Plant Breeding Reviews, Volume 46

List of Contributors xi

1 Dani Zamir: Pioneer in Tomato Genetics and Quantitative Trait Dissection 1 Irwin L. Goldman

I. Introduction 2

II. Understanding Quantitative Genetic Variation 4

III. Cloning of Quantitative Trait Loci 6

IV. Characterization of Genetic Phenomena 7

V. Sequencing the Tomato Genome 9

VI. Practical Plant Breeding 10

VII. Scientific Impact 13

VIII. List of Scientific Journal Publications of Dani Zamir 14

Literature Cited 30

2 Muscadine Grape Breeding 31 Patrick J. Conner and Margaret L. Worthington

I. Introduction 32

II. History of Improvement 38

III. Breeding Techniques 49

IV. Molecular Breeding Resources 52

V. Breeding for Specific Characters 58

VI. Intersubgeneric Hybridization 79

VII. Future Prospects 104

Literature Cited 106

3 Breeding Intermediate Wheatgrass for Grain Production 119 Prabin 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. DeHaan

I. Introduction 122

II. Plant Biology and Behavior 125

III. History of IWG Breeding 140

IV. Breeding Methodologies by Program 146

V. Breeding Goals and Progress 162

VI. Modern Breeding Tools 175

VII. Rate of Intermediate Wheatgrass Domestication 190

VIII. Future Directions 195

Literature Cited 197

4 Understanding Environmental Modulation of Heterosis 219 Zhi Li, Jiabin Sun, and Candice N. Hirsch

I. Introduction of Heterosis 220

II. Models and Mechanisms to Explain Heterosis 221

III. Genotype-by-Environment Interaction 224

IV. Inbred Lines Generally Have More Instability Across Environments than Hybrids 226

V. Higher Heterosis Levels are Observed Under Stress Conditions 227

VI. Variation in Heterosis is also Observed Under Natural Conditions 231

VII. Conclusion and Future Prospects 232

Literature Cited 233

5 Breeding of Hemp (Cannabis sativa) 239 Lawrence B. Smart, Jacob A. Toth, George M. Stack, Luis A. Monserrate, and Christine D. Smart

I. Introduction 240

II. Taxonomy and Domestication of Hemp 245

III. Sex Determination in Hemp 247

IV. Control of Pollination 250

V. Breeding and Selection Schemes 255

VI. Target Traits for Genetic Improvement 259

VII. Germplasm Resources 277

VIII. Genomic Resources 278

IX. Future Directions 279

Literature Cited 279

6 Genetic Resources and Breeding Priorities in Phaseolus Beans : Vulnerability, Resilience, and Future Challenges 289 Travis 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 Gepts

I. Description of Crop Vulnerability and Its Relevance in Phaseolus 294

II. Background on the Origin, Diversification, and Domestication of the Genus Phaseolus 296

III. Urgency and Extent of Crop Vulnerabilities and Threats to Food Security 318

IV. Genetic Erosion in the Centers of Origin 325

V. Status of Plant Genetic Resources in the NPGS 352

VI. Genomic and Genotypic Characterization Data 361

VII. Prospects, Future Development, and Gaps in Genetic Diversity 371

VIII. Epilogue 381

Literature Cited 385

7 Club Wheat -- A Review of Club Wheat History, Improvement, and Spike Characteristics in Wheat 421 Kimberly A. Garland-Campbell

I. Introduction 423

II. Spike Architecture in Grasses 424

III. Club Wheat History 426

IV. Club Wheat Breeding 432

V. Major Genes for Control of Spike Charactersitics in Wheat 444

VI. Conclusion 454

Literature Cited 455

8 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 467 Mark Cooper, Carlos D. Messina, Tom Tang, Carla Gho, Owen M. Powell, Dean W. Podlich, Frank Technow, and Graeme L. Hammer

I. Three Perspectives of G x E x M Interactions 470

II. Foundations for G x E x M Prediction 476

III. The Breeder's Equation and Beyond 480

IV. G x E x M Considerations for Designing Multi-Environment Trials 482

> G x (E x M) 510

> M x (E x G) 520

> (G x M) x E 525

VIII. Integrating the Different G x E x M Perspectives 531

IX. G x E x M Predictions Beyond the Training Data Boundaries 548

X. Prediction-Based Crop Improvement: Future Prospects 555

Literature Cited 560

9 Root Phenes for Improving Nutrient Capture in Low-Fertility Environments 587 Christopher F. Strock and Hannah M. Schneider

I. The Need for Nutrient-Efficient Crops 589

II. Root Phenes are Important for Resource Aqusition and Plant Growth 590

III. Root Ideotypes for Improved Nutrient Acquisition 596

IV. Phenotyping Methodology and Technology 605

V. Deployment Strategies for Root Phenes in Crop Breeding Programs 610

VI. Conclusions 614

Literature Cited 615

10 Role of the Genomics--Phenomics--Agronomy Paradigm in Plant Breeding 627 Chunpeng James Chen, Jessica Rutkoski, James C. Schnable, Seth C. Murray, Lizhi Wang, Xiuliang Jin, Benjamin Stich, Jose Crossa, Ben J. Hayes, and Zhiwu Zhang

I. Introduction 630

II. Agronomy and Genomics (A-G) 631

III. Genomics and Phenomics (G-P) 636

IV. Phenomics and Agronomy (P-A) 641

V. Merge G-P-A through GWAS 644

VI. Merge G-P-A through Blup 647

VII. Merge G-P-A through Bayesian Methods 649

VIII. Merge G-P-A through Ml 654

IX. Conclusion and Future Prospects 658

Literature Cited 659

Cumulative Contributor Index 675

Cumulative Subject Index 685