• Introduction

• Component I.   Genetic Resource Management

• Component II.  Genomic Characterization and Genetic Improvement

• Component III. Genome Databases and Bioinformatics

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 and Genetic Improvement (including molecular marker analyses, nucleotide sequencing, gene mapping, comparative and, to a limited extent, functional genomics, plant breeding, and genetic enhancement); and Genome Databases and Bioinformatics (developing new software tools for analyzing and managing genomic and genetic resource information and delivering the former via databases implemented on up-to-date 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 2003 this program produced many important discoveries and advances.  Some of these are described below, grouped by program component.

Selected Accomplishments by Component

Component I.   Genetic Resource Management

Broad spectrum of plant genetic diversity accessible to researchers.  The USDA/ARS National Plant Germplasm System (NPGS), composed of more than 20 genebanks throughout the United States, now manages more than 456,000 samples of more than 10,300 plant species, and distributes annually more than 100,000 samples upon request to researchers worldwide.  NPGS sites recently increased substantially the quality and quantity of information available online in the GRIN database, especially digital images of plants, and genetic marker profiles of key samples. 

Record number of maize genetic stocks distributed.  Genetic stocks, specialized germplasm lines with specific genetically characterized traits (often mutants), comprise a vitally important tool for plant genetic and genomic research.  During this reporting period, the USDA/ARS Maize Genetics Cooperation-Stock Center (the world’s largest and highest quality collection of maize genetic stocks) in Urbana, Illinois, distributed a record number of stocks (15,000+) to fill a number of requests (more than 300).  These stocks have enabled research worldwide that will enhance understanding of maize as a biological organism, and could ultimately lead to maize crop improvement.

Key plant genetic resources acquired via explorations and associated capacity-building partnerships.  ARS scientists at Beltsville, Maryland, coordinated fifteen foreign plant explorations to Latin America, Central Asia, Southeast Asia, and Russia that acquired rare types of grains, tree fruits, small fruits, forages, legumes, oilseeds, and vegetables.  Several projects included innovative capacity-building partnerships, e.g., funding from USDA-Foreign Agricultural Service enabled ARS scientists to assist counterparts in Uzbekhistan with renovating and upgrading that nation’s genebank, and training its personnel.  The preceding exchange projects secured key plant genetic resources for the NPGS, which will safeguard and distribute them for breeding and research worldwide.

Innovative partnerships with organic producers to conserve “heirloom”germplasm.  Thousands of “heirloom” (traditional cultivars) varieties of vegetables and fruit are threatened by extinction unless they are incorporated into genebanks and/or readily available in the trade.  In partnership with Cornell University colleagues, ARS scientists at Geneva, New York, trained more than 800 organic farmers and seed producers in small-scale seed production of heirloom varieties.  The preceding effort has increased the availability of heirloom and publicly-bred germplasm to organic and/or small producers.

Enhanced research and service capacity for crucial national microbial genebank.  The ARS Culture Collection in Peoria, Illinois, maintains a large, world-recognized genebank for microbes of industrial and agriculture significance.  ARS researchers in Peoria, Illinois, incorporated into this genebank several hundred key samples of bacteria with food safety significance (e.g. Clostridium) and fungi highly important as plant pathogens or producers of mycotoxins (e.g., Fusarium).  Furthermore, the collection database was re-programmed to facilitate easy use.  The preceding advances have enhanced this genebank’s capacity for serving the scientific public by providing ready access to needed cultures and associated descriptive information.

Comprehensive genetic resource characterizations.  Without adequate genetic characterization, genetic resources cannot be managed optimally in genebanks, and their utility to potential users is constrained.  NPGS genebanks, such as that at Davis, California, have significantly expanded their programs to genetically characterize germplasm.  ARS and collaborating university researchers at Davis, California, developed effective molecular genetic markers and completed “genetic fingerprints” for many samples of wine grapes and walnuts.  This research revealed the genetic structure for key elements of these crops’ genepools that will enable geneticists, breeders, and genebank managers to develop genetically-sound germplasm management strategies, and to exploit the genetic potential in genebank samples more efficiently and effectively.

Component II.  Genomic Characterization and Genetic Improvement

Smarter, more precise corn improvement for consumers needs.  Corn varieties differ genetically, but until genetic variation in the genes for starch quality and protein are identified at the molecular level, it will be difficult to improve corn for specific cooking purposes and nutritional value.  ARS scientists at Raleigh, North Carolina, have characterized the molecular variation for seven genes controlling starch quality and protein content.  These genes are associated with pasting quality, starch to protein ratio and environmental effects on grain quality.  These new findings can help design new corn varieties for specialized cooking purposes and improved nutritional value.

New pear variety released.  Fire blight is the single most devastating disease of pear, resulting in significant crop and tree loss.  A new pear variety, 'Shenandoah', was released by the USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia, in collaboration with The Ohio State University, Wooster, Ohio.  'Shenandoah' combines a moderately high degree of fire blight resistance and excellent fruit quality in a late maturing pear with long storage life.  This variety with a high fruit quality and fire blight-resistance may reduce grower losses, expand areas of pear production and reduce pesticide usage.

