Table Of ContentHORTICULTURAL PLANT BREEDING
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HORTICULTURAL
PLANT BREEDING
Thomas J. Orton, Ph.D.
Professor and Extension Specialist
Department of Plant Biology
School of Environmental and Biological Sciences
Rutgers, The State University of New Jersey
New Brunswick, NJ, United States
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Contents
Preface and Acknowledgments ix 4. Engineered Population Structures
Introduction: The Nature of Populations 73
I
Pure Lines and Multi-Lines 76
Random Mating with Truncated Allelic Frequencies 78
ELEMENTS AND UNDERPINNINGS
Hybrid and Synthetic Populations 78
OF PLANT BREEDING
Asexually Propagated Populations (Clones) 80
References 83
Introduction to Section 1
5. Mass Selection and the Basic Plant Breeding
Plants and People 3 Algorithm
Brief History of Plant Breeding 3
Future Challenges to Plant Breeders 4 Introduction 85
Agronomic vs. Horticultural Plant Breeding 5 Mass Selection and Plant Domestication 85
References 7 The Plant Breeding Algorithm 88
Germplasm 89
1. Introduction
Mating and Selection 91
New Populations with Prospective Improvements 92
The Beginning 9
Testing of Candidate Populations 92
Historical Perspective 12
Large-Scale Seed Production 93
References 26
Post-Seed Modifications 94
2. The Context of Plant Breeding References 94
Introduction 27 6. Breeding Objectives
Evolution and Speciation 27
Systematics and Nomenclature 29 Introduction 97
Plant Growth and Development 30 Plant Ideotypes and Ideotype Breeding 101
Plant Reproduction 31 Intergenic Interactions and Pleiotropy 105
Population Biology and Ecology 33 Interspecific Interactions 107
Social and Political Sciences 35 Return on Investment 108
References 37 References 110
3. Review of Genetics (From The Perspective 7. Germplasm and Genetic Variability
of A Plant Breeder)
Introduction 113
Mendelian Inheritance 39 Extant Gene Pools 115
Linkage 45 Biodiversity: Genetic Variability in Natural Ecosystems 117
Population Genetics 46 Genetic Variability Maintained In Situ 117
Quantitative Genetics 47 Germplasm Repositories 117
Heritability 50 Biotechnology to Foster and Characterize Phenotypic
Implications of Quantitative Genetics to Population Diversity and Genetic Variability 123
Gene Frequencies 52 References 126
Cytogenetics 53 Further Reading 128
Structure and Function of Chromosomes 59
Supernumerary or B Chromosomes 67 8. Enhancement of Germplasm
Maternal Inheritance 67
Genome Mapping 68 Introduction 129
References 70 Ploidy Changes and Chromosome Engineering 130
v
vi CONTENTS
Induced Mutations 134 12. Protection of Proprietary Plant Germplasm
Cell Culture Strategies 138
Genetic Transformation 140 Introduction 221
Genome Editing 144 Plant Patents 222
References 145 Plant Variety Protection 223
Further Reading 148 Trade Secrets 225
Copyrights, Trademarks, and Service Marks 225
9. Improvement of Selection Effectiveness Utility Patents 226
Material Transfer Agreements 227
Introduction 149
Intellectual Property Rights in the Public Sector 227
Heritability and Response to Selection 151
Summary 228
Enhanced Heritability: Open Field Production 152
Enforcement of PVP and Patents 228
Enhanced Heritability: Enclosures 153
Acknowledgment 229
Enhanced Heritability: Environmental Chambers 154
References 230
Selection Based on Progeny Tests 154
Selection on Trait Components 155 II
Selection Based on Composite Phenotypic Score 155
Selection of Linked Molecular Markers: Marker-Assisted BREEDING METHODS
Selection (MAS) 156
Alternative Methods for the Imputation of Marker
Introduction to Section 2
Breeding Values 165
Genome Selection 166
Preliminary Steps 235
Functional Genomics 169
References 236
References 169
Further Reading 173 13. The Pedigree Method
10. Natural Mating Systems and Review of the Genetic Implications of Self-Pollination
Controlled Mating or Other Assortative Mating Schemes 237
The Pedigree Method Introduction 242
Introduction 175 History of the Pedigree Method 244
Natural Plant Mating Systems 175 Choice of Parents 244
Generalized Flower Structure and Function 179 The Method 244
Floral Development and Transcription Factors (MADS-Box) 180 Pedigree Breeding Examples 249
Self-Incompatibility 182 Use of QTL and MAS to Enhance Pedigree Method
