Irwin Goldman, University of Wisconsin-Madison, Madison, Wisconsin, USA.

• List of Contributors xi1 Dani Zamir: Pioneer in Tomato Genetics and Quantitative Trait Dissection 1Irwin L. GoldmanI. Introduction 2II. Understanding Quantitative Genetic Variation 4III. Cloning of Quantitative Trait Loci 6IV. Characterization of Genetic Phenomena 7V. Sequencing the Tomato Genome 9VI. Practical Plant Breeding 10VII. Scientific Impact 13VIII. List of Scientific Journal Publications of Dani Zamir 14Literature Cited 302 Muscadine Grape Breeding 31Patrick J. Conner and Margaret L. WorthingtonI. Introduction 32II. History of Improvement 38III. Breeding Techniques 49IV. Molecular Breeding Resources 52V. Breeding for Specific Characters 58VI. Intersubgeneric Hybridization 79VII. Future Prospects 104Literature Cited 1063 Breeding Intermediate Wheatgrass for Grain Production 119Prabin Bajgain, Jared L. Crain, Douglas J. Cattani, Steven R. Larson, Kayla R. Altendorf, James A. Anderson, Timothy E. Crews, Ying Hu, Jesse A. Poland, M. Kathryn Turner, Anna Westerbergh, and Lee R. DeHaanI. Introduction 122II. Plant Biology and Behavior 125III. History of IWG Breeding 140IV. Breeding Methodologies by Program 146V. Breeding Goals and Progress 162VI. Modern Breeding Tools 175VII. Rate of Intermediate Wheatgrass Domestication 190VIII. Future Directions 195Literature Cited 1974 Understanding Environmental Modulation of Heterosis 219Zhi Li, Jiabin Sun, and Candice N. HirschI. Introduction of Heterosis 220II. Models and Mechanisms to Explain Heterosis 221III. Genotype-by-Environment Interaction 224IV. Inbred Lines Generally Have More Instability Across Environments than Hybrids 226V. Higher Heterosis Levels are Observed Under Stress Conditions 227VI. Variation in Heterosis is also Observed Under Natural Conditions 231VII. Conclusion and Future Prospects 232Literature Cited 2335 Breeding of Hemp (Cannabis sativa) 239Lawrence B. Smart, Jacob A. Toth, George M. Stack, Luis A. Monserrate, and Christine D. SmartI. Introduction 240II. Taxonomy and Domestication of Hemp 245III. Sex Determination in Hemp 247IV. Control of Pollination 250V. Breeding and Selection Schemes 255VI. Target Traits for Genetic Improvement 259VII. Germplasm Resources 277VIII. Genomic Resources 278IX. Future Directions 279Literature Cited 2796 Genetic Resources and Breeding Priorities in Phaseolus Beans : Vulnerability, Resilience, and Future Challenges 289Travis A. Parker, Jorge Acosta Gallegos, James Beaver, Mark Brick, Judith K. Brown, Karen Cichy, Daniel G. Debouck, Alfonso Delgado-Salinas, Sarah Dohle, Emmalea Ernest, Consuelo Estevez de Jensen, Francisco Gomez, Barbara Hellier, Alexander V. Karasev, James D. Kelly, Phillip McClean, Phillip Miklas, James R. Myers, Juan M. Osorno, Julie S. Pasche, Marcial A. Pastor-Corrales, Timothy Porch, James R. Steadman, Carlos Urrea, Lyle Wallace, Christine H. Diepenbrock, and Paul GeptsI. Description of Crop Vulnerability and Its Relevance in Phaseolus 294II. Background on the Origin, Diversification, and Domestication of the Genus Phaseolus 296III. Urgency and Extent of Crop Vulnerabilities and Threats to Food Security 318IV. Genetic Erosion in the Centers of Origin 325V. Status of Plant Genetic Resources in the NPGS 352VI. Genomic and Genotypic Characterization Data 361VII. Prospects, Future Development, and Gaps in Genetic Diversity 371VIII. Epilogue 381Literature Cited 3857 