USDA, Plant Genome Research Programme: Problems and Solutions

J.P. Miksche, M.K. Berlyn, and S. R. Heller

Biotechnology products are not in the market place as promised by the hype of the middle and late 1970's. Gene mapping research will help in meeting those promises, because the genes must be found first before they can be used. As a result of gene mapping and associated research, much information will be generated and it must be recorded and stored and easily accessible to others. In anticipation of the increased information, planning prototype analysis, and experimentation to establish a relational data base for all plant species as related to the USDA Plant Genome Research Program is underway.

Plant science applied to agriculture harnesses plant's potential by helping to insure an adequate supply of agriculturally based food, fiber, industrial products, and clean air for the earths ever-growing population.

Genetics and other sciences have played a major role in agriculture over the years. Humans have improved cultivated plants by selection over several millennia and more scientifically for the past one hundred through application of the principles of heredity. The use of these genetic principles enabled the rapid improvement of many crop varieties in the twentieth century through hybridization and selection techniques.

Early progress produced substantial increases in yield, pest resistance, and other genetic traits of economic importance. But the giant steps are getting rarer, and traditional plant breeding technologies in some crops are reaching limits. Efficient methods to identify, isolate, and transfer desirable genes need development to overcome these limitations of conventional breeding methods.

Since the late 1970's, the rapidly evolving tools of molecular biology have promised further improvement in crop and forest species. A decade of genetic engineering research, however has yet to yield the full potential of molecular biology as related to crop improvement.

The major problem facing agriculture today in the developed countries is production efficiency. A strong need to reduce grower input cost with concomitant increase in yield and quality with reduced environmental impact is mandatory. Solution of this agricultural challenge hinges upon the tools of the "new biotechnology". Recognition of this is manifested by the world wide interest and thrust of the public and private sectors. The major countries of the world have a more than six thousand large and small firms investing resources in the field, a number six times than observed in 1987. Despite major "buy-outs," shifts, and failures there has been an increase in the number of firms entering the competition since 1980. It is evident therefore that the

interest in advancements of biotechnology and associated products for the market place is not declining. However, the release of new plant varieties "for sale" via biotechnology applications have occurred.

The key points of this paper are, 1) A need to locate genes that code for desirable characteristics to produce plants that possess disease, heat, cold, drought tolerances and other yield deterrents is pressing. Genomic mapping will increase farming efficiency in yielding food and non-food products for the consumer. 2) Genomic research, associated molecular biology techniques and other related to agricultural sciences will generate much information that requires input, storage, retrieval and exchange by users.


The problems before us in agriculture are complex scientifically, economically, politically, and they are intimately linked with sociological changes through altering agricultural practices and policies. It is not possible to specifically cover all of the above problems, but a general panorama of the problems portray familiar scenes and challenges of increased world population with related food/fiber needs, which in turn, is directly related to efficient crop productivity, quality, increased petroleum energy cost, related petrochemical production fertilizer, environmental quality and improving the economic base of agricultural products. Specifically for this paper, the major problem facing agriculture today is plant production efficiency.

A strong need to reduce grower input cost with concomitant increase in yield and quality with reduced environmental impact is the need. This low cost grower input with high quality and yield output with an enhanced environment will take a rather long time to reach. Considerable research in plant science must be done to overcome the impediments of biotechnology product advancement and development.

Today, the precise tools afforded by molecular biology and genetic engineering can aid in determination of factors or key molecules that regulate carbohydrates, proteins, and fats. Opportunities in this field include changing chemical composition of the plant product, improving processing quality, enhancing resistance to stress altering plant size, and changing the ratio of the nutrient distribution in grain, fruit, leaves, stems or roots. However, many of the genes related to growth form and yield are multiple and operate in a complex developmentally regulated fashion. The significance of a complex integrated gene system is difficulty in gene transfer compared with single gene constructs and delivery. The related enzyme systems and metabolic pathways coupled with complex gene cascade systems presents a serious scientific problem to unravel.

Elucidation of the biochemistry and metabolism of several key compounds and pathways in higher plants is mandatory to implement effective transfer of complex genes. This is particularly relevant to directing the regulatory enzymes systems that are related to partitioning and distribution of desirable carbohydrates, lipid, and protein molecules to specific plant organs. The emphasis of many studies, for

example, is directed toward the movement of lipids and proteins to filling soybean seeds, sugar molecules to sugar beet root, and rubber to leaves or stems of guayule or hevea.