Agamospermy and Apomixis 186 Effectiveness 251
Heterogamy and Dioecy 190 Pedigree Method: Other Considerations 252
Gynoecy and Male Sterility 191 References 252
Controlled Mating in Plant Breeding Programs 194 Further Reading 253
Maternal Inheritance 195
Mating of Individuals 196 14. Other Breeding Methods for Self Pollinated
Matings Among and Within Populations 200 Plant Species
References 202
Further Reading 206 Introduction 255
The Bulk Population Method 255
11. Cultivar Testing and Seed Production Single Seed Descent 261
The Doubled Haploid Method (via Microspore Culture) 263
Introduction 207 Haploids from Interspecific Hybrids 267
Cultivar Testing 208 Heterosis and Hybrid Cultivars in Self-Pollinated
Cultivar Release 211 Crop Species 268
Transient and Durable Population Names 212 Genome Selection in Self-Pollinated Crop Species 270
Seed Production 213 Summary of Breeding Methods for Self-Pollinated Crop
Testing the Genetic Purity of Seed and Clonal Populations 217 Species 270
References 219 References 271
CONTENTS vii
15. Breeding Methods for Outcrossing Plant 18. The Backcross Method
Species: I. History of Corn Breeding and Open
Pollinated Populations Introduction 327
Historical Perspective 329
Introduction 275 Theoretical Considerations 330
Brief History of Corn Breeding 276 Transfer of Genes Across Species Barriers 333
Hybrid Corn Cultivars 278 Change of Cytotype 335
Combining Ability and Estimation Methods 281 Increasing the Number of Recurrent Parents or Traits
Population Improvement for Outcrossing Species 282 Under Transfer 336
Open Pollinated Populations 284 Modifications to the Backcross Method 337
References 285 Applications of Molecular Markers and MAS in the Backcross
Further Reading 286 Method 337
Comparisons of Backcross to Molecular Transformation 341
16. Breeding Methods for Outcrossing Plant References 343
Species: II. Hybrid Cultivars
19. Breeding for Disease and Insect Resistance
Introduction 287
Introduction 345
Inbreeding Depression 289
The Disease Concept 347
Heterosis 293
The Gene-for-Gene Theory 352
Applications of MAS for Heterosis 296
Horizontal and Vertical Resistance 354
Breeding Strategies for Hybrid Cultivars 296
Ploidy and Disease Resistance 356
Sources of Breeding Populations 297
Breeding for Disease Resistance 357
Recurrent Selection Schemes 298
Screening Methods 358
Cell and Molecular Biology Tools in Recurrent Selection 301
Marker-Assisted Breeding (MAS) for Disease
Production of Hybrid Seed 301
Resistance Breeding 359
References 305
Molecular Bases and Approaches to the Breeding of
Further Reading 307
Plant Disease Resistance 361
17. Breeding Methods for Outcrossing Plant Detailed Examples of Breeding Horticultural Crops
Species: III. Asexual Propagation for Disease Resistance 362
Examples of and Experiences with Disease Resistance
Introduction 309 in Other Horticultural Crop Species 370
Breeding of Selected Clonally-Propagated Crop Species 311 Insect Resistance and Tolerance 372
The Special Circumstances of Long-Lived Woody Perennials 313 MAS and Breeding for Insect Pest Resistance 374
Interspecific and Intergeneric Hybrids 314 Examples of and Experiences with Nematode and Insect
Applications of Cell and Tissue Culture in Breeding Herbivore Resistance in Horticultural Crop Species 374
Asexually Propagated Crop Species 316 Methods to Minimize New Resistant Genotypes of
Marker-Assisted Selection in Clonally-Propagated Pathogens and Pests and Also Avoid Damage
Crop Species 317 to Beneficial Species 376
Apomixis 318 References 377
The Plant Chimera 319
Grafting 321
Glossary 383
Tissue and Cell Culture and Artificial Seeds 322
References 323 Index 393
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Preface and Acknowledgments
Everyone takes a unique pathway through life that is a consequence of circumstances, opportunities, conscious
decisions, relationships, and plain luck. My decision to become a plant breeder was in response to a job opportunity
at the University of California, Davis in 1978. I had not been formally trained as a plant breeder, nor was I attracted
to the discipline as an undergraduate or graduate student. My academic training at Michigan State University was
primarily in plant biology with an emphasis on genetics, although I had enrolled in a few plant breeding courses.