Club Wheat -- A Review of Club Wheat History, Improvement, and Spike Characteristics in Wheat 421Kimberly A. Garland-CampbellI. Introduction 423II. Spike Architecture in Grasses 424III. Club Wheat History 426IV. Club Wheat Breeding 432V. Major Genes for Control of Spike Charactersitics in Wheat 444VI. Conclusion 454Literature Cited 4558 Predicting Genotype x Environment x Management (G x E x M) Interactions for the Design of Crop Improvement Strategies: Integrating Breeder, Agronomist, and Farmer Perspectives 467Mark Cooper, Carlos D. Messina, Tom Tang, Carla Gho, Owen M. Powell, Dean W. Podlich, Frank Technow, and Graeme L. HammerI. Three Perspectives of G x E x M Interactions 470II. Foundations for G x E x M Prediction 476III. The Breeder’s Equation and Beyond 480IV. G x E x M Considerations for Designing Multi-Environment Trials 482V. Breeder’s Questions: G E x M --> G x (E x M) 510VI. Agronomist’s Questions: G x E x M --> M x (E x G) 520VII. Farmer’s Questions: G x E x M --> (G x M) x E 525VIII. Integrating the Different G x E x M Perspectives 531IX. G x E x M Predictions Beyond the Training Data Boundaries 548X. Prediction-Based Crop Improvement: Future Prospects 555Literature Cited 5609 Root Phenes for Improving Nutrient Capture in Low-Fertility Environments 587Christopher F. Strock and Hannah M. SchneiderI. The Need for Nutrient-Efficient Crops 589II. Root Phenes are Important for Resource Aqusition and Plant Growth 590III. Root Ideotypes for Improved Nutrient Acquisition 596IV. Phenotyping Methodology and Technology 605V. Deployment Strategies for Root Phenes in Crop Breeding Programs 610VI. Conclusions 614Literature Cited 61510 Role of the Genomics--Phenomics--Agronomy Paradigm in Plant Breeding 627Chunpeng James Chen, Jessica Rutkoski, James C. Schnable, Seth C. Murray, Lizhi Wang, Xiuliang Jin, Benjamin Stich, Jose Crossa, Ben J. Hayes, and Zhiwu ZhangI. Introduction 630II. Agronomy and Genomics (A-G) 631III. Genomics and Phenomics (G-P) 636IV. Phenomics and Agronomy (P-A) 641V. Merge G-P-A through GWAS 644VI. Merge G-P-A through Blup 647VII. Merge G-P-A through Bayesian Methods 649VIII. Merge G-P-A through Ml 654IX. Conclusion and Future Prospects 658Literature Cited 659Cumulative Contributor Index 675Cumulative Subject Index 685

Irwin Goldman, University of Wisconsin-Madison, Madison, Wisconsin, USA.

• List of Contributors xi1 Dani Zamir: Pioneer in Tomato Genetics and Quantitative Trait Dissection 1Irwin L. GoldmanI. Introduction 2II. Understanding Quantitative Genetic Variation 4III. Cloning of Quantitative Trait Loci 6IV. Characterization of Genetic Phenomena 7V. Sequencing the Tomato Genome 9VI. Practical Plant Breeding 10VII. Scientific Impact 13VIII. List of Scientific Journal Publications of Dani Zamir 14Literature Cited 302 Muscadine Grape Breeding 31Patrick J. Conner and Margaret L. WorthingtonI. Introduction 32II. History of Improvement 38III. Breeding Techniques 49IV. Molecular Breeding Resources 52V. Breeding for Specific Characters 58VI. Intersubgeneric Hybridization 79VII. Future Prospects 104Literature Cited 1063 Breeding Intermediate Wheatgrass for Grain Production 119Prabin Bajgain, Jared L. Crain, Douglas J. Cattani, Steven R. Larson, Kayla R. Altendorf, James A. Anderson, Timothy E. Crews, Ying Hu, Jesse A. Poland, M. Kathryn Turner, Anna Westerbergh, and Lee R. DeHaanI. Introduction 122II. Plant Biology and Behavior 125III. History