New genetic tools for rice improvement.  ARS scientists at Beaumont, Texas, in cooperation with the U.S. Rice Foundation, have developed molecular markers for rice cooking quality, grain aroma, and disease resistance.  These markers, which are more accurate than standard breeding methods, may enable breeders to select simultaneously for several economically important traits.  Conveying these molecular markers to U.S. rice breeders will help bridge the technology gap for many conventional breeding programs and result in new specialty rice desired by consumers.

Rapid method to detect lycopene developed.  Lycopene is an important human health target for horticultural crop breeding, but typical assays for lycopene content are time consuming and require hazardous chemicals.  A simple, inexpensive and rapid method to detect lycopene content in tomatoes was needed so that growers, breeders, and scientists could test for it.  Scientists at the USDA-ARS South Central Agricultural Research Laboratory, Lane, Oklahoma, produced an accurate assay that is faster, less expensive and requires no hazardous chemicals as it uses a high intensity light spectrophotometer.  This technology offers the tomato industry a potentially simple method for attaining consistently high lycopene content in tomatoes and tomato products.

Dry bean with rust resistance.  Rust diseases pose serious challenges for dry bean production.  ‘Merlot’, a small red dry bean developed and released cooperatively by the USDA-ARS Sugarbeet and Bean Research Unit, East Lansing, Michigan, and the Michigan Agricultural Experiment Station is an upright, short-vine (Type IIA), full season cultivar with consistent and desirable canning quality, and the first small red commercial cultivar with resistance to bean rust disease.  ‘Merlot’ improves the seed characteristics, canning quality, and disease resistance of the small red market class.  Grower interest in Merlot is considerable, as determined by the quantity of foundation seed ordered through commercial channels.

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

Genetic approaches to improve drought tolerance in soybean crops.  Drought is the greatest single limitation to soybean yield in the United States, but no drought tolerant cultivars are available for commercial production.  ARS scientists at Raleigh, North Carolina, coordinated a national program to develop drought tolerant soybean varieties and, through DNA marker analysis, discovered genes that partially control drought resistance in new drought-tolerant soybean lines. 

Genes affecting seed germination identified.  ARS scientists at Pullman, Washington, Washington State University and Duke University have discovered how a gene called “Sleepy” controls how fast and well seeds germinate.  The researchers discovered that the molecular interaction of ‘Sleepy’ with another gene controls hormonal processes that trigger germination.  This information can be used to reduce losses to gardeners, homeowners, and producers due to poor seed germination.

Rhizoctonia root rot resistant sugar beet.  Monogerm, O-type sugar beet germplasm, FC724, was developed and released by ARS scientists at Fort Collins, Colorado, in cooperation with the Beet Sugar Development Foundation, Denver, Colorado.  FC724 has high resistance to Rhizoctonia root rot and has good to moderate resistance to Cercospora leaf spot.  FC 724 will help beet seed industry breeders produce hybrids that will reduce crop losses to Rhizoctonia root rot.

Development and release of commercial sugarcane varieties.  ARS scientists at New Orleans, Louisiana, in collaboration with sugarcane researchers at the Louisiana State University Ag Center and the American Sugar Cane League released the cultivar HoCP 96-540.  This high yielding variety will reduce genetic vulnerability to new disease and insect pests that presently threaten the U.S. sugar industry.

‘WhipperSnapper’ southernpeas.  ARS scientists at Charleston, South Carolina, in cooperation with Louisiana State University at Calhoun, Louisiana, and Lincoln University at Jefferson City, Missouri, developed a superior yielding American-type southernpea with snap-type characteristics of Asian ‘vegetable cowpea’.  The new variety, tentatively named `WhipperSnapper', will provide home gardeners and farmers, who produce hand or machine-harvested snaps and fresh-shell peas with a single variety for both purposes.

New late season strawberry variety.  ARS scientists at Beltsville, Maryland, in collaboration with North Carolina State University, Cornell University, Iowa State University, Pennsylvania State University, the New Jersey Ag Experiment Station, Ag Canada at Nova Scotia, and ARS at Poplarville, Mississippi, released ‘Ovation’ a new late-season strawberry cultivar.  ‘Ovation’ has high yield, excellent fruit size and quality, and exceptional vigor.  This new variety is expected to replace the current late-season standard from the Mid-Atlantic northward.

Strawberry with bacterial angular leafspot disease (BALD) resistance.  ARS scientists at Beltsville, Maryland, developed precise assays to demonstrate that the inheritance of BALD resistance is conferred by recessive alleles at three to four genetic loci in two wild relatives of cultivated strawberry.  This information will facilitate more efficient development of new resistant varieties adapted to their localities.

