress factors associated with commercial dilute acid hydrolysis of lignocellulosic biomass.


ACCOMPLISHMENTS:  Identified binary mixtures of oxidation inhibitors (antioxidants) exhibiting synergistic effects when applied to improve oxidative stability of biodiesel.


IMPACT/OUTCOME:  A lower cost method has been identified to protect biodiesel fuel from oxidative degradation and maintain fuel quality.


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


ACCOMPLISHMENTS:  Demonstrated that a new submersible pump powered by wind or solar energy can pump water from a deep well while requiring little maintenance, that is less costly to install than a mechanical windmill.


IMPACT/OUTCOME:  A more economical method has been identified for farmers and ranchers to provide water for 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 2004, ARS will develop scientific information that contributes to improved efficiency and environmental stewardship of food animal production systems.


ACCOMPLISHMENTS:  Previous work by ARS researchers at Ithaca, New York, has shown that Clostridium sporogenes, the primary detrimental bacteria involved in the fermentation of silage for dairy cattle, could be inhibited by a specific bacteriocin that is produced by the ruminal bacterium S. bovis.  The research team has now shown that the activity of the bacteriocin is at least tenfold higher under the relevant conditions experienced during silage production.


IMPACT/OUTCOME:  The dairy industry relies heavily upon the use of silage as a feedstuff, but silage preservation is often inadequate to ensure quality.  One of the critical control points impacting silage quality is the control of detrimental amino acid degrading bacteria during the ensiling process.  These results suggest that the bacteriocin producing bacteria S. bovis, has the potential to improve silage quality.


ACCOMPLISHMENTS:  Research conducted at the Grazinglands Research Laboratory, El Reno, Oklahoma, demonstrated that producers can substitute perennial cool season grasses for wheat, or use a combination of these grasses with wheat, to buffer highly variable wheat forage production and simultaneously meet the nutritional demands of stocker calves.


IMPACT/OUTCOME:  These farm scale studies of stocker calf weight gains indicate that a variety of grasses can be grazed a full month later in the spring than wheat pasture, extending the marketing date of stocker calves past the seasonal lows in beef prices associated with the end of the wheat pasture grazing season.  These findings allow livestock producers to more consistently meet the forage needs of stocker calves and reduce the economic losses associated with livestock production in the southern Great Plains.


ACCOMPLISHMENTS:  ARS scientists developed advanced oxidation processes for controlling and mitigating microbial populations and critical water quality parameters within a re-circulation fish production system.  They developed a disease challenge model for a rainbow trout pathogen (Yersinia ruckeri) at Leetown, West Virginia, and developed and applied for U.S. patents on fish vaccines against the fish pathogens, Flavobacterium columnare, Edwardsiella tarda, and Streptococcus agalactiae at Auburn, Alabama.


IMPACT/OUTCOME:  These health management accomplishments will reduce the risk of losses from diseases and improve profitability of warm and cold water aquaculture.


ACCOMPLISHMENTS:  ARS researchers developed a technique for measuring the palatability of shrimp feeds needed to implement the use of plant protein sources in their diets at Hilo, Hawaii.  Also, scientists showed that poultry byproduct meal supplemented with two amino acids could replace fish meal in diets for hybrid striped bass at Stuttgart, Arkansas.


IMPACT/OUTCOME:  This research will help demonstrate the feasibility of replacing fishmeal in aquaculture diets.  Replacing fishmeal in aquaculture feeds improves the sustainability of aquaculture and reduces the cost of the feed.


ACCOMPLISHMENTS:  ARS showed that stressing pregnant sows carried over to their off-spring an altered physiology, demonstrated that dopamine and serotonin are useful indicators of stress in chicken genetic improvement, and demonstrated an alterative to forced molting (feed removal).  A patent application is being pursued at West Lafayette, Indiana.


IMPACT/OUTCOME:  This information provides livestock producers with methods for reducing stress in swine and chickens.


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 2004, ARS will


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


ACCOMPLISHMENTS:  Research work conducted in the Breeding and Genetics Unit at the U.S. Meat Animal Research Center, Clay Center, Nebraska, has determined that variation in the thyroxine-binding globulin gene causes a 30 to 40 percent reduction in the size of the mature testes with a concomitant reduction in average backfat thickness. 


IMPACT/OUTCOME:  This discovery has identified a new biochemical pathway regulating testes size, a trait that is directly related to the number of sperm cells that a boar produces in a day.  Since the swine industry relies heavily upon artificial insemination, maximizing the number of sperm cells produced daily by a boar will minimize the number of boars required in boar studs.