of IWG Breeding 140IV. Breeding Methodologies by Program 146V. Breeding Goals and Progress 162VI. Modern Breeding Tools 175VII. Rate of Intermediate Wheatgrass Domestication 190VIII. Future Directions 195Literature Cited 1974 Understanding Environmental Modulation of Heterosis 219Zhi Li, Jiabin Sun, and Candice N. HirschI. Introduction of Heterosis 220II. Models and Mechanisms to Explain Heterosis 221III. Genotype-by-Environment Interaction 224IV. Inbred Lines Generally Have More Instability Across Environments than Hybrids 226V. Higher Heterosis Levels are Observed Under Stress Conditions 227VI. Variation in Heterosis is also Observed Under Natural Conditions 231VII. Conclusion and Future Prospects 232Literature Cited 2335 Breeding of Hemp (Cannabis sativa) 239Lawrence B. Smart, Jacob A. Toth, George M. Stack, Luis A. Monserrate, and Christine D. SmartI. Introduction 240II. Taxonomy and Domestication of Hemp 245III. Sex Determination in Hemp 247IV. Control of Pollination 250V. Breeding and Selection Schemes 255VI. Target Traits for Genetic Improvement 259VII. Germplasm Resources 277VIII. Genomic Resources 278IX. Future Directions 279Literature Cited 2796 Genetic Resources and Breeding Priorities in Phaseolus Beans : Vulnerability, Resilience, and Future Challenges 289Travis A. Parker, Jorge Acosta Gallegos, James Beaver, Mark Brick, Judith K. Brown, Karen Cichy, Daniel G. Debouck, Alfonso Delgado-Salinas, Sarah Dohle, Emmalea Ernest, Consuelo Estevez de Jensen, Francisco Gomez, Barbara Hellier, Alexander V. Karasev, James D. Kelly, Phillip McClean, Phillip Miklas, James R. Myers, Juan M. Osorno, Julie S. Pasche, Marcial A. Pastor-Corrales, Timothy Porch, James R. Steadman, Carlos Urrea, Lyle Wallace, Christine H. Diepenbrock, and Paul GeptsI. Description of Crop Vulnerability and Its Relevance in Phaseolus 294II. Background on the Origin, Diversification, and Domestication of the Genus Phaseolus 296III. Urgency and Extent of Crop Vulnerabilities and Threats to Food Security 318IV. Genetic Erosion in the Centers of Origin 325V. Status of Plant Genetic Resources in the NPGS 352VI. Genomic and Genotypic Characterization Data 361VII. Prospects, Future Development, and Gaps in Genetic Diversity 371VIII. Epilogue 381Literature Cited 3857 Club Wheat -- A Review of Club Wheat History, Improvement, and Spike Characteristics in Wheat 421Kimberly A. Garland-CampbellI. Introduction 423II. Spike Architecture in Grasses 424III. Club Wheat History 426IV. Club Wheat Breeding 432V. Major Genes for Control of Spike Charactersitics in Wheat 444VI. Conclusion 454Literature Cited 4558 Predicting Genotype x Environment x Management (G x E x M) Interactions for the Design of Crop Improvement Strategies: Integrating Breeder, Agronomist, and Farmer Perspectives 467Mark Cooper, Carlos D. Messina, Tom Tang, Carla Gho, Owen M. Powell, Dean W. Podlich, Frank Technow, and Graeme L. HammerI. Three Perspectives of G x E x M Interactions 470II. Foundations for G x E x M Prediction 476III. The Breeder’s Equation and Beyond 480IV. G x E x M Considerations for Designing Multi-Environment Trials 482V. Breeder’s Questions: G E x M --> G x (E x M) 510VI. Agronomist’s Questions: G x E x M --> M x (E x G) 520VII. Farmer’s Questions: G x E x M --> (G x M) x E 525VIII. Integrating the Different G x E x M Perspectives 531IX. G x E x M Predictions Beyond the Training Data Boundaries 548X. Prediction-Based