·        Introduction

·        Analysis and Modification of Plant Genomes

·        Biological Processes That Determine Plant Productivity and Quality

·        Mechanisms of Plant Interactions with Other Organisms

Introduction

This program includes much of the Agricultural Research Service s fundamental research that is necessary for practical advances but is too far upstream to provide solutions for practical problems.  The research focuses on mechanistic understanding of specific plant processes and properties.  The knowledge and tools developed can be used to improve functions and properties of plants. The program is divided into three components: Analysis and Modification of Plant Genomes (functional genomics, focusing on the molecular end of the spectrum; technology for modifying plant genomes); Biological Processes that Determine Plant Productivity and Quality (plant growth and development, photosynthesis, productivity, and environmental responses (that relate processes and attributes of the whole organism to their genetic and metabolic underpinnings and provide the context for molecular manipulations); and Mechanisms of Plant Interactions with Other Organisms (plant defensive reactions to pests and pathogens, emphasizing those that reduce the need for applied pesticides; interactions with beneficial organisms; secondary metabolism and products).  Together, the results of these research approaches provide a continuum of understanding from genes to phenotype (plant attributes and performance).

During the year, ARS scientists operating in this program prepared research plans for peer review. Following a workshop in June 1999, where customers and stakeholders stated their needs and priorities to ARS (see 1999 Program Annual Report), scientists wrote an Action Plan to address the identified needs.  After public review and revision, this Action Plan was made available in January 2000, and was used as the guide to direct scientists into high-priority research areas for their new projects.  After internal discussion and revision, project plans were submitted in October 2000, for impartial review by independent panels of peer experts.  The peer panels met in November 2000.  Projects will be revised to meet criticisms, and the revised projects, after concurrence by the peer panels, will be implemented on June 1, 2000.

During 2000, there were many important discoveries and advances.  Some of them are described below.  By no means do these selected accomplishments display the important achievements of the entire research program.  Instead, they highlight the type of activities carried out under this program and the type of benefits that result.

Selected Accomplishments (Listed by Component) 

Analysis and Modification of Plant Genomes

With today's rapid developments in genetics and genomics, many possibilities for improving plants exist now that were unimaginable even a few years ago.  Barriers to movement of single genes or small numbers of genes across unrelated species are being breached, allowing transfer of key genetic capabilities not just among higher plants, but across classes of organisms (such as from bacteria to plants).  New information about DNA structure provides insights into how gene activities are regulated and coordinated with other related genes.  Soon, there may be ways to direct rearrangements of DNA by the plants internal mechanisms, without introducing any new genes.  Part of a broad approach to plant performance, the research in this component of the program develops an understanding of the molecular mechanisms underlying plant functions.

Improving the process of genetic engineering.  Although biotechnology has succeeded in integrating foreign genes into host DNA, the process is not easily controlled and results in very low success rates of site-specific integration (that is, putting the gene exactly where it is wanted). ARS research has now developed a process that greatly increases the success rate of site-specific integration of single-copy DNA.  This advance will greatly facilitate site-specific integration, making the process of genetic engineering much more controlled than is was with previous technologies.

Expanding genetic engineering technology to blueberries.  Although a few genetically engineered crops have been highly successful, most crops are extremely difficult to transform.  A widespread and serious problem is that cells, once transformed, often cannot be induced to form whole plants again.  Blueberries are an important crop, which have been difficult to genetically engineer.  Researchers have now developed a highly efficient way to regenerate blueberry shoots for several commercially important cultivars.  This long-awaited breakthrough means that it is now possible to conduct genetic engineering studies with important blueberry cultivars.  Introduction of cold hardiness and disease resistance genes in blueberries is now under way. 

Biological Processes That Determine Plant Productivity and Quality

Crop plants do not use, or inefficiently use, all of the resources available to them.  In many cases, the governing traits involve the growth and development of the intact organism.  In this program component, research is focused on the complex processes of plant growth and development, productivity, and efficiency, and how they are related to gene action and metabolism.  The responses of these processes to the environment, especially stressful (non-optimal) environments, are especially important because environmental limitations to efficiency are the major reason for poor and variable yields.  Research conducted under this component of the program identifies specific genes or gene products that control plant functions, enabling improvements to be focused on the appropriate targets.

Key enzyme for starch utilization improved in barley.  An enzyme involved in starch degradation can be damaged by heat during industrial processing of cereal grains.  ARS researchers and colleagues at the University of Wisconsin at Madison have enhanced the thermostability of the enzyme using site-specific mutation and transgenic methods.  The potential benefits of this research are increased sugar production during industrial processing of cereal grains, along with reduced raw material costs and less waste production.