ACCOMPLISHMENTS:  Research conducted by ARS scientists at Athens, Georgia, is seeking to understand the functional relationships between the numerous proteins associated with the growth and development of fat tissue in pigs.  Over 30 genes that code secreted proteins were reported for the first time in pig adipose tissue including agouti, nerve growth factor, several interleukins, brain derived neurotrophic factor, and IFNA2. 


IMPACT/OUTCOME:  One of the major goals of swine improvement is to change the proportion of lean to fat content of pork while maintaining eating quality.  This information provides a better understanding of the molecular mechanisms controlling fat tissue secretory function that in turn provides opportunities for genetic improvement in body composition.


ACCOMPLISHMENTS:  ARS completed two early growth evaluations of five different genetic stocks of North American Atlantic Salmon at Franklin, Maine; established broodyear lines of top performing families of rainbow trout for breeding at Leetown, West Virginia, and Hagerman, Idaho; and refined the protocols to produce all reproductively-sterile rainbow trout at Leetown.


IMPACT/OUTCOME:  These accomplishments increase the probability of improving the economically important traits for farmed salmonids, and provide a method to nearly eliminate risk of escapes to the environment.


ACCOMPLISHMENTS:  ARS conducted aquaculture research on the mechanisms of stress response and performance, important information on fish health.


IMPACT/OUTCOME:  This knowledge will be used to develop superior genetic lines of fish, effective nutrient conversion, and health management and production systems to reduce operating costs.


ACCOMPLISHMENTS:  ARS developed a technology for artificial insemination spawning of southern flounder and pompano at Stuttgart, Arkansas.


IMPACT/OUTCOME:  This technology is critical for making fingerlings available to producers.


develop technologies leading to improved marketability of animal products.


ACCOMPLISHMENTS:  Retail yield of beef carcasses in the beef industry is predicted through the assignment of a visually determined yield grade by a USDA official grader prior to carcass fabrication.  Due to the inherent subjectivity of this system, ARS researchers at Clay Center, Nebraska, in collaboration with the National Cattlemen’s Beef Association and Tyson Fresh Meats, have developed an image analysis system for use on-line in commercial packing plants to predict boneless, closely trimmed sub-primal cutout yields. 


IMPACT/OUTCOME:  One of the targeted areas to increase production efficiency in the beef industry is improved lean retail yield of carcasses.  Application of this on-line instrument allows more objective and accurate prediction of beef retail yield under commercial conditions.  Two of the four major beef processors have now implemented this system with others considering it for future implementation.


ACCOMPLISHMENTS:  ARS scientists demonstrated that a previously thought harmless alga caused fish kills.  They developed a management remedy at Stoneville, Mississippi.


IMPACT/OUTCOME:  The management remedy was communicated to fish farmers; has the potential for saving thousands of dollars in losses.


ACCOMPLISHMENTS:  ARS identified a natural algicide in laboratory screening.  Tests in field evaluations confirmed its capability to control algae-related off favors in catfish.


IMPACT/OUTCOME:  A U.S. patent application has been filed, and a Cooperative Research and Development partner has been identified to commercialize the discovery.  The product has the potential to be more economical and environmentally sound than the two provisional controls being used.


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 2004, ARS will


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


ACCOMPLISHMENTS:  Advances in cattle genomics have enabled scientists to identify genes affecting a wide array of traits of economic importance (so-called Quantitative Trait Loci (QTL)).  ARS researchers at Beltsville, Maryland, working collaboratively with scientists at the University of Illinois, have recently reported the first QTL detected affecting the pregnancy rate in U.S. holstein germplasm.  Additional QTLs were also detected for somatic cell score, an indicator of mastitis incidence.


IMPACT/OUTCOME:  One of the most critical issues facing the U.S. dairy industry is a decline in fertility, thought to be associated with a gradual accumulation of in-breeding depression over the past forty-five years, largely due to widespread use of genetically superior sires through artificial insemination.  Discovery of these QTLs will lead to improved efficiency of genetic selection for fertility traits in dairy and beef cattle. 


ACCOMPLISHMENTS:  Swine and beef reproduction research over the past 20 years at the U.S. Meat Animal Research Center, Clay Center, Nebraska, has been focused on identification of physiological mechanisms contributing to increased reproductive capacity.  Researchers have validated that a previously identified genetic marker for the pig erythropoieten receptor gene is associated with a two to three pig difference in ultimate litter size, and for the first time, two QTLs for male reproductive traits in cattle (testes size and follicle stimulating hormone). 


IMPACT/OUTCOME:  One of the primary selection criteria in genetic improvement programs in the livestock industry is reproductive rate.  By increasing the total production per female in the breeding herd, profitability is enhanced significantly for the individual producer through increased output over static fixed costs.  Identification of these QTLs will lead to enhanced efficiency of genetic improvement programs for reproductive rates in swine and cattle germplasm.


