• Introduction
• Genetic Resource Management
• Genomic Characterization, Manipulation, and Genetic Improvement
• Bioinformatics and Genome Databases

Introduction

National Program 301, Plant, Microbial, and Insect Genetic Resources, Genomics, and Genetic Improvement, is divided into three components: Genetic Resource Management (conserving a broad spectrum of genetic resources and facilitating their use in genetic improvement and scientific research); Genomic Characterization, Manipulation, and Genetic Improvement (including molecular marker analyses, nucleotide sequencing, gene mapping, genetic enhancement, plant breeding, and to a limited extent, functional genomics; and Bioinformatics and Genome Databases (developing new software tools for analyzing and managing genomic and genetic resource information and delivering the former via databases on computer networks).  Together, these components are yielding breakthroughs in understanding genome composition, manipulating genetic material, and providing genetically diverse gene pools with sustained and enhanced agricultural value.  During 2000, this program produced many important discoveries and advances.  Some of these are described below.

Selected Accomplishments (Listed by Component)

Genetic Resource Management

The USDA/ARS collections of genetic resources represent the largest and highest quality source of raw genetic material for ensuring continued worldwide progress in genomic research and genetic improvement of agricultural commodities.  One component of National Program 301 is the USDA/ARS plant, microbial, and insect genetic resource management program, which is conducted with university and corporate partners and other national and international genetic resource programs, especially those at international agricultural research centers.  There are very few publicly accessible germplasm collections maintained by the private sector, so all segments of worldwide agricultural research and genetic improvement rely on the USDA/ARS public collections of genetic resources.

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

The website for the NPGS public database, the Germplasm Resources Information Network (GRIN) was queried thousands of times per day through the World Wide Web at www.ars-grin.gov .  An average of more than 4000 new visitors queried GRIN everyday.  This high frequency indicates the database is a key resource for plant researchers and breeders worldwide.

USDA/ARS Microbial Germplasm Collections .  The collections now manage more than 100,000 different strains of bacteria, fungi, and related microbes.  The largest collection at Peoria, Illinois, manages more than 80,000 different strains, including germplasm vouchers of patented microbes.  The collections serve as an important reference standard for microbial identification, as biocontrol agents, and as sources of natural products for pharmaceutical and other industrial uses.

Detection methods for blueberry diseases .  Blueberry stunt disease is among the most serious diseases of highbush blueberries throughout the United States, which cause substantial economic losses.  A highly sensitive and accurate diagnostic test for blueberry stunt phytoplasma was developed by USDA/ARS scientists in Chatsworth, New Jersey, and Beltsville, Maryland.  The new test will be essential for developing strategies for minimizing the spread and economic impact of the disease.

New methods for evaluating sugar content and disease resistance in beet germplasm .  Sugar beets are one of the most important sources of domestic sugar and a mainstay of the agricultural economy in the Northern Great Plains.  Sugar content and disease resistance are key productivity factors for sugar beets.  USDA/ARS scientists at East Lansing, Michigan, developed new methods for assaying sugar content of single plants (via high-performance liquid chromatography) and single plant assays for disease resistance to an important sugar beet seedling disease.  These new techniques may accelerate the pace of sugar beet genetic improvement.

Detection methods for avocado diseases .  Avocado sun blotch is one of the most devastating diseases of this fruit crop.  USDA/ARS scientists at Miami, Florida, developed an improved method for detecting in a single assay different virulent strains of the viroid that causes this disease.  This new detection method will increase the efficiency of germplasm management efforts and may help prevent spread of the disease.

Evaluating cotton germplasm for insect resistance .  By evaluating hundreds of cotton germplasm lines, USDA/ARS researchers at Starkville, Mississippi, identified non-United States germplasm with resistance to tobacco budworm, one of the most serious cotton pests.  These resistant materials will provide the basis for breeding resistance into cotton germplasm adapted to the United States.

New methods for evaluating cereal germplasm for aluminum tolerance .  High concentrations of aluminum in soils severely limit agricultural productivity worldwide, especially for cereals.  USDA/ARS researchers at Columbia, Missouri, developed a rapid, hydroponic screening laboratory method for identifying wheat resistant to high concentrations of aluminum.  The results of the lab test correlated highly with field tests conducted in Brazil.  This new germplasm evaluation tool may improve the efficiency of breeding wheat for aluminum tolerance, thereby improving its productivity on marginal soils throughout the world.

New diagnostic tests for aflatoxin-producing fungi.   Aflatoxin-producing fungi are a major threat to the safety of United States and world food and feed supplies.  USDA/ARS scientists at Peoria, Illinois, determined the sequences of particular genes of aflatoxin-producing fungi that will enable development of a rapid detection system.  During this research, a new aflatoxin-producing fungus associated with silkworm rearing was discovered.  This research broadens the number of species known to produce aflatoxin, and provides addition information needed for DNA detection systems.

