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 (activated only when needed) and coordinated with other related genes. Gene function can differ depending upon location in the genome, and this variability often determines success or failure of crop improvement efforts. Knowledge of these fundamental processes is important to the future of agriculture, because the knowledge will allow increased production of food, fiber, medicines, and other products, in a way that is important deterioration.

Functional genomics is the science that relates variability in DNA sequences to the function, expression, and regulation of genes, and ultimately to the phenotype. The Plant Biological and Molecular Processes Program concentrates on long-term discovery research to improve the manipulation of genes and gene expression for agricultural purposes. Research goals include, but are not limited to, identifying sources of new genes; recognizing and modifying important genes and the mechanisms for regulation of their expression; characterizing and manipulating the cell signals that govern the patterns of gene activities; altering the processes of recombination to improve transgene expression and provide specificity to its genomic location; and tailoring the temporal, spatial, and environmental regulation of transgenes to meet specific needs. Intensive research is aimed at genes important to agricultural purposes, such as those coding for plant growth and development, disease and stress resistance, nutrient absorption, seed development, grain-quality traits, nutritional properties, and flowering expression. Under this National Program the research is aimed at developing an understanding of the continuum from DNA to phenotype and the mechanisms that provide that continuum.

Biological Processes that Determine Plant Productivity and Quality.  Crop production potential is much greater than currently realized, in part because crop plants do not use, or they inefficiently use, all of the available resources. In many cases, the governing traits involve the growth and development of plant organs or of the whole organism, and the processes are governed by many different genes so that molecular mechanisms cannot be easily analyzed. In this component, research is focused on the processes of plant growth and development, productivity, and efficiency, and their metabolic underpinnings. The responses of these processes to environment, especially stressful (non-optimal) environments, is especially important because environmental limitations to efficiency are the major reason for poor and variable yields. The role of plant growth and development in determining productivity and efficiency needs to be described. The nature of environmental, physical, or chemical messengers that trigger developmental changes also needs to be understood, including how the messengers work (at the molecular and gene level, if possible). These concepts must be integrated at the cellular, whole-plant, and community level so that the consequences of changes in a process can be predicted reliably.

Mechanisms of Plant Interactions with Other Organisms.  Much of plant metabolism produces compounds with a role in defense against pathogens or predators, as attractants for pollinators, or the like. In the 'real world,' 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 means to protect crops; to enhance nutritional balance, flavor, or other attributes of quality; or to promote important symbioses between crop plants and other organisms. Importantly, 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 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 that underlie those relationships. Most of this work will be targeted to specific identified needs, such as resistance to an identified pest or enhancement of a specific phytonutrient, and the knowledge will be intended to lead to new technology to satisfy those needs. Processes under investigation include sensing of pests and pathogens by the host plant, triggering of plant defense reactions, signaling processes within or between plants that govern gene expression contributing to plant health, transfer and expression of defense or quality genes, useful natural products of plant metabolism, and other fundamental plant functions.