The USDA Plant Genome Research Program

Jerome P. Miksche and Stephen R. Heller
US Department of Agriculture
Agricultural Research Service,
Plant Genome Research Program
Beltsville, MD 20705 USA

Introduction:

As we near the 21st century the world's supplies are not growing as fast the world's population. As this problem becomes more evident in the coming years, it is believed that genetic engineering holds the best promise for a solution to this upcoming dilemma. The purpose of the USDA Plant Genome Program is to enhance the long-term viability and competitiveness of United States crop and livestock production by developing systems to improve the profitability of agriculture while protecting environmental quality.

Agricultural genetic engineering differs in two major ways from the human genetic engineering. First, in agriculture, where conventional breeding has been going on for centuries, the changes being made are evolutionary, not revolutionary. There is no "killer application" potential, like some of the possible new drugs which, someday, will come from the human genome project. Second, the ability to actually undertake genetic experiments and produce products today, allows the agriculture genome project to

actually be 1-2 decades ahead of the human genome project in actual practical results.

Program Goal and Anticipated Outcomes:

The goal is to improve the genetic makeup of important plant species. Accomplishments are made by locating marker DNA or genes on chromosomes, determining molecular gene structure, and transferring genes to improve plant performance. The improved plants will have reduced environmental impacts and meet specific marketplace needs. Placements of gene constructs or DNA markers in the hands of plant breeders is of paramount importance for full implementation of the program. The new breeder-developed cultivars offer pest and disease resistance. Disease resistant plants reduce the use of agricultural chemicals. They display tolerance to abiotic stresses such as heat, cold, and drought conditions and have enhanced performance when grown under adverse conditions. Cultivars will also be produced to yield non-traditional traits for use in renewable biomaterial.

The program is one effort composed of two parts: 1) the USDA National Research Initiative (NRI) Competitive Grants and 2) the USDA/ARS/NAL Plant Genome Database. Total appropriation from Congress for 1991 through 1994 was some $59 million for the program. The NRI and ARS received about $47 and $12 million, respectively, for the grants and database efforts. The NRI awards covered research on 51 agronomic, horticultural, forest tree species, and 4 non-agricultural taxa. Within the 55 taxa, 84% of the research award dollars went to 5 plant groups: (1) tree species - $1.8 million; (2) crucifers - $4.3 million; (3) legumes - $5.9 million; (4) Solanaceae $9.8 million; and (5) grasses - $16.6 million. Over 80 gene/trait/metabolic phenomena are at various stages of progress.

Genome Mapping Applications address and help in solving major agricultural problems. Crop production limits are becoming evident in some major crops. Some limitations related to the plant genome DNA and its interaction with the physical environment. Others represent challenges to plants by other organisms. Limitations include such factors as total yield, amount and amino acid composition of seed proteins, resistance to wind and rain damage, and ability to grow under extreme conditions of temperature, of salinity, or in marginal soils. Biological agents that limit crop production are primarily insects, fungal, bacterial, or viral pathogens, and competing plants, which we call weeds.

Major Program Objectives:

The major objectives of the Plant Genome Research Program are:

(1)Construction of saturated molecular genetic linkage maps with sufficient localization of sequencing and the transfer of important genes through several molecular methods for controlling yield, heat and cold tolerance, pest resistance, and product quality traits. Linkage maps of several major crop species will be developed with emphasis placed on homology between species to accelerate the use of available DNA markers from one species to be used in a range of related species. Development of new mapping, sequencing, and DNA transfer technologies.

(2)Development of automated technical information systems and technological robotics laboratory procedures for processing and electronic data gathering and exchange, coordinate with hardware and software development.Development and improvement of ACEDB and WWW software, b) modification of database design to accommodate software and hardware evolution, c) development and validation of strategies and techniques for data interpretation, analysis, and input, d) offer education programs for scientists, customers/donors.

Some Important Accomplishments:

1. For the first time ever, a disease resistant gene was located and removed from the genome by map-based cloning technology. Bacterial Speck resistance trait was transferred to a susceptible variety of wheat resulting in resistance.

2. One researcher is part of a team that discovered a new class of genes that allows plants to recognize bacterial, fungal, and viral pathogens.

3. Quantitative trait loci (QTL) methods have been used to develop a barley line resistant to barley stripe rust and another researcher demonstrated an increase of 15% in corn yield.

4. Forest researchers have analyzed the loblolly pine genome and mapped over 200 genetic markers as part of a tree improvement program in the Southeastern USA. Tree breeders can now expedite the improvement of loblolly pine by time compression and use of genetic resources with meaningful parents and desirable offspring.

5. Structure alikeness and or gene synteny has been detected, so far, in 4 plant families - grasses, Solanaceae, crucifers, and legumes.

Practical Results:

To date there have been seven genetically engineering crops which are currently being sold in the USA. They are: canola, corn, cotton, potato, soybean, squash, and tomato. The altered traits respectively include: oil composition, corn borer resistance, herbicice resistance, Colorado potato beetle resistance, virus resistance, delaying ripening, and thickening.

The companies selling these products are: Asgrow Seed, Calgene, Ciba-Geigy, DNA Plant Technology, Monsanto, Mycogen, Peto Seed, Rhone-Poulenc Rorer, and Zeneca. More corps are now being developed and additional companies are expected to enter the market in the coming years.

Plant Genome Program Information:

The Plant Genome Project has, as its fundamental principle, the rapid delivery and easy access to the scientific results of the project. With this in mind the project has funded the National Agriculture Library (NAL) to be the focal point for the electronic and printed information of the project. A massive set of databases and associated search, retrieval, and display software has made the data and information easy to access from around the world. The current Plant Genome System include the following thirteen databases:

AAtDB--Arabidopsis
Alfagenes--alfalfa (Medicago sativa)
BeanGenes--Phaseolus and Vigna
ChlamyDB--Chlamydomonas reinhardtii
CottonDB--Gossypium hirsutum
GrainGenes--wheat, barley, rye and relatives
MaizeDB--maize
RiceGenes--rice
SolGenes--Solanaceae
SorghumDB--Sorghum bicolor
SoyBase--soybean

TreeGenes--forest trees
Mendel--plant-wide gene names

Each month there are hundreds of scientists and others accessing these databases via the Internet. In the most recent month, August 1995, there were over 150,000 computer accesses of the system via the Internet (the Internet url is http://probe.nalusda.gov), up from some 80,000 a year earlier. Figure 1 shows the web site home page for the project, with various major database categories and other documents available. Figure 2 shows an example of some of the data resources, which include links to searching the National Agriculture Library (NAL) AGRICOLA bibliographic database, the GRIN Germplasm database, the Enzyme Data Bank, the Enzyme Metabolic Pathways database, the Kyoto Ligand database, Prosite, the Protein Identification Resource (PIR), the Online Mendelian Inheritance in Man (OMIM) database, the Protein Data Bank (PDB), GenoBase, and SwissProt. There are also links to and from the NIH/NLM/NCBI GenBank sequence database which contains both human, plant, and animal sequences. For those wishing to contact the NAL Plant Genome Data and Information Center can contact the head of the center, Dr. Susan McCarthy by e-mail (smccarthy@nalusda.gov), phone (301-504-6613), or by FAX (301-504-7098). In addition the project coordinates a yearly Plant Genome conference every January in San Diego, CA. Further information on this meeting can be obtain from Dr. McCarthy.