Genomic Characterization, Manipulation, and Genetic Improvement

USDA/ARS researchers apply traditional and contemporary technologies to harness the inherent genetic potential of germplasm.  To harness this genetic potential most effectively, novel, rapid, and more efficient methods must be developed for identifying useful properties of genes and genomes, for determining the function of genomic segments, and for manipulating genetic material and genomic information.  Through genomic characterization, the structural and functional features of genomic segments or entire genomes can be elucidated nearly simultaneously, providing knowledge that will help create new agricultural products, ensure food safety and security, and furnish new ways of boosting agricultural productivity.  Consequently, sequencing genomes or genomic components of agriculturally important organisms and determining their function via functional genomic analyses are priorities for USDA/ARS and a goal for this component of National Program 301.

The information generated by this National Program component, when combined with more effective breeding strategies, will help ARS scientists more rapidly attain high. priority genetic improvement objectives.  All of the preceding tools and information furnish the bases for more effective assessments of genetic diversity, diagnostic and varietal/strain identification tests, and superior methods of genetic improvement.  Optimal progress in genetic improvement will result from marrying the preceding technologies with genetic resources, bioinformatics technology, and genomic/genetic information (see below).  The result will be superior, genetically improved organisms for agriculture and additional genetic stocks to enable future research.

Genome sequencing .  Precise knowledge of the location, composition, and function of plant genes is key for accelerating enhanced crop productivity.  Determining the exact arrangement of genetic building blocks--technically known as nucleotide sequences--is one of the first steps in the process.  At the end of 2000, an international scientific team that included ARS researchers in Albany, California, determined the first essentially complete genome sequence for a plant, Arabidopsis , an experimental . model plant..   It was sequenced first because of its small genome and rapid life cycle.  Knowledge of its genome is already helping to elucidate the structure and function of crop genomes and their constituent genes.

A petunia with red corollas .  The only naturally occurring species of Petunia with red corollas (flowers) from Brazil was scientifically characterized.  The unusual color results from a biochemical pathway different than that of the common garden petunia.  This discovery by ARS scientists in Beltsville, Maryland, is important because it may provide a second potential source of genes for red corolla color for this crop, one of the most important bedding ornamental plants in the United States.

New disease-resistant dry bean released .  USDA/ARS researchers and university cooperators at East Lansing, Michigan, released a high-yielding, black-seeded dry bean that incorporates resistance to a variety of fungal diseases, including white mold, the most serious disease of this crop in the Great Lakes region.  Cultivation of this bean may reduce fungicide use, while increasing profits for small producers, who generally rely on good production to offset profit risks.  

Valuable source of oat disease resistance identified .  Crown rust is a devastating disease of oats, and previous sources of resistance to the disease were governed by one gene, which often became ineffective soon after deployment.  USDA/ARS researcher and university cooperators at St. Paul, Minnesota, identified a more general type of resistance, conferred by many genes acting in concert, that is effective against all strains of the disease, as opposed to specific strains.  Researchers found DNA markers, which will facilitate incorporation of the resistance genes into oat breeding lines.

New, superior potato varieties .  The farmgate value of potatoes is worth several billion dollars in the United States, but the cost of production is high because of diseases, pests, and suboptimal quality.  USDA/ARS researchers at Prosser, Washington, and university cooperators in the Pacific Northwest released several superior potato varieties that should increase producer profitability.  Bannock Russet and Gem Russet have improved disease resistance and yield for the french fry and fresh markets.  Idarose is a superior red-skinned variety for boiling and salads.

Low phytic acid grains are nutritionally superior .  USDA/ARS researchers at Aberdeen, Idaho, initially developed grains with low phytic acid to decrease phosphorus run-off from animal feed operations.  Later research with university cooperators has shown that humans retained 70 percent more zinc from foods prepared from low phytic acid maize, and cattle gained up to 33 percent more weight per day when fed low phytic acid barley as compared to regular barley.  These results suggest that low phytic acid grains are not only important in phosphorus nutrient management, but that they also may be superior for food and feed.

  New, superior landscape plants developed .  Two new woody ornamental landscape plants, a lilac and a redbud, were developed by scientists at Washington, D.C., and released to nurseries for propagation.  The redbud is seedless, and the lilac is better adapted to warmer climates.  Both new varieties can be propagated readily by standard techniques and furnish United States gardeners a wider diversity of well-adapted landscape plants.