ACCOMPLISHMENTS:  Research in the Growth Biology Laboratory at Beltsville, Maryland, has involved the study of the chicken proglucagon gene that produces five different peptide hormones functioning in tissue growth, gastrointestinal function, regulation of insulin and blood glucose levels, and appetite control.  This work has recently led to the cloning and sequencing of the gene, and to the identification of four distinct protein transcripts produced by this one gene through alternative splicing and alternate promoter usage.  The types and levels of specific proglucagon transcripts were determined in pancreatic, intestinal, and brain tissues collected from chickens that had been deprived of feed and/or refed to induce changes in energy status. 


IMPACT/OUTCOME:  Development of a more complete understanding of the biological mechanisms regulating feed intake in poultry and livestock is needed in order to better tailor production systems to available genetic lines to improve production efficiency.  This research provides new information necessary to understand how the peptide hormones are produced and what impact changes in the expression of this gene might have on glucose metabolism and appetite regulation in poultry.


ACCOMPLISHMENTS:  ARS researchers identified genes expressed in rainbow trout oocyte using a successfully constructed cDNA library from rainbow trout oocyte, identified immune genes of rainbow trout, and identified genes that expressed calpain protein in rainbow trout.  They also identified genes expressing toll-like receptors believed to be involved in disease resistance of catfish.  Insulin–like growth factors I and II showed promise as markers for selection of channel catfish broodstock for superior growth.


IMPACT/OUTCOME:  Gene identification and marker development are important steps in integrating molecular technology and genetic selection in breeding of superior performing fish.


ACCOMPLISHMENTS:  ARS was issued a patent for a diagnostic test to detect bacterial kidney disease in rainbow trout at Aberdeen, Idaho.


IMPACT/OUTCOME:  This diagnostic test will be commercialized and useful to trout producers in identifying sick fish.


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


ACCOMPLISHMENTS:  ARS researchers at the U.S. Meat Animal Research Center have:  1) added 800 genes to the integrated bovine map via single nucleotide polymorphism (SNP) mapping in introns; 2) increased the number of microsatellite markers in the bovine linkage map from 1,500 to 3,800; 3) deposited 680 sheep, 4,429 cattle, and 5,445 swine SNPs in the public database, GenBank, at NCBI (prior to these submissions no more than 100 SNP had been deposited for any of the species); 4) deposited 13,922 bovine and 65,866 porcine expressed sequence tags (ESTs) in GenBank; 5) developed a set of 14,000 ESTs with unique 3-prime end sequences for use in developing a commercial cattle microarray; and 6) developed and tested a pipeline for identification, complete sequencing, and annotation of full-length cDNA clones for livestock genes through which 500 bovine full length cDNAs were identified.


IMPACT/OUTCOME:  2004 was a milestone year in livestock genomics with the completion of the chicken genome sequence and the release of the first draft of the bovine genome sequence.  ARS research has laid much of the path for this development and in the past year has significantly enhanced the information contained in the livestock genetic maps. These tools are enabling the more rapid discovery of genes and their functions, required to build genomic tools to improve production efficiency, animal health, and well-being of beef and dairy cattle, swine, and sheep.


ACCOMPLISHMENTS:  When the first case of BSE, more commonly referred to as “mad cow disease,” was reported in Washington State in December of 2003, it became one of the first major applications of genomic technology in providing a valuable and rapid solution in a crisis situation in animal agriculture.  Records identified the sire and other relatives of the BSE index case and their tissues were available for genetic analyses.  ARS scientists at Clay Center, Nebraska, used a panel of single nucleotide polymorphism DNA markers, under development for animal identification, to quickly verify the pedigree of the affected cow, which was traced back to a Canadian origin.    


IMPACT/OUTCOME:  Using this genotyping test, scientific evidence was made available to show that the affected animal was one of a group of 81 females that had crossed the U.S. border from Canada several years earlier.  This provided the missing link in the traceability of this female to verify that she was born prior to the 1997 implementation of a full ban on animal protein feeding in Canada.


ACCOMPLISHMENTS:  Research conducted in the ARS Bovine Functional Genomics Laboratory at Beltsville, Maryland, has resulted in the development of bioinformatic software called EST-PAGE.  It allows researchers to easily process large volumes of data on ESTs and more importantly, to submit their data to the public databases for worldwide application and use. 


IMPACT/OUTCOME:  The volume of data being generated from analysis of DNA sequence and downstream applications in functional genomics and proteomics research is growing exponentially as the genomes of the major livestock species are being added to the sequence infrastructure.  This software will facilitate ease of transfer and access to such data by researchers worldwide working across many species, especially the 25 groups around the world who have already requested and received the source code.


