Objective 3. Translational Plant Genomics – Application of Genomics Tools
As functions are assigned to genes in a few key plant species, the next, and most significant, opportunity will be to use this information to address questions of basic biology and to develop technologies that will produce plants with enhanced economic value and expanded utilities.
Application of genomics tools to understand traits of biological and economic importance
Humans have long exploited the unique biochemical, structural and physiological diversity of the plant world for agriculture and other benefits. Genomics has greatly increased the potential for understanding the basis for this diversity. Some of the many examples of specialized traits of both fundamental biological interest and economic importance are:
Tuber and bulb development: Many useful plant traits are not found in reference species, such as
Arabidopsis or rice. For example, potato tubers are underground stems that are uniquely modified as starch-storing organs. Sweet potatoes are roots modified as starch-storing organs; and onions are leaves modified to form bulbs as nutrient-storing organs. Understanding the genetic networks that guide the development of these unique structures could yield important information for improving or further modifying these crop plants.
Wood formation: Production of softwood and hardwood is unique to woody plants. The composition and final stages of wood production are biologically and chemically complex, and expected to require the coordinated expression of many genes. Therefore, an understanding of the genetic networks for wood formation will contribute to future improvements in silviculture and natural resource management.
Fruit development: Edible fruits have been developed from wild species for differences in shape, size, texture, color, flavor, and chemical composition. The physiological and developmental processes yielding fruits such as peaches, apples, berries, oranges, papaya, bananas, peanut and others cannot be studied directly in reference species. However, as genome resources increase for a few key species, the biological processes for diverse species can be better understood.
Phosphate and nitrogen nutrition: Some plants are more capable of utilizing nutrients from the soil than others, especially nitrogen and phosphate, the main ingredients of fertilizers. Legumes form specialized association with microorganisms to utilize nitrogen from the air. Many plants including legumes and trees associate with a special group of fungi to utilize phosphate in the soil efficiently. Understanding howthese plants
accomplish efficient uptake and utilization of nitrogen and
phosphate would help in the design of plants that require less
chemical input for optimal performance in the field.
Expansion of genomics approaches to
biodiversity, ecology and ecosystem studies
Understanding biodiversity is very likely to lead us to discover
new mecha-nisms and higher order principles of biology. What are
the key switches that have allowed plants to develop into such a
vast array of morphological types and occupy such a wide range of
environmental niches? How and why do plants produce the widest
array of chemical compounds in the natural world, and how is it that the spectrum of chemicals in plants can adjust so rapidly to
environmental changes? How have gene functions changed as plant species have evolved to meet the challenges of new environments and new ecosystems? The NPGI project
portfolio should include significant and broad efforts to understand plant interactions with pathogenic,
mutualistic, and symbiotic organisms. New alliances among basic and applied biologists, plant and animal breeders, and computational experts will allow us to understand plants within the context of their biotic and abiotic environment.
Expansion of genomics approaches to renewable resources and novel biomaterials
Renewable resources hold the promise for stabilizing the losses incurred from our accelerated use of nonrenewable resources. Ultimately, whole genome analysis will allow us to develop rational strategies for optimizing renewable resources and for facilitating environmental remediation. For example, a small increase in the efficiency of photosynthetic energy capture and conversion, stimulated by translation of genomic information to an applied context, would have a major impact on plant production. Similarly, the discovery of new plant-based materials or the introduction of new genetic processes could revitalize plant improvement strategies in renewable resources.