USDA and DOE Project Director Meeting AFRI Plant Genome, Genetics and Breeding Program AFRI Plant Breeding and Education Program USDA-DOE Feedstock Genomics for Bioenergy Program Town and Country Resort and Convention Center San Diego, CA January 13, 2011 Table of Contents Speaker Abstracts (In Presentation Order) .................................................................................................. 7 Genomics-Based Breeding in Forest Trees: Are We There Yet and Why We Need a Reference Genome to Finish the Job; David B. Neale .............................................................................................................. 7 Genome-Wide Patterns of SNP Variation in Wheat: Tools and Resources for Breeding and Studying Genetics of Agronomic Traits; Eduard Akhunov ...................................................................................... 8 Oat SNP Development and Identification of Loci Affecting Key Traits in North American Oat Germplasm Using Association Genetics; Eric Jackson .............................................................................. 9 Advanced Pine Breeding Through Association Genetics and Biotechnology; Matias Kirst ................... 10 Improving Maize Against Aflatoxin and Drought: Translational Plant Breeding, Education, and Extension; Seth C. Murray ...................................................................................................................... 12 An Integrated Approach to Breeding Resistance to Phytophthora Capsici In Pepper; Allen Van Deynze ................................................................................................................................................................ 13 Building Improved Crown and Rhizome Transcriptomes to Evaluate Seasonal Changes in Switchgrass Populations with Divergent Winter Survival; Gautam Sarath ................................................................ 13 Accelerating the Domestication of Miscanthus for Biofuel Production; Andrew Paterson .................. 14 Genome-Wide Analysis of miRNA Targets in Brachypodium and Biomass Energy Crops; Pamela J. Green ...................................................................................................................................................... 16 Plant Genome, Genetics and Breeding Program Project Reports (Alphabetical Order of Lead Project Director) ...................................................................................................................................................... 17 Single Nucleotide Polymorphism (SNP) Markers for High-Throughput Genotyping to Advance Genomic, Genetic and Breeding Research in Wheat; Eduard Akhunov ................................................ 17 Genome-Wide Selection to Introgress Exotic Dwarf-Corn Germplasm into U.S. Corn Belt Germplasm; Rex Bernardo .......................................................................................................................................... 20 Understanding the Mechanisms that Define Cereals: Unraveling the Function of Lineage Specific Genes within the Poaceae; C. Robin Buell ............................................................................................. 21 Advancing the Barley Genome; Tim Close .............................................................................................. 24 The Douglas-Fir Climate Change Transcriptome Observatory (CCTO) for the Pacific Northwest; Richard Cronn ...................................................................................................................................................... 26 Translating Solanaceae Sequence Diversity and Trait Variation into Applied Outcomes through Integrative Research, Education, and Extension; David Douches .......................................................... 28 Comparative Protein Networks Controlling Disease Resistance in Rice and Wheat; Jorge Dubcovsky 37 Triticeae CAP: Improving Barley and Wheat Germplasm for Changing Environments; Jorge Dubcovsky and Gary Muehlbauer ............................................................................................................................ 42 2 Simultaneous Genetic Analysis of Winter Hardiness Traits and Development of Winter Malting Barley Varieties; Patrick Hayes .......................................................................................................................... 51 Oat SNP Development and Identification of Loci Affecting Key Traits in North American Oat Germplasm Using Association Genetics; Eric Jackson ............................................................................ 53 A Genome Sequence for Common Bean, Phaseolus vulgaris; Scott Jackson ......................................... 56 Common Bean Coordinated Agricultural Project (CAP); Phil McClean .................................................. 58 Development of a High Resolution SNP Chip (600K) and Genotyping of 850 Diverse rice (Oryza sp.) Accessions; Susan McCouch ................................................................................................................... 61 Barley Coordinated Agricultural Project; Gary J. Muehlbauer ............................................................... 64 Conifer Translational Genomics Network Coordinated Agricultural Project; David Neale .................... 81 Loblolly Pine Genome Project; David Neale ........................................................................................... 83 Scanning for Yield: High-Throughput Discovery of Candidate Agronomic Loci for Marker-Assisted Selection in Maize; Jeffrey Ross-Ibarra .................................................................................................. 86 Evaluating Genomic Selection for Applied Plant Breeding; Kevin P. Smith ........................................... 89 Expanding the Scope of Association Mapping in Important Crop Species with Methodology Development in Statistics; Dong Wang .................................................................................................. 92 Defense versus Symbiosis: Host Genetic Control of Nodulation Specificity in Soybeans; Hongyan Zhu ................................................................................................................................................................ 94 Plant Breeding and Education Program Project Reports (Alphabetical Order of Lead Project Director) . 96 Assessing the Cost of Pyramiding Host Resistance to Biotic Stress in Crop Species; William Berzonsky ................................................................................................................................................................ 96 Translational Genomic Approaches for Enhancing Disease Resistance in Plants, an Internet-Facilitated Education Program for Training Plant Breeders; Charles Brummer ...................................................... 98 Enhancing Education and Research Capacity in Plant Breeding for Drought Tolerance; Pat Byrne .... 101 Building Expertise in Plant Breeding that Focuses on Drought Tolerance in Common Bean (Phaseolus vulgaris L.); James D. Kelly .................................................................................................................... 103 Advanced Pine Breeding Through Association Genetics and Biotechnology; Matias Kirst ................. 106 Enhancing Education and Research in Breeding for Plant Disease Resistance; Michael Mazourek .... 109 New Vistas in Plant Breeding Education: Investigating the Genetics Underlying the Ability to Yield Under High Planting Density in Maize; Rita H. Mumm ........................................................................ 111 Improving Drought Tolerance and Aflatoxin Resistance in Maize; Education, Extension, and Translational Breeding via Altered Lipid Metabolism; Seth C. Murray ................................................ 118 Partnership for Research & Education in Plant Breeding and Genetics at Purdue University; Herbert Ohm ...................................................................................................................................................... 121 3 Genetics of Calcium Uptake by Potato Tuber; Jiwan P. Palta .............................................................. 124 Marker-Assisted Breeding to Enhance Disease Resistance in Corn, Rice, and Sugarcane; Prasanta K. Subudhi ................................................................................................................................................. 126 Enhancing Leaf Spot Resistance in Peanut; Barry L. Tillman ................................................................ 129 An Integrated Approach to Breeding Resistance to Phytophthora Capsici in Pepper; Allen Van Deynze .............................................................................................................................................................. 131 USDA-DOE Feedstock Genomics for Bioenergy Program Project Reports (Alphabetical Order of Lead Project Director) ........................................................................................................................................ 137 Functional Interactomics: Determining the Roles Played by Members of the Poplar Biomass Protein- Protein Interactome; Eric Beers............................................................................................................ 137 Alfalfa Transcript Sequencing and SNP Discovery to Improve Biomass Composition; Charles Brummer .............................................................................................................................................................