ACCOMPLISHMENTS:  A new normalized cDNA library has been synthesized from lactating dairy cow and calf intestinal tissue to facilitate gene discovery in ruminant metabolism by researchers at Beltsville, Maryland.  The library, called 8BOV, has been synthesized, sequenced, and characterized.  It is having a direct impact as evidenced by the 19,110 new ESTs which have now been deposited in the public database GenBank.  A total of 1,123 sequence elements from the ESTs represent genes encoding proteins in other animal systems that can now be exploited in the bovine.


IMPACT/OUTCOME:  The production of meat, milk, and wool products is considered to be relatively inefficient due to the fact that upwards of two-thirds of the input costs are expended for feed energy required for maintenance of body tissues largely attributable to energy expended by the visceral tissues (liver and gut).  This library will facilitate the search for specific metabolic pathways, transporters, growth factor receptors, and growth factors that have profound effects on ruminant visceral energy and protein metabolism, paving the way for improvements through precision management and genetics.


ACCOMPLISHMENTS:  ARS characterized a rainbow trout bacterial artificial base chromosome library made up of about 135,000 base pair DNA segments for use in constructing physical maps.  Subsequent sequencing evaluations and measures of stress are being studied for use in development of biomarkers and strategies to manage disease.


IMPACT/OUTCOME:  This accomplishment has great potential to expedite the genetic improvement and production efficiency of rainbow trout.


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 2004, ARS will


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


ACCOMPLISHMENTS:  ARS scientists at Miles City, Montana, have been working for a number of years to develop a framework for application of selection indexes in the beef cattle seedstock industry.  In the past year, selection indexes based on this research were made available to the American International Charolais Association, American Hereford Association, American Simmental Association, North American Limousin Foundation, the Angus Sire Alliance, and the South African Agricultural Research Council.


IMPACT/OUTCOME:  Genetic improvement programs in the beef cattle industry are complex due to the need to select a wide array of performance criteria.  This research enables beef cattle breeders to use an optimal approach to genetic improvement where breeding values for a variety of economically important traits are appropriately weighted according to their economic value, genetic variation, and genetic relationships into an aggregate “overall” index breeding value.


ACCOMPLISHMENTS:  The beef cattle industry has widely capitalized upon the characterization of germplasm representing 34 breeds through the Germplasm Evaluation Project conducted at the U.S. Meat Animal Research Center.  Results from the project provided evidence that the genetic variation observed amongst Continental European and British breeds for growth performance has significantly decreased over the past decade.   


IMPACT/OUTCOME:  These results are critically important to beef cattle breeders as they design selection objectives within breeds and crossbreeding systems using multiple breeds to make genetic improvement.


ACCOMPLISHMENTS:  Research conducted at the U.S. Meat Animal Research Center, Clay Center, Nebraska, has concluded that ewes sired by Romanov rams were 59 percent more productive than ewes sired by traditional sheep breeds used for out of season breeding (Dorset and Finnsheep).  Greater use of Romanov-crossbred ewes in maternal roles of terminal crossbreeding systems would contribute to enhanced profitability of sheep production.


IMPACT/OUTCOME:  Length of seasonal fertility largely determines the effectiveness of accelerated lambing systems and annual systems that breed females in the spring of the year.  Efficiency of commercial sheep production could be markedly improved through the use of Romanov germplasm in maternal line development to enhance seasonal fertility. 


ACCOMPLISHMENTS:  ARS researchers at Leetown, West Virginia, determined that the performance of domesticated strains of rainbow trout were not different in flow-through versus recirculation systems.  Also, researchers at Stoneville, Mississippi, demonstrated with performance evaluations of blue catfish and blue x channel catfish crosses the benefits of improved growth and survival.


IMPACT/OUTCOME:  This information was made available to fish producers to aid in their decisions about which strains or lines of fish to grow.


ACCOMPLISHMENTS:  ARS researchers developed a large scale facility for genetic evaluation of oysters.  They established a collaborative genetic project to reduce cadmium in oysters, a long-term objective toward breeding improved oysters for the Pacific Coast.


IMPACT/OUTCOME:  The large scale rearing facility will enable more rapid progress of the genetic selection project.  A discriminatory factor in international trade will be eliminated for Pacific Coast oysters, if a trait for lower cadmium is found.


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:  The National Animal Germplasm Program, located at Fort Collins, Colorado, was formally established in 1999 to better protect the U.S. livestock industry.  The number of germplasm and tissue samples in the collection was increased by 114 percent and the number of breeds represented by 50 percent in the past year.  This growth is far ahead of original plans and expectations.  Two breeds of dairy cattle, four lines of chickens, and one line of pigs were increased to a level considered as secure in the collection.  Additionally, six important fish species were added to the collection for the first time.


