Plant Breeding Reviews, Volume 41 Plant Breeding Reviews Series

Plant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops.

1. Hari Deo Upadhyaya: Plant Breeder, Geneticist and Genetic Resources Specialist 1
Sangam L Dwivedi

Abbreviations 3

I. Introduction 3

II. Biographical Sketch 5

III. Contributions 5

A. Genetic Resources Management and Use 6

1. Representative Subsets 6

2. Climate]resilient Germplasm 8

3. Seed Nutrient]dense Germplasm 8

4. Bioenergy 9

5. Germplasm Use in Breeding 9

6. On]farm Conservation and Use of Diversity 10

7. Wild Relatives and Cultigen Genepool 10

8. Gaps in Collections 12

B. Molecular Biology and Biometrics 13

1. Population Structure and Diversity 13

2. Genome]wide Association Mapping 13

3. Candidate Genes Associated with Agronomically Useful Traits 15

4. Ethnolinguistic Groups Shaped Sorghum Diversity in Africa 15

5. Genome Sequencing 16

C. Groundnut Breeding 16

1. Early Maturity 16

2. Drought Tolerance 18

3. Aflatoxin Resistance 18

4. Farmers Participatory Varietal Selection 19

D. Chickpea Breeding 20

IV. Upadhyaya, the Man 20

A. Personality 20

B. Educator and Leader 27

C. International Collaborations 28

D. Recognition 28

1. Awards 28

2. Honours 30

3. Service 30

V. Publications 30

VI. Products 31

A. Cultivars 31

B. Registrations 31

References cited and further reading 33

2. Crop Improvement Using Genome Editing 55
Nathaniel M Butler, Jiming Jiang and Robert M Stupar

Abbreviations 56

I. Introduction 57

II. Conceptual Framework for Genome Editing 60

A. Development of Sequence]Specific Nucleases 60

1. Early Nucleases 62

2. Designer Nucleases 62

3. RNA]guided Nucleases 65

B. DNA Repair Pathways 66

1. Non]homologous End]joining 66

2. Homologous Recombination 69

C. Modes of Modifications 70

1. NHEJ]mediated Modifications 70

2. HR]mediated Modifications 71

III. Plant Transformation Strategies 72

A. Agrobacterium]mediated Transformation 73

B. Protoplasts and Biolistics 75

C. Plant Viral Systems 76

IV. Harnessing Breaks for Targeted Mutagenesis 77

A. Detecting and Stabilizing Targeted Mutations 78

B. Targeted Mutagenesis in Polyploids 81

V. Precision Gene Editing via HomologousRecombination 82

VI. Genome Editing at the Genome Level 85

A. Large Deletions 85

B. Chromosomal Rearrangements 86

C. Epigenetic Remodelling and Base Editing 87

VII. Future Perspectives 88

A. Nuclease Decisions and Considerations 89

B. Crop Challenges and Advantages 90

C. Regulation of Nuclease Technology 91

Acknowledgements 92

Literature Cited 92

3. Development and Commercialization of CMS Pigeonpea Hybrids 103
KB Saxena, D Sharma, and MI Vales

Abbreviations 105

I. Introduction 106

II. Reproductive Cycle and Morphology of Pigeonpea 108

A. Induction of Flowering 108

B. Maturity Range 109

C. Flower Structure 110

D. Flowering Pattern 111

E. Pollination and Fertilization 111

F. Natural Cross]pollination 112

1. Cross]pollinating Agents 112

2. Extent of Out]crossing 114

III. Crop Production 115

A. General Agronomy 115

B. Major Production Constraints 115

1. Diseases 115

2. Insect Pests 117

3. Waterlogging 117

IV. Extent and Nature of Heterosis in Pigeonpea 118

V. Genetic Male Sterility]based Hybrid Technology 119

A. Genetic Male Sterility Systems 119

B. Heterosis in GMS]based Hybrids 121

C. Release of the First GMS]based

Pigeonpea Hybrid 121

D. Hybrid Seed Production Technology 122

E. Assessment of GMS]based Hybrid Technology 123

VI. Temperature]sensitive Male Sterility 124

VII. Cytoplasmic]nuclear Male Sterility]based Hybrid Technology 125

A. Early Efforts to Produce CMS System 126

B. Breakthrough in Breeding Stable CMS Systems 126

C. Diversification of Cytoplasm 127

1. A1 CMS System from Cajanus sericeus (Benth. ex Bak.) van der Maesen 128

2. A2 CMS System from Cajanus scarabaeoides (L.) Thou 128

3. A3 CMS System from Cajanus volubilis (Blanco) Blanco. 128

4. A4 CMS System from Cajanus cajanifolius (Haines) Maesen 129

5. A5 CMS System from Cajanus cajan (L.) Millsp 129

6. A6 CMS System from Cajanus lineatus (W & A) van der Maesen 130

7. A7 CMS from Cajanus platycarpus (Benth.) van der Maesen 130

8. A8 CMS System from Cajanus reticulatus (Aiton) F. Muell 130

9. A9 CMS System from Cajanus cajan (L.) Millsp 131

D. Effect of Pigeonpea Cytoplasm on Yield 131

E. Fertility Restoration of A4 CMS System 132

VIII. Breeding New Hybrid Parents 133

A. Fixing Priorities 133

B. Selection of Hybrid Parents from Germplasm and Breeding Populations 134

C. Isolation of Fertility]Restoring Inbred Lines from Heterotic Hybrids 136

D. Breeding Dwarf Parental Lines 137

E. Breeding Determinate/Non]determinate Parental Lines 137

F. Disease]resistant Parental Lines 138

G. Use of a Naked]Eye Polymorphic Marker in Hybrid Breeding 139

H. Formation of Heterotic Groups 140

I. Inbreeding Depression 141

IX. Application of Genomics in Breeding Hybrids 142 A. Understanding the Molecular Genetics Basis of the A4 CMS System 143