Crop Improvement: Future Prospects 555Literature Cited 5609 Root Phenes for Improving Nutrient Capture in Low-Fertility Environments 587Christopher F. Strock and Hannah M. SchneiderI. The Need for Nutrient-Efficient Crops 589II. Root Phenes are Important for Resource Aqusition and Plant Growth 590III. Root Ideotypes for Improved Nutrient Acquisition 596IV. Phenotyping Methodology and Technology 605V. Deployment Strategies for Root Phenes in Crop Breeding Programs 610VI. Conclusions 614Literature Cited 61510 Role of the Genomics--Phenomics--Agronomy Paradigm in Plant Breeding 627Chunpeng James Chen, Jessica Rutkoski, James C. Schnable, Seth C. Murray, Lizhi Wang, Xiuliang Jin, Benjamin Stich, Jose Crossa, Ben J. Hayes, and Zhiwu ZhangI. Introduction 630II. Agronomy and Genomics (A-G) 631III. Genomics and Phenomics (G-P) 636IV. Phenomics and Agronomy (P-A) 641V. Merge G-P-A through GWAS 644VI. Merge G-P-A through Blup 647VII. Merge G-P-A through Bayesian Methods 649VIII. Merge G-P-A through Ml 654IX. Conclusion and Future Prospects 658Literature Cited 659Cumulative Contributor Index 675Cumulative Subject Index 685

Irwin Goldman, University of Wisconsin-Madison, Madison, Wisconsin, USA.

• List of Contributors xi1 Dani Zamir: Pioneer in Tomato Genetics and Quantitative Trait Dissection 1Irwin L. GoldmanI. Introduction 2II. Understanding Quantitative Genetic Variation 4III. Cloning of Quantitative Trait Loci 6IV. Characterization of Genetic Phenomena 7V. Sequencing the Tomato Genome 9VI. Practical Plant Breeding 10VII. Scientific Impact 13VIII. List of Scientific Journal Publications of Dani Zamir 14Literature Cited 302 Muscadine Grape Breeding 31Patrick J. Conner and Margaret L. WorthingtonI. Introduction 32II. History of Improvement 38III. Breeding Techniques 49IV. Molecular Breeding Resources 52V. Breeding for Specific Characters 58VI. Intersubgeneric Hybridization 79VII. Future Prospects 104Literature Cited 1063 Breeding Intermediate Wheatgrass for Grain Production 119Prabin Bajgain, Jared L. Crain, Douglas J. Cattani, Steven R. Larson, Kayla R. Altendorf, James A. Anderson, Timothy E. Crews, Ying Hu, Jesse A. Poland, M. Kathryn Turner, Anna Westerbergh, and Lee R. DeHaanI. Introduction 122II. Plant Biology and Behavior 125III. History of IWG Breeding 140IV. Breeding Methodologies by Program 146V. Breeding Goals and Progress 162VI. Modern Breeding Tools 175VII. Rate of Intermediate Wheatgrass Domestication 190VIII. Future Directions 195Literature Cited 1974 Understanding Environmental Modulation of Heterosis 219Zhi Li, Jiabin Sun, and Candice N. HirschI. Introduction of Heterosis 220II. Models and Mechanisms to Explain Heterosis 221III. Genotype-by-Environment Interaction 224IV. Inbred Lines Generally Have More Instability Across Environments than Hybrids 226V. Higher Heterosis Levels are Observed Under Stress Conditions 227VI. Variation in Heterosis is also Observed Under Natural Conditions 231VII. Conclusion and Future Prospects 232Literature Cited 2335 Breeding of Hemp (Cannabis sativa) 239Lawrence B. Smart, Jacob A. Toth, George M. Stack, Luis A. Monserrate, and Christine D. SmartI. Introduction 240II. Taxonomy and Domestication of Hemp 245III. Sex Determination in Hemp 247IV. Control of Pollination 250V. Breeding and Selection Schemes 255VI. Target Traits for Genetic Improvement 259VII. Germplasm Resources 277VIII. Genomic Resources 278IX. Future