Indispensable to gene transfer of desirable single and complex gene systems are plant cell and tissue culture techniques. Predictable regeneration of plants with desired genotypes is of prime importance to successful application of crop improvement through molecular gene transfer. The cardinal factor to regeneration of agronomically important crops from cells rely in the technology to control the mutation and destruction rate of genes in culture stress cells. The general result of cell culture is somaclonal variation, which is not desirable when the engineered crop plants with uniform genotype and phenotype are the wanted. Scientist are addressing the molecular bases of variation to improve plant tissue culture techniques, but the results are a long way off. In the mean time, trail and error reigns.

Protection of plants from weeds, fungi, insects, and bacteria with pesticides and herbicides and other agricultural chemicals is a costly grower input and the challenge is to reduce cost of this agronomic practice. Pesticide use has been the most effective control of disease and pest control over the years. Overall, the use of pesticides to control disease infestations is rapidly changing because of the following reasons: 1) pesticide cost; 2) pesticide impact on the environment, that is humans, animals and other plants; 3) registration of pesticides and associated regulatory problems; 4) increased resistance of pest and pathogens to pesticides.

Genetics and breeding are the desired approach to solving pest problems, many of which have been successful, but the results are generally slow to attain. It is evident that a lack of basic information about pathogens exist as well as host-pathogen interaction mechanisms. Part of the answers to the challenges before us can be met with tissue culture and molecular gene transfer technology coupled with continued breeding and genetic studies. Techniques involving in vitro methods that address disease problems are successful as tissue culture systems to do work in serving as a select in system to determine resistance to fungal and bacterial diseases of plants.

Biological control may provide an opportunity to replace some pesticides for control of specific pests. In addition to the classical biocontrol techniques of collecting and release, the challenge is to develop new technologies to develop biocontrol agents. Specifically, the use of genetic engineering and other manipulative techniques may be useful in transferring biocontrol molecules. Basic research on host pathogens and host insect interactions will also be needed to make this approach successful.

The above impediments to biotechnology advancement are the paucity of basic knowledge of plant biochemistry, physiology, and pathology and lack of uniformally effective DNA transfer technologies and reproducible tissue culture procedures. Perhaps, however the most important of all of these is desirable gene identification and location in plant genomes. The ability to locate and isolate specific genes will lead to more efficient breeding for important agronomic traits such drought and heat tolerance, pest resistance, reduced water contamination by pesticides and fertilizer, and an increase quality in yield. Until those genes are located, precisely characterized, and transferred, systematic and predictable production of plants with useful characteristics will continue to be developed through trail-and-error research.

Plant gene mapping research is the key to effective use of the new molecular biology techniques and realization of biotechnology potentials. Explicit knowledge about genes and rapid exploitation of that knowledge can anticipate or neutralize disease and problems with the interaction of harmful genotypes in the environment. With mapping information, new breeding schemes incorporating differently specified engineered gene complexes can be devised to help crop performance in each growing area. Plant genome research will also enable manipulation of genetic resources to achieve desirable variations. Scientist will be able to capitalize more effectively on natural pest resistance in plant; even where this resistance is initially weak, genetic manipulation can make it more effective. The benefits of such capabilities will be lower cost to farmers and consumers, and less chance of harming the environment with chemical pesticides.

The goal of the USDA Plant Genome Research Program is to find important genes and markers on chromosomes, isolate those genes from the genome, and transfer them rapidly to improve plant varieties. We have little knowledge of many important genes and their expressions. However, what we do know opens the way to a concerted genome research program. The National Plant Genome Research Program will address single and multigenetic traits that relate to agriculture, forestry, and environmental concerns (i.e. global change and water quality). It will help maintain production stability and profitability and improve quality of agricultural products, maintain germplasms resources, and develop new crop resources. To accomplish these goals the National Plant Genome Research Program will foster and coordinate research. This research will lead to the ability to identify, characterize, alter, and rapidly and precisely manipulate genes controlling traits of agricultural importance to meet societies needs. Another goal is to establish a relational plant genomic database system to handle the mass of generated data.