B. Tagging Fertility]restoring Genes 143

C. Assessment of Genetic Purity 144

D. Potential Role in Breeding Two]line Hybrids 145

X. Commercialization of Hybrid Pigeonpea Technology 146

A. Standard Heterosis 146

1. Early]maturing Hybrids 146

2. Medium] and Late]maturing Hybrids 147

B. Release of the World’s First Commercial Legume Hybrid 149

C. Hybrid Seed Production Technology 152

D. Economics of Hybrid Seed Production 153

XI. Outlook 154

Acknowledgements 157

Literature Cited 157

4. The Evolution of Potato Breeding 169
Shelley H Jansky and David M Spooner

Abbreviations 170

I. Introduction 170

II. Classification of Cultivated Potato 171

III. Origin of the Cultivated Potato 173

IV. Dynamics of Potato Landrace Evolution 176

V. Origin of the European Potato 178

VI. Nineteenth Century Potato Breeding 179

VII. Early Twentieth Century Potato Breeding 184

VIII. Conventional Potato Breeding 189

IX. Late Twentieth Century Potato Breeding 191

X. Twenty]first Century Potato Breeding 196

A. Is Tetraploidy Necessary for High Tuber Yield in Potato? 196

B. What are the Advantages of Moving to the Diploid Level and Developing Inbred Lines? 198

C. Is It Possible to Develop Diploid Inbred Lines in Potato? 200

XI. Conclusions 202

Literature Cited 203

5. Flavour Evaluation for Plant Breeders 215
JC Dawson and GK Healy

Abbreviations 217

I. Introduction 217

A. Scope of the Chapter 218

B. Justification for Rapid Sensory Methods 219

C. History 220

II. Types of Rapid Sensory Analysis Methods 221

A. Performance Relative to Conventional Methods 222

B. Methods of Rapid Sensory Evaluation 224

1. Evaluation of Individual Product Attributes 224

Method 1: Intensity Scales 224

Method 2: Flash Profiling 225

Medhod 3: Check All That Apply (CATA) 226

2. Evaluation of Global Differences 227

Method 4: Sorting 227

Method 5: Projective Mapping 228

3. Evaluation in Comparison to a Reference 230

Method 6: Paired Comparisons 230

Method 7: Polarized Sensory Positioning 231

Method 8: Open]ended Evaluations 232

4. Use of Professional Experts in Evaluation 232

C. Numbers of Assessors and Numbers of Samples for Trained, Untrained and Expert Panels 235

III. Data Analysis for Rapid Sensory Methods 236

A. Principal Component Analysis 237

B. Multi]dimensional Scaling 237

C. Multiple Correspondence Analysis 238

D. Generalized Procrustes Analysis 239

E. Multiple Factor Analysis 239

IV. Example of Using Sensory Analysis for Breeding 241

A. Background, Goals and Partners 241

1. Participant Recruitment and Priority Setting 241

2. Cultivar Trials 243

B. Flavour Evaluation Methods Used 243

1. Evolution of Flavour Evaluation Methods 243

2. Intensity Scaling Methods Used with Crew Members 244

3. Chef Projective Mapping Evaluation 245

C. Statistical Methodology 246

1. ANOVA with Intensity Scaling Methods 246

2. Principal Component Analysis of Field Crew Flavour Evaluation Means 246

3. Multiple Factor Analysis of Chef Projective Mapping Data 247

D. Results 247

1. Field Crew Flavour Evaluation with Intensity Scaling 247

2. Chef Flavour Evaluations 250

3. Participant Feedback and Next Steps 253

V. Outlook 254

Acknowledgements 256

Literature Cited 256

6. The Genetic Improvement of Black Walnut for Timber Production 263
James R McKenna and Mark V Coggeshall

Abbreviations 264

I. Introduction 265

II. Biology of Black Walnut 268

A. Leafing Date 268

B. Flowering 268

1. Female Flowers 269

2. Male Flowers 270

C. Pollen Collection 270

D. Artificial Pollination 271

III. Breeding 272

A. Breeding Strategies 272

B. Selection 272

C. Age]to]Age Correlations 273

D. Improvement 274

E. Analysis 274

IV. Evaluation of Heritable Traits 274

A. Geographic Variation 274

B. Growth 275

C. Timber Quality 275

D. Wood Quality 276

V. Host Plant Resistance to Pathogens and Insect Pests 277

A. Insect Resistance 277

B. Anthracnose 277

C. Thousand Cankers Disease 278

D. Bunch Disease – Witches Broom 278

VI. Propagation 279

A. Seed Propagation 279

B. Grafting 280

C. Rooting 281

VII. Plot Management 281

A. Progeny Tests 281

B. Clone Banks 282

C. Seed Orchards 283

VIII. Future Directions 283

Literature Cited 283

7. A Life in Horticulture and Plant Breeding: The Extraordinary Contributions of Jules Janick 291
Irwin L Goldman and Rodomiro Ortiz

Abbreviations 292

I. Introduction 292

II. Honors and Commendations 297

III. Students and Teaching 297

IV. Editorial Work 299

V. Books and Proceedings 303

VI. Research 306

A. Patents 307

B. Book Chapters, Reviews and Introductions 307

C. Journal Publications 310

D. Popular and Extension Articles 320

E. Book Reviews 329

F. Encyclopaedia Articles 331

VII. Public Addresses, Invited Seminars and Speeches 332

VIII. Service Contributions 355

IX. Epilogue 358

Literature Cited 360

Index

Irwin L. Goldman, Professor and Chair, Department of Horticulture, University of Wisconsin-Madison, USA.