Directions 279Literature Cited 2796 Genetic Resources and Breeding Priorities in Phaseolus Beans : Vulnerability, Resilience, and Future Challenges 289Travis A. Parker, Jorge Acosta Gallegos, James Beaver, Mark Brick, Judith K. Brown, Karen Cichy, Daniel G. Debouck, Alfonso Delgado-Salinas, Sarah Dohle, Emmalea Ernest, Consuelo Estevez de Jensen, Francisco Gomez, Barbara Hellier, Alexander V. Karasev, James D. Kelly, Phillip McClean, Phillip Miklas, James R. Myers, Juan M. Osorno, Julie S. Pasche, Marcial A. Pastor-Corrales, Timothy Porch, James R. Steadman, Carlos Urrea, Lyle Wallace, Christine H. Diepenbrock, and Paul GeptsI. Description of Crop Vulnerability and Its Relevance in Phaseolus 294II. Background on the Origin, Diversification, and Domestication of the Genus Phaseolus 296III. Urgency and Extent of Crop Vulnerabilities and Threats to Food Security 318IV. Genetic Erosion in the Centers of Origin 325V. Status of Plant Genetic Resources in the NPGS 352VI. Genomic and Genotypic Characterization Data 361VII. Prospects, Future Development, and Gaps in Genetic Diversity 371VIII. Epilogue 381Literature Cited 3857 Club Wheat -- A Review of Club Wheat History, Improvement, and Spike Characteristics in Wheat 421Kimberly A. Garland-CampbellI. Introduction 423II. Spike Architecture in Grasses 424III. Club Wheat History 426IV. Club Wheat Breeding 432V. Major Genes for Control of Spike Charactersitics in Wheat 444VI. Conclusion 454Literature Cited 4558 Predicting Genotype x Environment x Management (G x E x M) Interactions for the Design of Crop Improvement Strategies: Integrating Breeder, Agronomist, and Farmer Perspectives 467Mark Cooper, Carlos D. Messina, Tom Tang, Carla Gho, Owen M. Powell, Dean W. Podlich, Frank Technow, and Graeme L. HammerI. Three Perspectives of G x E x M Interactions 470II. Foundations for G x E x M Prediction 476III. The Breeder’s Equation and Beyond 480IV. G x E x M Considerations for Designing Multi-Environment Trials 482V. Breeder’s Questions: G E x M --> G x (E x M) 510VI. Agronomist’s Questions: G x E x M --> M x (E x G) 520VII. Farmer’s Questions: G x E x M --> (G x M) x E 525VIII. Integrating the Different G x E x M Perspectives 531IX. G x E x M Predictions Beyond the Training Data Boundaries 548X. Prediction-Based Crop Improvement: Future Prospects 555Literature Cited 5609 Root Phenes for Improving Nutrient Capture in Low-Fertility Environments 587Christopher F. Strock and Hannah M. SchneiderI. The Need for Nutrient-Efficient Crops 589II. Root Phenes are Important for Resource Aqusition and Plant Growth 590III. Root Ideotypes for Improved Nutrient Acquisition 596IV. Phenotyping Methodology and Technology 605V. Deployment Strategies for Root Phenes in Crop Breeding Programs 610VI. Conclusions 614Literature Cited 61510 Role of the Genomics--Phenomics--Agronomy Paradigm in Plant Breeding 627Chunpeng James Chen, Jessica Rutkoski, James C. Schnable, Seth C. Murray, Lizhi Wang, Xiuliang Jin, Benjamin Stich, Jose Crossa, Ben J. Hayes, and Zhiwu ZhangI. Introduction 630II. Agronomy and Genomics (A-G) 631III. Genomics and Phenomics (G-P) 636IV. Phenomics and Agronomy (P-A) 641V. Merge G-P-A through GWAS 644VI. Merge G-P-A through Blup 647VII. Merge G-P-A through Bayesian Methods 649VIII. Merge G-P-A through Ml 654IX. Conclusion and Future Prospects 658Literature Cited 659Cumulative Contributor Index 675Cumulative Subject Index 685