New hop variety with resistance to powdery mildew.  ARS scientists at Corvallis, Oregon, used traditional breeding methods to combine hop powdery mildew resistance genes from the cvs Nugget, Early Green and Cascade into a new disease resistant variety with high brewing quality.  Adoption of this variety by brewers will reduce production costs by nearly 12 percent for U.S. growers.

Anthracnose resistant pinto bean.  ARS scientists at Prosser, Washington, in cooperation with Michigan State University, North Dakota State University, and University of Idaho, developed an anthracnose resistant pinto bean named USPT-ANT-1.  The cultivar possesses resistance against all known North American strains of anthracnose.  Public and private bean breeders across the United States are now using USPT-ANT-1 to deploy resistance into new pinto bean cultivars.

Mapping disease resistance genes in wild potato.  ARS scientists at Madison, Wisconsin, mapped a disease resistance gene of the wild potato (Solanum bulbocastanum) that confers resistance to late blight.  Molecular markers were used to determine the location of the resistance gene in the potato genome.  This enables eventual gene insertion into a susceptible potato variety to reduce the need for spraying with fungicides.

Increasing health-enhancing compounds in onions.  ARS scientists at Madison, Wisconsin, studied the genetic control for pungency and two major classes of health-enhancing compounds in onions, thiosulfinates and fructans, carbohydrates associated with lower rates of colon/rectal cancers.  Flavor and health-enhancing attributes of onion are controlled by genes that regulate the synthesis of fructans.  Another gene strongly affects the amount of sucrose in onion bulbs.  This information will now enable plant breeders to select for higher sucrose content in onion bulbs so as to combine a sweeter flavor with relatively high thiosulfinate and fructan concentrations, thus creating more nutritious onions with a pleasant flavor and aroma.

Increasing genetic diversity in ornamental pepper germplasm.  In cooperation with an industry partner, ARS scientists at Beltsville, Maryland, have released a new dual-purpose ornamental/culinary pepper cultivar named ‘Tangerine Dream’.  This new cultivar is distinguished by a unique gene combination for beneficial plant morphological traits and improved fruit quality.  Ornamental peppers have the highest per unit value of any pepper product.  They provide a profitable way for small farmers to produce a high value alternative crop.

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

Component III. Genome Databases and Bioinformatics

Developing genetic tools to explore the soybean genome.  Highly detailed genomic maps may accelerate the genetic improvement of soybeans and help better position U.S. producers in competitive global oilseed markets.  ARS scientists at Beltsville, Maryland, and Ames, Iowa, in collaboration with the Universities of Nebraska, Utah, and the Monsanto Company, developed and used nearly 2000 DNA markers to create a new soybean genome map that encompasses all 20 soybean chromosomes.  The newly constructed map is an essential tool for discovering genes affecting important soybean traits, for marker assisted selection to identify superior breeding lines, and for basic studies aimed at the cloning of genes.

User-friendly web site serves as a vital genetic tool and resource for maize researchers.  ARS scientists at Columbia, Missouri, and researchers at Iowa State University have developed a central web interface for maize (corn) research called MaizeGDB (maize genetics and genomics database).  Up-to-date genetic and genomic data are delivered from the site, along with software tools, literature references, and instructions about how to access the data.  This “one-stop” site for maize researchers insures that the most recent genetics and genomics discoveries are widely accessible to maize crop improvement and genetics programs worldwide. 

More effective means for identifying biocontrol fungi.  Strains of Trichoderma serve as some of the most important fungal biocontrol agents for combating plant disease, e.g., diseases of cacao (the source of chocolate).  ARS scientists in Beltsville, Maryland, developed an online, interactive identification key for Trichoderma species that enables a wide spectrum of users (e.g., scientists, regulatory officials, producers, etc.) to identify these key fungi more rapidly and reliably.  This tool may help accelerate regulatory decisions, enhance progress of biocontrol programs, and facilitate a broad spectrum of agricultural research.

New, more effective proteomic analysis.  Traditional proteomic analytical methods involve matching mass spectrophotometric peptide fingerprints against a list of “known” genes, but the preceding relies on the correct identification for the “known” genes.  ARS scientists at Ithaca, New York, developed a simple but broadly applicable method for constructing proteomic databases with “all possible translation products” (APTP).  The technique predicts all possible proteins directly from nucleic acid sequences, is compatible with standard proteomic database research tools, and has enabled the precise location of protein “translation start sites,” without requiring a reference list, in the genome of the plant pathogenic bacterium P. syringae.

Enhanced genomic maps and bioinformatic tools for rice and maize.  ARS scientists and their collaborators at Cold Spring Harbor Laboratory, New York, created a high-density integrated map that displays the genomic relationships between rice and maize.  This new bioinformatic tool has enabled researchers to correlate the genomic similarities between these species with key phenotypes (i.e., morphological mutations and known quantitative trait loci “QTLs”) for both species, an important initial step for attaining the ultimate goal of applying knowledge of the rice genome to elucidating structure and function of the maize genome.