IMPACT/OUTCOME:  Breeding populations of livestock have narrowed considerably in their genetic diversity over the past several decades prompting concerns regarding adequate levels of genetic variability and biosecurity.  This progress provides increased security of farm animal genetic resources and maintenance of animal genetic variation.


ACCOMPLISHMENTS:  Scientists in the ARS Biotechnology and Germplasm Laboratory at Beltsville, Maryland, have exploited the recent release of the chicken genome sequence applying proteomics techniques to identify 40 proteins that are expressed in the turkey sperm storage tubule epithelium.  Four proteins were uniquely expressed when sperm were absent while three additional proteins were only expressed when sperm were present. 


IMPACT/OUTCOME:  The commercial turkey industry relies exclusively on artificial insemination (AI) for production.  Due to low success of cryopreservation of semen, these AI procedures rely on the use of fresh semen, which requires costly maintenance of male populations on production farms.  A unique aspect of turkeys is that they have the ability to store live sperm in the oviduct of the hen for extended periods of time in sperm storage tubules.  These results are the first step in identifying novel proteins for maintenance of poultry sperm viability and provide one of the first examples of the power of having a whole genome sequence available from the chicken.


ACCOMPLISHMENTS:  ARS confirmed that ghrelin, a hormone involved with growth and feed intake in terrestrial animals was in rainbow trout, tilapia, and catfish.  It was identified as a new regulatory pathway for controlling growth hormone secretion.  Researchers found that feed efficiency of groups of related fish was adequately large to use in improving performance.


IMPACT/OUTCOME:  These accomplishments will be used for developing more efficient strains of finfish for aquaculture.


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 2004, 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:  Demonstrated that post-plant application of a hydrophobic kaolin clay mulch provided excellent weed control during the establishment year of blackberries with no adverse effects.


IMPACT/OUTCOME:  An environmentally safe and economical weed management technique for small fruit and horticultural crops was identified.


ACCOMPLISHMENTS:  Papaya and plum trees have been genetically engineered to resist virus pathogens (papaya ring spot virus and plum pox virus) that otherwise threaten to eliminate the production of these fruits.  In both cases there is no other known method available to generate resistance to these devastating diseases.


IMPACT/OUTCOME:  The resistant papaya tree has restored papaya production in Hawaii to pre-disease levels, and ARS (Hilo, Hawaii) is cooperating with scientists from many other countries to develop their own locally adapted resistant varieties of this fruit, a dietary staple with excellent nutritional value in much of the tropical world.  The pox-resistant plum variety developed by ARS (Kearneysville, West Virginia) is undergoing biosafety evaluations, and when approved for distribution, will provide the only source of virus resistance for fruit breeders.


ACCOMPLISHMENTS:  ARS scientists at Raleigh, North Carolina, have led a cooperative project to develop high yielding soybeans with low phytate content.  When plants were grown with excess phosphorus, seed phytate concentrations in normal soybeans doubled whereas levels in the low phytate line remained constant.  This result led to the discovery that two different genes control phytate concentration in soybeans.


IMPACT/OUTCOME:  In southern States, there are many large poultry and swine feeding facilities which are sources of phosphorus pollution from livestock waste.  Soybeans that are naturally low in phytate (a major cause of phosphorus in animal wastes) are a great advantage in reducing pollution.  The new information makes it possible to devise efficient plant breeding methods to transfer the low phytate genes to soybean varieties.


ACCOMPLISHMENTS:  ARS scientists at Beaumont, Texas, have developed “Neches,” a new sweet or waxy rice cultivar.  The rice can be used as dessert rice and has novel starch and flour properties.  ARS researchers at Lincoln, Nebraska, in cooperation with the University of Nebraska have released two new hard white winter wheat varieties for Asian noodles.


IMPACT/OUTCOME:  These new varieties will help diversity and expand markets for U.S. producers.


ACCOMPLISHMENTS:  ARS researchers at Mississippi State, Mississippi, have identified new molecular markers for aflatoxin resistance and released an inbred line of corn with improved aflatoxin resistance.  ARS scientists at Raleigh, North Carolina, discovered that resistance to fumonisin contamination is highly heritable and linked with ear rot resistance. 


IMPACT/OUTCOME:  Contamination of corn grain with mycotoxins (aflatoxin and fumonisin) can cause food safety problems and major losses to U.S. corn producers.  These new genetic resources will expedite the transfer of fungal mycotoxin resistance into superior corn hybrids for U.S. producers.


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


ACCOMPLISHMENTS:  ARS researchers at Albany, California, and Ithaca, New York, have developed a new web site, “GrainGenes 2.0.”  Large scale genomics and genetic data are provided to cereal researchers from this web site along with new bioinformatics software tools and genetic mapping information.