  New, superior genetic markers for improving tomato. s nutritive quality .  In tomatoes, beta carotene confers superior nutritive properties.  USDA/ARS scientists at Beltsville, Maryland, identified DNA genetic markers for accurately predicting beta carotene content.  These markers may improve the efficiency of tomato breeding and hasten the development of varieties with superior nutritional content.

Alfalfa gene flow tracked .  Quantifying the actual or potential gene flow via pollen transfer is a vital task for scientifically based risk assessments of transgenic crops.  USDA/ARS scientists at Manhattan, Kansas, discovered that alfalfa pollen could be transferred more than 1,000 meters by pollinating insects.  This distance is far greater than originally reported; suggesting that absolute containment of transgenic, insect-pollinated alfalfa is highly unlikely.

Potatoes with superior nutritive value .  The chemical compound lutein may help ameliorate age-related macular degeneration, a major cause of blindness and related compounds may also protect against cancer and cardiovascular diseases.  USDA/ARS scientists at Beltsville, Maryland, developed experimental lines of potatoes with high concentrations of lutein, providing the raw material for improving the nutritive value of commercial potatoes.

New USDA/ARS variety tops the Ohio soybean yield trials .  Continued improvement in yield of soybeans is needed to enable United States farmers to maintain a competitive edge in world markets.  In 1999 field trials, ARS researchers in Wooster, Ohio, found that a newly released semidwarf soybean cultivar topped the maximum yield trials at 97 bushels per acre.  The results confirmed the potential of a well-managed subirrigation/drainage system, when used in combination with a high-yield soybean cultivar, to produce consistent yields of 70 to 80 bushels per acre.

Nematode-resistant carrots.   Nematicides are very expensive, especially for small producers, and those who produce vegetables such as carrots for organic or low-input niche markets.  Consequently, carrots with genetic resistance to nematodes are highly desirable, since nematodes pose the largest threat to production worldwide. USDA/ARS scientists in Madison, Wisconsin, and their university cooperators identified and characterized genes conferring genetic resistance to nematodes in carrots.  They began breeding the resistant traits into standard carrot germplasm.

Disease resistance for cocoa .  Cocoa, the raw material for chocolate, represents a $5 billion dollar industry in the United States.  It is also an essential cash crop for small farmers in the tropics.   Cocoa production is seriously threatened by three diseases, and the crop is further endangered by over-reliance on a few West African producers.  The cocoa genome is poorly understood; characterization of existing collections is often inaccurate; and the genetic mechanisms underlying disease resistance are poorly documented.  USDA/ARS researchers in Miami, Florida; Mayaguez, Puerto Rico; and Beltsville, Maryland, along with international public and private-sector cooperators have begun to genetically characterize cocoa germplasm, and thereby identify genetic markers associated with disease tolerance, quality, and productivity. To date, genes for disease resistance have been mapped to three genomic regions.

  New peach for the Southeastern United States.   Peaches in the southeastern United States are generally grown by small producers in relatively small volumes.  The profitability of southeastern growers may be enhanced by . Gulfprince. an early-season peach with superior quality and shipping characteristics that was bred by USDA/ARS researchers and their university cooperators at Byron, Georgia.

New superior cool-season grain legumes .  Grain legumes are important rotational crops in cereal-based cropping systems of the Pacific Northwest.  But many diseases, insect pests, and environmental stress reduce their seed yield and quality.  USDA/ARS scientists in Pullman, Washington, released two new varieties of peas, two new varieties of lentils, and a new variety of chickpeas.  These superior, new varieties incorporate high yields and levels of disease resistance. 

Plum-pox-resistant plums .  Plum pox virus, the most serious virus disease of plums and other stone fruit, recently entered the United States and may threaten the United States stone fruit industry.  USDA/ARS researchers at Kearneysville, West Virginia, genetically engineered plums for resistance to the virus, thereby providing producers with a way to combat that disease.

Soybeans with highly unsaturated oil .  USDA/ARS researchers at Raleigh, North Carolina, developed soybeans with high concentrations of oleic acid, (that is with highly unsaturated oil) using traditional breeding methods.  Highly unsaturated oil is considered healthier than highly saturated oils.  Such varieties bred using traditional approaches may help United States farmers to remain competitive in exporting soybeans to nations that restrict use of transgenic crops.

Rice with improved seedling vigor .  At present, herbicides are applied to control weeds prior to flooding rice fields.  USDA/ARS researchers at Beaumont, Texas, have identified and characterized genes that accelerate seedling growth up to four times.  When these genes are incorporated into standard germplasm, it may result in more vigorous rice that will establish itself more rapidly, thereby reducing the need for herbicide application. 