After taking the position at UCD as an Assistant Professor/Geneticist/Plant Breeder, my transition from esoteric sci-
ence into the world of plant breeding started with on-the-job learning experiences starting a program in cool-season
vegetables and teaching the UCD plant breeding class.
My pathway diverted in 1982 when I made a conscious decision to leave UCD for a position in the rapidly ex-
panding agricultural biotechnology industry. Ultimately, I remained in the agricultural biotech industry for 12 years,
starting with forging applications of cellular and molecular biology in crop improvement. I gravitated progressively
to the product development and commercialization facet of the business since there was no shortage of scientists, but
there was a paucity of broadly trained professionals to bridge the gap from research to products and services. Along
the way, I experienced the entire biotechnology spectrum from basic science to marketing and sales. I learned to re-
spect the challenges and rigors of all links in the product development chain from basic sciences to finished products.
None of them are trivial or easy.
My return to academia in 1995 came as an administrator at the School of Environmental and Biological Sciences (SEBS),
Rutgers University, a position I held until 2002. Following two years as an acting county extension agent, I returned to
the research/extension/teaching faculty at Rutgers after an absence of 22 years as a practicing academic. I assumed the
responsibility to co-teach Plant Breeding, and embarked on applied plant breeding efforts in processing and fresh market
tomatoes. Over time, I also initiated targeted breeding efforts at Rutgers in Capsicum sp. and seedless table grape.
My Plant Breeding co-instructor and I experienced difficulty in selecting a textbook that could serve as an effective
resource to students; to reinforce the topics we covered in class and fill in the details we did not. The plant agricul-
tural industry in New Jersey is driven heavily by horticultural species, but most plant breeding textbooks focused
only on agronomic species. Further, available textbooks were woefully outdated with regard to the integration of cell
and molecular biology applications.
During the transition year from extension agent to research/extension/teaching (2005), I decided to write this
book. Time was available while the research program was planned and launched, but I knew it would soon disap-
pear as the program expanded. I had a vision for how the book would be crafted and a lot of ideas spiraling in my
head, so I simply drafted a table of contents and started writing. By late 2005, a very rough draft of the book had
been completed. It consisted of a download of virtually everything that was in my memory banks, rife with personal
experiences. The draft was not replete, however, with documentation or visual examples. It needed a lot of work to
become a finished product.
I was correct that available discretionary time would quickly vanish. My attempts to keep the book project on the
front, then the back burners, after 2005 were unsuccessful. Research, extension, and teaching obligations occupied
progressively more of my calendars and the book project was correspondingly shelved. My department chair urged
me to rekindle my interest in the project and, in 2017, I took a 6-month sabbatical leave to finish the book. I had al-
ready expended a lot of time and effort on the draft, and did not want the investment to be squandered.
After a couple of chapters were completed to my satisfaction, I sought a publishing partner. Academic Press/
Elsevier responded quickly with interest. I’d published before with Elsevier, and the experience had been a good one.
We came to an agreement by August, 2017.
The original project was more ambitious than what ended up between these covers. A third section with
specific crop species examples was planned and partially written. I underestimated the time requirements par-
ticularly of documentation of facts presented in the book. Many chapters consumed over a month to re-write,
document, and illustrate. The sabbatical ended in December 2017, and the book was far from completed. The third
section was suspended in the interests of getting the book finished and published in a reasonable time frame.
Plant breeding is accelerating, and new discoveries are changing the discipline almost daily. I couldn’t afford to
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