USDA Plant Genome Research Program

USDA Plant Genome Research Program Progress Report

Published in Probe Volume 4(3-4): August 1994-January 1995

Anne Datko and Ed Kaleikau
National Research Initiative, CSREES, USDA
Steve Heller, Jerry Miksche and Garry Smith
Plant Genome Research Program, ARS, USDA
Doug Bigwood, Genome Informatics Group, NAL, ARS, USDA

The Plant Genome Research Program (PGRP) addresses agricultural problems. Solution of the problems will lead to efficient production of food, feed, and fiber while concurrently reducing the environmental impact associated with farming practices and manufacturing processes.

The goal of the program has remained the same for the past four years. It was established to speed the improvement of plants - agronomic, horticultural, and forest tree species. This is accomplished by locating and characterizing agriculturally important genes and by subsequent transfer of those genes to plants to improve performance. The products, through the hands of the breeder, will be new cultivars. These new cultivars will offer pest and disease resistance and tolerance to abiotic stresses, such as heat, drought, and cold. They will meet future marketplace needs and niches, as well as strengthen endeavors to enhance the environment.

The Plant Genome Research Program is a cooperative effort among several USDA agencies - the Agricultural Research Service (ARS) (which now includes the National Agricultural Library (NAL)) is the lead agency, and the Cooperative State Research, Education, and Extension Service (CSREES). ARS coordinates with the Human Genome Projects of the National Institutes of Health (NIH) and the Department of Energy (DOE), as well as the Arabidopsis thaliana effort of the National Science Foundation (NSF). The Plant Genome Research Program is in the process of establishing official cooperation with some of the European Union (EU) countries and informal but promising interactions with several Pacific Rim countries.

The USDA Plant Genome Research Program is a single program with two components:

I. Competitive grants through CSREES, National Research Initiative.
II. The Plant Genome Database through ARS.

The total appropriation from Congress for this program from 1991 through 1994 was $58.79 million. This amount represents $46.55 and $12.24 million dollars designated for the National Research Initiative competitive grants and the Agricultural Research Service, respectively.

I. COMPETITIVE GRANTS NRI COMPONENT

Grant proposals are oriented towards improving agronomic qualities through genomic research. The Request For Proposals (RFP) proposals addressing three categories: 1. Broad genome maps; 2. Fine maps, including physical mapping; and 3. Technology development to increase the efflciency of mapping and sequencing desirable genes.

Competitive grants were awarded to 381 scientists from 84 public, private, and government research institutions from 43 states. (Table 1). The average award per year over the four years was $127,177 with an average rate of success of 32.8% and an average of 2.2 years per award (Table 2). Fifty-one agronomic, horticultural, and forest tree species and three non-agricultural taxa are included in the plant genome effort (Table 3). Eighty four percent of the grant funding went to members of five plant groups: 1. Tree species - $1.8 million; 2. Crucifers - $4.3 million; 3. Legumes - $5.9 million; and grasses - $16.6 million. Nearly 100 gene/trait/genetic phenomena are at various stages of progress as listed in Table 4. Table 5 lists some of the molecular biology technology pursued by the awardees of the technology over the past four years.

Several important accomplishments have been made by the Program grant awardees:

For the first time ever, a disease resistance gene was isolated by map-based cloning technology. The bacterial speck resistance gene was molecularly transferred to a susceptible variety, resulting in resistance.
One awardee is part of a team that discovered a new class of genes that allows a plant to recognize a diverse group of pathogens.
Quantitative trait loci (QTL) methods have been used to develop a barley line resistant to barley stripe rust which increased the yield of corn by 15%.
Researchers have analyzed the loblolly pine genome and mapped over 200 genetic markers as part of a tree improvement program in the Southeastern United States. Tree breeders can now expedite the improvement of loblolly pines by shortening the time necessary to select desirable characteristics and by using these genetic markers to identify trees with desirable traits.

The above achievements represent only a small fraction of the program's effort. Development of molecular genomic maps for corn, wheat, sorghum, soybean, cotton, tomato, peanut, lettuce, apple, and other commodities is progressing rapidly and the association of the markers with desirable genetic traits will facilitate plant breeding and crop improvement efforts. This activity of placing the DNA gene locations in the hands of the breeder is a paramount goal of the USDA Plant Genome Research Program.

II. PLANT GENOME DATABASE COMPONENT

With the aid of molecular geneticists and breeders, the PGRP is achieving its aims by locating and using genes that improve plants. The program uses the intellectual prowessof government, university, and private sector researchers.

Collaboration of many researchers throughout the country and the world necessitates the need for electronic media communication. Plant genome research generates voluminous data and the handling of large amounts of information requires researchers to have computer expertise.

Performing experiments in the laboratory or field and publishing results in regular scientific journals will not adequately meet the information demands of the 21st century. The ability to rapidly assimilate, analyze, and compare research findings in an electronic form will be needed.

Voluminous data generation requires a Plant Genome Database (PGD). It is divided into three components:

Stock Center Databases - These databases consist of data necessary to enhance genomic research. They are located throughout the United States and elsewhere and are of utmost importance to the USDA PGD and plant breeders in general to making the desired genetic variation available to address agricultural problems. At present, there is a database called GRIN, Germplasm Research Information Network, and while not a direct part of the plant genome research program, it provides a valuable link between germplasm and the genetic information from the other databases (See "Germplasm Resources Information Network (GRIN)" in this issue).
Genome Mapping Database includes physical, genetic, RAPDs, RFLPs, and other map types of many agricultural plant species and some model systems from non-agricultural taxa. These databases are being developed for the first time in a coordinated manner under the direction of the program. At present, ARS is funding directly and indirectly the databases for Arabidopsis thaliana and Chlamydomonas species (model systems), apple, barley, beans, corn, cotton, oats, peas, pepper, petunia, pine, poplar, potato, rye, sorghum, sugarcane, tobacco, tomato, Triticum species -- and the list is expanding.
DNA Sequences - Since this data is the same as those which are being placed into GenBank/GenInfo/European Molecular Biology Laboratories (EMBL) and DNA Databank of Japan (DDBJ), it was the consensus not to have a separate independent sequence database. Hence, all plant DNA sequence data from the USDA Plant Genome Research Program are being placed in the above sequence database efforts of the Plant Genome Database program.

The Agricultural Research Service is concerned only with mapping databases through a rather simple but efficient process. Funding, direct and indirect, is supplied by ARS to "database curators" for the various species. These researchers take the lead for their respective species, perform some evaluation and quality control of their databases, and hold that information in the home laboratories of their institution. The information is sent to the USDA National Agricultural Library, where it is integrated into a master or central database system with data from all of the species. The priority database topics include disease/ pathology, genetic resources, germplasm, genetic maps, quantitative traits, and other factors as decided upon by the database operators. Links are made to relevant databases such as GenBank/EMBL/ DDJB, SwissProt, and AGRICOLA.

All of the information in the database is accessible to the public. The Plant Genome Database is now a real and functioning information and data resource for agricultural genome researchers. As the system increases in size and intellectual content, its value will greatly increase and enhance the abilities of researchers to undertake more sophisticated genome research, which will ultimately benefit the agricultural community and all consumers.