Table of Contents

Page Background and General Information 1

Planning and Coordination for NP 302 2

ARS Crop Production and Protection Research 3

How This Report was Constructed and What it Reflects 7

Research Component 1: Functional Utilization of Genomes 8

Problem Area 1A: Advancing From Model to Crop Plants 8

Problem Area 1B: Applying Genomics to Crop Improvement 12

Research Component 2: Biological Processes that Improve Crop Productivity 20 and Quality

Problem Area 2A: Understanding Growth and Development 21

Problem Area 2B: Understanding Plant Interactions with Their Environment 28

Problem Area 2C: Developing High-Value Products 39

Research Component 3: Plant Biotechnology Risk Assessment 48

Problem Area 3A: Improving and Assessing Genetic Engineering Technology 49

Problem Area 3B: Interaction of Transgenic Plants with Their Environment 56

Appendix 1: Selected Supporting Information and Documentation for 66 Accomplishments and Impact of NP 302 Research

Appendix 2: NP 302 Research Projects 70

Appendix 3: NP 302 Publications 74

Cover Photo: Barley GeneChip probe assay data from a NP 302 research project (Ames, Iowa). Parallel profiling reveals a link between basal and gene-specific resistance. ―Cutting Edge TranscriptomeAnalysis: It‘s all about design‖. Plant Cell 16:2249-2251 (2004)

NATIONAL PROGRAM 302 Plant Biological and Molecular Processes

BACKGROUND AND GENERAL INFORMATION

The vision for the USDA-ARS National Program (NP) 302 Plant Biological and Molecular Processes is to conduct scientific research that leads to tomorrow‘s advances in crop production, quality, and safety. The NP 302 mission is to conduct fundamental research on plants that forms the basis for greater crop productivity and efficiency, better product quality and safety, improved protection against pests and diseases, and sustainable practices that maintain environmental quality. This National Program‘s mission follows the USDA, Agricultural Research Service Strategic Plan (see http://www.ars.usda.gov/SP2UserFiles/Place/00000000/ARSStrategicPlan2006-2011.pdf),which in turn, is directed towards achieving goals mandated by the USDA Research, Education, and Extension Mission Area Strategic Plan and the USDA Strategic Plan for 2006-2011 (see http://www.ocfo.usda.gov/usdasp/sp2005/sp2005.pdf).

The products of research conducted in this national program contribute toward broader goals (termed ―Actionable Strategies‖ or targets) associated with the following specific Performance Measures from the ARS Strategic Plan for 2006-2011 and the previous ARS Strategic Plan for 2003-2007. These include:

ARS Strategic Plan 2006-2011 Objective 2.2: Increase the Efficiency of Domestic Agricultural Production and Marketing Systems

Performance Measure 2.2.3: Expand, maintain, and protect our genetic resource base, increase our knowledge of genes, genomes, and biological processes, and provide economically and environmentally sound technologies that will improve the production, efficiency, health, and value of the Nation‘s crops.

Examples of Actionable Strategies:

Describe the structure, function, and regulation of agriculturally important genes and their protein products in model plants and crop plants. Identify new genetic methods and tools to identify specific genes that mediate end product traits desired by consumers, such as nutritional content, oil, grain quality, disease resistance, and stress tolerance in agricultural crops. Improve plant genetic transformation systems to expand their usefulness, and improve exploitation of genome sequence information to identify valuable genes in raw germplasm collections.

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ARS Strategic Plan 2003-2007 Objective 1.2: Contributions to the Efficiency of Agricultural Production Systems

Performance Measure 1.2.5: Provide produce