Published in Probe Volume 1(1-2): Spring-Summer 1991
Jerome Miksche, Director
Plant Genome Research Program, USDA
USDA's (U.S. Department of Agriculture) Plant Genome Research Program, established last October, will facilitate the improvement of plants--agronomic, horticultural, and forest species--by locating important genes and markers on chromosomes, determining the structure of those genes, and transferring the genes to improve performance. The end product will be superior plant varieties that more closely meet marketplace needs and niches, while creating a positive effect on the environment.
The program is a cooperative effort of USDA agencies, the Agricultural Research Service (ARS), the National Agricultural Library (NAL), the Cooperative State Research Service (CSRS), and the Forest Service (FS). ARS has the lead role in directing the program. With a budget of $14.7 million for FY 9l, the Plant Genome Research Program is managed through grants, contracts, and inter- and intra-agency transfers of funds.
Competitive Grants
CSRS' Competitive Grants Research Office will manage the grants portion of the program in cooperation with ARS. Grants will be peer reviewed and mission oriented. Scientists from industry, academia, and government may apply for grant funding. Multidisciplinary submissions will be given favorable consideration.
The program grants consists of three components: l) Support will be committed to constructing broad maps that locate important genes or gene systems in crops and forest species. This will be achieved using a technology that allows scientists to determine rather broad genetic similarities and differences, initiate assignment of DNA fragments on chromosomes, and then begin the mapping process. Budgeted dollars will not be allocated on a commodity basis, but on targeted gene systems or traits of some of the commodities that yield economic gain to American agriculture. Knowledge acquired from one commodity can be transferred to another crop species.
In this phase of the program, proposals anticipated will represent the following commodities: corn, soybean, tomato, wheat, barley, rice, pine (conifers), potato, garden bean, cotton, pea, peaches, oats, sorghum, sweet potato, carrots, onions, apple, rose, sugarcane, citrus crops, and other agriculturally important species.
2) Grants will be awarded to develop more specific information on crops for which some data has already been acquired. Many of the major acreage crop species such as corn, soybean, wheat, and rice come under this category.
Scientists will determine gene construction relative to important specific traits such as yield, heat and cold tolerance, disease resistance, quality changes, drought tolerance, gene transfer, and expression. This objective is important in that it will generate results that offer products to the agricultural community. The analysis of factors in gene systems or gene families that regulate gene expression is required.
3) Progress in the Plant Genome Research Program is tied to developing new mapping and sequencing technologies. The following are examples of new technologies that need development: A new method to tag sequences, which will eliminate the need to store mapping probes, innovative applications of the polymerase-chainreaction (PCR), new methodology to identify Quantitative Trait Loci (QTL's), creative computer software designed specifically for plant gene systems, in situ hybridization technologies for plant chromosomes, methods that allow mapping of polyploid genomes, chromosomal sorting and separation technologies specifically designed for complex plant genomes, and methods to overcome obstacles for plant regeneration and transformation.
Contracts and Agency Funds
The program's contracts and agency funds portion will support informatics and technological laboratory procedures. A high priority for the Plant Genome Research Program is the management of mapping/sequencing data and biological resources produced through genome research. These results will be of value only if they are made readily available to the community.
Plans are underway to establish a centralized plant genome database system to manage the expected enormous volume of research information to be generated and the diverse biological resources. The database will be located in NAL's new Plant Genome Data and Information Center, which provides information on plant genome research to users. A standardized database management system will enable researchers to easily deposit and retrieve mapping and sequencing data. Database development will focus on four agricultural commodities: corn, wheat, soybean, and pine. Work groups organized in these areas will address user needs, define database file structures and elements, and assume responsibility for quality control on the acquired data.
An equally urgent need is to enhance current stock centers. The deposition and distribution of new biological resources such as seeds, mutants, antibodies, protein and DNA probes are important considerations for the program. A major program challenge is to establish new centers as materials accumulate.
In addition, the increased innovative technologies that will automate DNA laboratory procedures from extraction and purification through data analysis are important challenges needed to make the program effective.
USDA staff are pleased with the support demonstrated thus far for the program throughout government, industry, and academia. For more information on the program, contact Jerry Miksche on (301) 344-2029.