IMPACT/OUTCOME:  This central site ensures that the most recent genetics and genomics discoveries are rapidly deployed to wheat, barley, and oats genetic improvement programs.


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 2004, 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 in Columbia, Missouri, have identified three soybean genes that control the enzymes that are responsible for linolenic acid production.  Two of these genes have mutations, bringing the total number to five mutant alleles.  The mutations in four of these genes are the result of single nucleotide changes, and a fifth allele actually has lost a significant part of its sequence, a natural genomic deletion.


IMPACT/OUTCOME:  This information enables the construction of very specific molecular markers that will facilitate the selection of very low linolenic acid germplasm from breeding populations.  Genetic reduction of linolenic acid in soybean oil is a major step that enables the manufacture of more healthful foods with low levels of ‘trans’ isomers.


ACCOMPLISHMENTS:  All aspects of plant biology hinge on their ability to perceive light.  Phytochrome is the major light receptor for plants.  ARS scientists at the Plant Gene Expression Center in Albany, California, have discovered genes that control the process called “phytochrome signaling.”  This gene encodes an intermediate signal that regulates red light induced changes in seedling growth (photomorphogenesis), by functioning as the central circadian oscillator of the plant biological clock.


IMPACT/OUTCOME:  The research may provide insight into the molecular mechanism by which light controls agriculturally relevant responses, such as floral induction.


ACCOMPLISHMENTS:  ARS scientists at Lubbock, Texas, have mapped a gene that is essential for signaling cold stress in plants.  At Raleigh, North Carolina, ARS scientists have developed methods to isolate specialized cells in winter wheat seedlings that survive extreme freezing temperatures.  Those cells can now be used to identify genes that confer freezing tolerance in winter wheat.  Scientists at the University of California, Davis, and ARS scientists at Albany, California, have identified the “vernalization” gene, which ensures that wheat plants will not flower and form grain until the greatest danger of killer frosts has passed. The ARS scientists successfully inserted the gene into wheat plants to test its effect, proving the essential role of the gene in freezing protection. 

IMPACT/OUTCOME:  Winterkill and cold temperatures cause major losses every year to horticultural plants and field crops.  These studies advance the science of freezing protection and identifying genes and methods that can be used to improve crop resistance.


ACCOMPLISHMENTS:  ARS scientists at Beltsville, Maryland; Ithaca, New York; and Albany, California, are characterizing the effects of genetic engineering on plant metabolism and environmental fitness and developing methods to reduce or eliminate identified risks.  Targets include changes in plant metabolic competency, spread of transgenes to sites where they are unwanted, and limiting expression of transgenes to non-harvested plant parts.


IMPACT/OUTCOME:  As a result of the research, we will be able to identify the risks associated with genetic engineering that need to be prevented or ameliorated.  The data is essential to regulatory agencies charged with oversight of agricultural biotechnology.  Consumers in the United States and in overseas marketplaces must have confidence in the genetically engineered products from U.S. agriculture.


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:  Scientists at the USDA-ARS Plant Gene Expression Center, Albany, California, have developed a strategy that will help prevent gene spread from genetically engineered crops.  The revised strategy incorporates three site specific recombination systems, one to insert the DNA precisely into the plant genome, a second to remove selectable markers (such as antibiotic resistance genes), and a third to remove transgenic DNA from pollen.


IMPACT/OUTCOME:  The three systems, when working together, will provide an unprecedented level of control over the potential environmental spread of transgenic DNA, one of the chief concerns voiced repeatedly by consumers.


ACCOMPLISHMENTS:  ARS scientists within the Plant Stress and Germplasm Development Unit in Lubbock, Texas, have identified a novel gene that is essential for heat tolerance in plants.  This finding advances ARS’ understanding of how cellular components impact the expression of heat tolerance.  The scientists used positional cloning to map the mutated gene within the thermo-sensitive mutant AtTS244.


IMPACT/OUTCOME:  Plant productivity in arid climates often is reduced by temperature stress.  This discovery will improve the ability to develop more heat tolerant crops.


ACCOMPLISHMENTS:  Identified the true sex pheromone of the female dogwood borer, an increasingly important wood-boring pest of apple, and developed pheromone lures for the capture of male moths.


IMPACT/OUTCOME:  A technology for mating disruption was identified that could control the pest insect of apples and reduce or eliminate the need for use of insecticides.


Performance Measure 1.2.7:    Identify genes responsible for plant product quality and resistance to diseases, pests, and weather losses.