Aluminum toxicity to plants reduced.   Soils contain large amounts of the element aluminum, which is inactive at normal soil pH.  Acid soils, though, solubilize toxic forms of aluminum, which react with phosphorus-containing minerals and make the phosphorus unavailable.  Acid soils are one of the greatest restrictions on crop yields in the southeastern United States and are also a major global problem, especially in the tropics.   ARS researchers have identified a process in alfalfa roots that detoxifies the aluminum present in acid soil solutions, enabling roots to grow more vigorously and absorb phosphorus.  Genetic engineering to enhance the activity of one enzyme in roots has enhanced the detoxification process, improved alfalfa growth, and increased phosphorus absorption.  The enhanced plants can be used to produce forage in soils that are currently considered too toxic and infertile.

Tomatoes with increased lycopene content.  Tomato plants were genetically enhanced to maintain higher levels than normal of a group of natural compounds called polyamines.   Tomatoes with high polyamines were found to have 2.5 times higher levels of lycopene, an antioxidant and anticarcinogen.  Lycopene is also a naturally occurring compound that is responsible for the red color of tomatoes.

Flood-tolerant soybean lines developed.  Soybeans in the United States are quite susceptible to flooding.  Even moderate water logging of the soil, such as low spots in a field, severely reduces yield.  American soybean cultivars are largely derived from plants collected in northern China, where flooding is a rare problem.  Soybeans collected from southern China, where rainfall is greater, display much better tolerance to flooding.  Five new, elite breeding lines have been developed, carrying a flooding tolerance gene discovered in plants from southern China and they are being tested in Arkansas and Mississippi.  The new lines are expected to substantially reduce the risk from short-term flooding.

Getting specific in controlling ethylene.  Ethylene is almost a universal growth regulator in plants, controlling processes from disease resistance to lateral root initiation to fruit ripening.  There are treatments available that inhibit or stimulate ethylene production very generally, but inevitably they affect many other plant processes in addition to the intended one.  For the first time, genes have been introduced into tomato and Arabidopsis plants that affect ethylene production in very specific sites.  This creates the specificity needed to inhibit or stimulate specific ethylene-dependent processes without damaging the plant-E/SPAN's overall metabolism.

Mechanisms of Plant Interactions with Other Organisms

Much of plant metabolism produces proteins or other compounds that play a role in defenses against pathogens or predators, as attractants for pollinators, or the like.   In nature, these processes are as essential to plant health and survival as are the primary processes of photosynthesis and respiration.  In many respects they present the most attractive opportunities for crop improvement because they offer ways to protect crops; to enhance nutritional balance, flavor, or other attributes of quality; or to promote important symbioses between crop plants and other organisms.  Opportunities to enhance these processes may often be generated by focusing on single genes or few genes, unlike the polygenic traits related to plant development, adaptation, and yield.  Research will develop knowledge of relationships among host plants, pests and pathogens, and beneficial organisms, and of the specific molecular, biochemical, and physiological events underlying those relationships.  Most of this work will be targeted to specific identified needs, such as resistance to a pest or enhancement of a specific phytonutrient; and the knowledge will be used to lead to new technology to satisfy those needs. 

Acid soil-tolerant rhizobia identified.  Commercially available rhizobia (bacteria that inhabit the nodules of legume plants and fix atmospheric nitrogen into plant-available N compounds) are very sensitive to acid soil conditions.  As a result, much of the acreage of the southeastern United States, which suffers from acid soils, has poor forage crop productivity.  Nearly 150 native strains of rhizobia were collected from white clover in acid soils in West Virginia, and these were demonstrated to be resistant to soil acidity.  Selected strains have potential to increase legume-based forage production in the area.

Test for purity of St. John's wort.  As dietary supplements, St. John's wort and other herbal products are not subject to regulatory oversight by the Food and Drug Administration.  These preparations can vary in potency and purity.  Now, a DNA-based test has been developed that will detect contamination or adulteration of St. John-E/SPAN's wort with other botanicals.  This is the first time such a robust, reliable, and efficient method has been developed and offered to the botanical supplement industry.

Indicator of nitrogen fixation capability of legumes .  Soybeans and other legumes depend upon bacteria in the nodules that fix nitrogen from the air (that is, convert it into a form that the plant can use for growth).  This process is highly variable, both during the season and across species and environments.  Research has determined that ureide transport to nodules has an important role in limiting nitrogen fixation by a metabolic feedback reaction.  In plants whose leaves are capable of degrading large quantities of ureides, delivery to the nodules is limited and nitrogen fixation rates are high.  This is the first efficient, simple test to be made available by which plant breeders can easily select legumes that sustain high levels of nitrogen fixation. 

Soybean allergenicity attacked.  Soybeans have a tremendous number of uses in foods, ranging from vegetable cooking oil from the seeds to a high-protein milk substitute.  The latter application is used largely for infants or children who are lactose-intolerant or allergic to cow's milk.  Unfortunately, a significant number of infants are also allergic to soybeans.  Researchers identified two gene products that account for almost all of the soybean seeds allergenic properties and they knocked out those gene products using biotechnology.  The result is a hypoallergenic soybean, which is currently undergoing testing as a safer, more suitable source of formula for allergic infants.