Wheat resistant to scab .  Fusarium head blight (scab) has devastated the hard red spring wheat producing areas of the Northern Great Plains.  USDA/ARS researchers and university cooperators at Fargo, North Dakota, released the scab-tolerant variety . Alsen. , which has high yields and greater scab resistance than current varieties.  It will likely be widely produced in regions previously devastated by this disease.

Guayule composite board foils termites and fungi .  Wood-destroying organisms cause several billion dollars worth of damage annually in the United States.  USDA/ARS researchers at Phoenix, Arizona, and their university cooperators developed composite boards made from guayule pulp and high-density plastic.  When exposed to termites or wood. rot fungi, the composite boards were not damaged, thereby demonstrating an important new potential use for guayule, a drought-tolerant crop known for its nonallergenic latex.  Commercial production of guayule as an alternative source of rubber and building material may help conserve United States water and forest resources.

New peanut breeding lines to resist nematodes and disease .  The peanut root-knot nematode and tomato spotted-wilt virus cause significant economic damage to peanuts in the Southeastern United States.  USDA/ARS researchers in Tifton, Georgia, have bred the first peanut that is highly resistant to root-knot nematode and tomato spotted-wilt virus pathogens,  Further agronomic evaluations and enhancement will develop this material into a commercially acceptable cultivar.

Sunflower variety with superior oil .  The United States frying industry requires sunflower oil with 50 to 60 percent monosaturated fatty acid, which ideally would be produced by a sunflower hybrid with high yield and superior agronomic properties.  USDA/ARS researchers in Fargo, North Dakota, developed a hybrid sunflower with this fatty acid profile, high yield, and disease resistance.  The germplasm was released to private and public breeding programs for varietal development.

Bioinformatics and Genome Databases

USDA/ARS researchers and their public-sector cooperators are developing new software tools for rapidly and readily analyzing and processing the torrent of genome sequence and map data issuing from various large projects that are analyzing crop and model plant genomes.  The processed data are managed in the USDA/ARS genome databases, bioinformatics focal points for the collection and dissemination of information relating to genomes, genetic improvement, genetic diversity, and their study.  Accessible through the World Wide Web, the databases contain research contacts; the sequences of genes and expressed sequence-tags (ESTs); genetic maps; descriptions of defined genes and DNA markers; genetic control of economically important traits; metabolic pathways and associated enzymes.  They also provide genetic information related to agriculturally important traits; links between separate model species and agricultural species databases; and links to relevant genetic resource databases and their extensive data on accession traits.  The combination of high-quality databases and software tools provided by this National Program component are optimizing the quantity and quality of genetic information available for research, breeding, and genetic resource management.

New ARS networks for bioinformatics research and development, and genome databases .  The flood of crop genome sequencing data issuing from various crop genome characterization efforts (especially sequencing of model species genomes, and gene segments termed ESTs) requires enhanced genome database and bioinformatic capabilities to convert the data to useful information for solving agricultural problems and to deliver that information to users.  With the USDA/ARS Center for Agricultural Bioinformatics at Cornell University, Ithaca, New York, serving as a hub, this national program has expanded its institutional network for developing and maintaining crop genome databases and bioinformatics tools to encompass strong partnerships with the University of Minnesota, the University of California-Davis, and Cold Spring Harbor Laboratory.  At Ithaca, USDA/ARS scientists established a new Internet server to widely distribute genetic and genomic information for more than a dozen crops and model plant species to the scientific community.

New software tools for more efficient genetic mapping .  USDA/ARS scientists and collaborators at Cornell University, Ithaca, New York, developed more efficient means for genetically mapping agriculturally important traits, which serves as a vital prerequisite for genetic improvement of that trait.  The scientists developed a new software tool, MapPop that enables high-quality genetic mapping with smaller scale genetic studies.  This new tool and approach may tangibly accelerate the generation of genetic data and the progress of crop genetic improvement.

New comparative maps between soybean and a model plant species .  The size and complexity of the soybean genome prevent it from being completely characterized in the near future.  USDA/ARS scientists in Ames, Iowa, correlated information in the USDA/ARS soybean genome database with genomic data from the model plant Arabidopsis , the first plant genome to be completely sequenced.  The arrangement of genes on these two genomes was somewhat similar, indicating that information derived from the Arabidopsis genome may help accelerate genetic research and crop improvement in soybeans, a major crop worldwide.

Diversity of gene sequences in corn breeding lines .  Efficient use of naturally occurring genetic variation in corn is difficult because most agronomic traits involve multiple genes.  ARS scientists at Raleigh, North Carolina, have used large-scale DNA sequencing of genes from diverse corn germplasm to associate specific genes with traits controlling nutrient utilization, flowering time, and plant height.  This information can be used to assess the diversity of United States corn breeding lines and to speed up the breeding of corn for a range of environments.