During FY 2004, 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 scientists are very active in identifying, characterizing, and transferring genes that provide resistance to pests and pathogens, combining modern genomic methods with traditional breeding, for use in developing resistant crop varieties.  Examples include:  resistance to reniform nematode in cotton (College Station, Texas; and Mississippi State, Mississippi); resistance to soybean cyst nematode (Beltsville, Maryland); resistance to Fusarium wilt in cotton (Shafter, California); resistance to soybean rust (national multi-location cooperative effort); resistance to Aspergillus flavus in cotton (New Orleans, Louisiana), corn (Mississippi State, Mississippi), and peanut (Tifton, Georgia); and resistance to Fusarium head blight in grains (Fargo, North Dakota; St. Paul, Minnesota; and Madison, Wisconsin).


IMPACT/OUTCOME:  Resistance genes, many of which are very difficult to transfer, will be the basis for improving resistance to pests and pathogens, thereby enhancing yields and quality, reducing dependence on pesticides, and improving profitability and sustainability of U.S. agriculture. 


ACCOMPLISHMENTS:  ARS researchers at Columbia, Missouri, have provided the majority of the molecular marker resources for trait mapping in corn.  More recently, these scientists, along with scientists at the University of Wisconsin and University of California, Irvine, have developed a new genomic approach to identify genes that control agronomic traits.


IMPACT/OUTCOME:  A major constraint for crop breeders is limited knowledge concerning which genes control valuable traits.  This new approach was developed to make breeding more efficient in selecting genes.  For the first time, it is now possible to exploit corn genomic discoveries to facilitate more targeted, efficient corn improvement.


ACCOMPLISHMENTS:  Genetic diversity in agricultural crops is thought to decline during their evolution from wild species to modern land races, and even more rapidly as man has selected elite cultivars from the land races for commercial production.  Recent findings by ARS scientists at Beltsville, Maryland, have shown that the loss of genetic diversity in the modern soybean genome was much less rapid than in maize or even Arabidopsis.  The decline in genetic diversity was significantly more rapid in wild soybean (the progenitor of cultivated soybean) versus unimproved cultivated soybean germplasm, typical of that in the USDA Soybean Germplasm Collection.


IMPACT/OUTCOME:  This unexpected discovery suggests that genetic association analysis using whole genome scans may be feasible for gene or QTL discovery.  This approach is based on the first application of “linkage disequilibrium” theory in a self-fertilized crop species, such as soybean, and suggests the possibility of a much more efficient approach to discover genes or QTL in the soybean germplasm collections, such as that maintained by the USDA.


ACCOMPLISHMENTS:  ARS researchers at Phoenix, Arizona, have bred Lequerella to improve seed oil content, harvest index, and seed yield.  A new germplasm line is being released this year with 33 percent oil content compared to 29 percent from the previously released line.  The new line provides high genetic diversity for future improvements to public and private researchers, and is an alternative domestic source of hydroxy fatty acids presently filled by imported castor.  Hybrid Lesquerella lines now produce above 80 percent hydroxyl fatty acid compared to 56 percent from non-hybrids.  These are significantly improved over the best lines available and will result in significantly lowering the cost for industrial use.


IMPACT/OUTCOME:  This research is being accelerated with the development of 20 single sequence repeat (SSR) molecular markers.  These tools will enable marker assisted selection for traits, such as high hydroxy fatty acids, improved oil content, and other yield related traits.  Lower oil costs for products, such as biodegradable motor oils, are needed to improve chances for commercialization of lesquerella.


ACCOMPLISHMENTS:  ARS scientists in Stillwater, Oklahoma, discovered new sources of genetic resistance to the bird cherry-oat aphid, a perennial pest of wheat.  Purdue scientists and ARS researchers at West Lafayette, Indiana, developed wheat lines that are resistant to barley and cereal yellow dwarf virus.  ARS scientists at Aberdeen, Idaho, and Stillwater, Oklahoma, developed a new barley variety, “Burton,” that is resistant to Russian wheat aphid.


IMPACT/OUTCOME:  Insects and diseases cause major losses to the U.S. wheat and barley industry.  These new lines and varieties will help U.S. producers combat serious pest and disease threats.


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


ACCOMPLISHMENTS:  ARS scientists at Fargo, North Dakota, constructed a gene linkage map with a set of 129 recombinant inbred lines (RILs) derived from the cross of 83HR4 x RHA345.  Linkage maps are desirable for the rapid location of genes governing simple and complex phenotypes or quantitative trait loci (QTLs), and for the development of DNA markers for marker-assisted breeding.  DNA samples were prepared in collaboration with A. Berville in France.  The linkage map consisted of 160 markers in 17 linkage groups plus four pairs of linked markers, and covered a total length of 1,140 centiMorgans (cM) with an average interval of 9 cM between two markers.


IMPACT/OUTCOME:  This map will be useful to define the QTLs affecting oleic acid composition in the sunflower seed oil.


ACCOMPLISHMENTS:  ARS scientists at Ames, Iowa, have developed techniques that help sort DNA fragments or ESTs.  These fragments were used to identify members of gene families and define locus defining polymporphisms that distinguish each family member.  This was followed by the identification of SNPs (alleles) between homologs in the germplasm used to construct the EST libraries.  In addition, bioinformatic software was developed to help position genes (gene ontology).  Analyses of BAC-end sequences from genetically anchored loci also provided insight into the structure and organization of the soybean genome.  BLAST analysis using BAC-end sequences revealed microsynteny between Medicago truncatual and Arabidopsis thaliana.


IMPACT/OUTCOME:  The soybean genome is composed of two duplicated sets of chromosomes.  This makes reassembly and assignment of gene sequences to the correct chromosome very difficult.  Statistical modeling of redundant BAC ‘hits’ using mapped genetic markers indicated that most soybean genes will be found in approximately 25 percent of the genome, thus making genome sequencing in soybean much more manageable and providing clues to the sequencing strategy that will save millions of dollars in sequencing costs.


ACCOMPLISHMENTS:  Relatively few breeding lines have been used in the parentage of most modern soybean varieties in commercial production.  This “narrow genetic” base does not take advantage of the great genetic diversity that exists in the soybean germplasm collection.  ARS scientists at Urbana, Illinois, have demonstrated the value of these “untapped” genes.  Four new quantitative trait loci (QTL) associated with high protein concentrations have been mapped in populations derived from three exotic sources of high protein.  Five of six putative QTLs associated with soybean seed yield were confirmed, two near isogenic line populations.  The favorable alleles at these QTLs were originally derived from exotic germplasm.


IMPACT/OUTCOME:  In the near isogenic populations the yield increases per QTL ranged from 2.9 to 4.5 bushels per acre.  A new germplasm release, LG00-3372, was the highest yielding entry in Uniform Preliminary Test IIIB in 2003.  This line is a selection from the cross of two Chinese varieties, Hui nan zi hua he jia (PI 561319A) x Fen dou 31 (PI 574477); and the pedigree is 87 percent exotic germplasm. 


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 2004, ARS will


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


ACCOMPLISHMENTS:  The 20+ genebanks in the USDA/ARS National Plant Germplasm System (NPGS) now conserve 460,000 separate samples of over 10,700 plant species.  During the last few years, scientific interest in this germplasm has increased significantly, with more than 130,000 samples distributed last year to requesters worldwide. 


IMPACT/OUTCOME:  These materials are key to enabling continued progress in crop genetics and breeding, requisite for future food security.


ACCOMPLISHMENTS:  ARS scientists at Cold Spring Harbor Laboratory, New York, improved bioinformatic tools for comparing the genomic structure of corn and rice.  Also, they incorporated sorghum and wheat “physical maps” into the grain genome database, Gramene.


IMPACT/OUTCOME:  These advances furnish new, more powerful bioinformatic/database tools for accelerating progress in understanding the detailed genetic structure of grain genomes.  The new insights gained may aid grain crop genetic improvement.


ACCOMPLISHMENTS:  ARS scientists at Ithaca, New York, successfully applied a new statistical genetic approach, termed “association mapping,” to characterizing the genetic control of starch and protein quality in maize.  They identified new genes and alleles associated with starch pasting quality, starch to protein ratios, starch content, and the interaction of those genes with environmental variability.


IMPACT/OUTCOME:  Not only was this a successful proof-of-concept for a new method, it also identified new genes potentially valuable for breeding corn tailored to meeting specific agronomic and industrial needs.


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


ACCOMPLISHMENTS:  ARS scientists at College Station, Texas, established in Louisiana an innovative plantation of pecan seedstocks selected for their combined horticultural and forestry merit. 


IMPACT/OUTCOME:  The research results in the first long-term pecan test system focused on pecan genetic improvement in a major U.S. production area and on the development of large-scale pecan production systems that simultaneously improve wildlife habitat and harvest yield.


ACCOMPLISHMENTS:  Scientists at ARS genebanks developed and/or applied new genetic markers, called “SSRs,” to a broad spectrum of crops, such as peanuts, citrus, grapes, tropical legumes, mangoes, paspalum, tropical ornamental bulbs, blueberries, and hazelnuts.  They developed a means for assaying genetic variability in DNA rapidly and inexpensively. 


IMPACT/OUTCOME:  The markers are molecular tools potentially useful for accelerating progress in crop genetic resource conservation and breeding.


ACCOMPLISHMENTS:  Developed techniques to effectively identify watercore and mealiness in apples by using spectral reflection of near infrared frequencies.


IMPACT/OUTCOME:  The new technology that was developed could form the basis for sorting and removing defective apples.




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.


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Last Modified: 8/17/2005
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