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DEDICATION PREFACE ACKNOWLEDGEMENTS INDUSTRY HIGHLIGHTS BOXES INDUSTRY HIGHLIGHTS BOXES: AUTHORS SECTION 1: OVERVIEW AND HISTORICAL PERSPECTIVES CHAPTER 1 INTRODUCTION 1.1 What is plant breeding? 1.2 The goals of plant breeding 1.3 The concept of genetic manipulations of plant attributes 1.4 Why breed plants? 1.5 Overview of the basic steps in plant breeding 1.6 How have plant breeding objectives changed over the years 1.7 The art and science of plant breeding 1.8 Training of plant breeders 1.9 The plant breeding industry 1.10 Duration and cost of plant breeding programs 1.11 The future of plant breeding in society 1.12 The organization of the book CHAPTER 2 HISTORY OF PLANT BREEDING 2.1 Origins of agriculture and plant breeding 2.2 The "Unknown Breeder" 2.3 Plant manipulation efforts by early civilizations 2.4 Early pioneers of the theories and practices of modern plant breeding 2.5 Later pioneers and trailblazers 2.6 History of plant breeding technologies/techniques 2.7 Genome-wide approaches to crop improvement 2.8 Bioinformatics and OMICs technologies in crop improvement 2.9 Summary of changes in plant breeding over the last half century 2.10 Achievement of modern plant breeders SECTION 2 POULATION AND QUANTITAVTIVE GENETIC PRINCIPLES CHAPTER 3 INTRODUCTION TO CONCEPTS OF POPULATION GENETICS 3.1 Concepts of a population and gene pool 3.2 Issues arising from Hardy-Weinberg equilibrium 3.3 Factors affecting changes in gene frequency 3.4 Frequency dependent selection 3.5 Summary of key plant breeding applications 3.6 Modes of selection 3.7 Effect of mating system on selection 3.8 The concept of inbreeding 3.9 Inbreeding and its implications in plant breeding 3.10 Concept of population improvement 3.11 Types of open pollenated populations CHAPTER 4 INTRODUCTION TO QUANTITATIVE GENETICS 4.1 What is quantitative genetics? 4.2 What is a quantitative trait? 4.3 Qualitative genetics versus quantitative genetics 4.4 The environment and quantitative variation 4.5 Polygenes and polygenic inheritance 4.6 Decision-making in breeding based on biometrical genetics 4.7 Gene action 4.8 Gene action and plant breeding 4.9 Variance components of a quantitative trait 4.10 The concept of heritability 4.11 Response to selection in breeding 4.12 Concept of correlated response 4.13 Selection for multiple traits 4.14 Concept of intuitive index 4.15 The concept of general worth 4.16 Nature of breeding characteristics and their levels of expression 4.17 Early generation testing 4.18 Concept of combining ability 4.19 Mating designs 4.20 The genetic architecture of quantitative traits 4.21 The effect of QTL on phenotype 4.22 Molecular basis of quantitative variation 4.23 Systems genetics 4.24 Predicting breeding value 4.25 Genomic selection (genome wide selection) 4.26 Mapping quantitative traits SECTION 3 REPRODUCTIVE SYSTEMS CHAPTER 5 INTRODUCTION TO REPRODUCTION 5.1 Importance of mode of reproduction to plant breeding 5.2 Overview of reproductive options in plants 5.3 Types of reproduction 5.4 Sexual reproduction 5.5 What is autogamy? 5.6 Self incompatibility 5.7 Male sterility 5.8 Dichogamy 5.9 Genetic and breeding implications of autogamy 5.10 Genotype conversion programs 5.11 What is allogamy? 5.12 Artificial pollination control techniques 5.13 Inbreeding depression 5.14 Mendelian concepts relating to the reproductive system 5.15 Complex inheritance CHAPTER 6 HYBRIDIZATION 6.1 Concept of gene transfer and hybridization 6.2 Application of crossing in plant breeding 6.3 Artificial hybridization 6.4 Artificial pollination control techniques 6.5 Flower and flowering issues in hybridization 6.6 Emasculation 6.7 Pollination 6.8 Number of F1 crosses to make 6.9 Genetic issues in hybridization 6.10 Types of populations generated through hybridization 611 Wide crosses 6.12 Issue of reproductive isolation barriers 6.13 Overcoming challenges of reproductive barriers 6.14 Bridge crosses CHAPTER 7 CLONAL PROPAGATION AND IN VITRO CULTURE 7.1 What is a clone? 7.2 Clones, inbred lines, and pure lines 7.3 Categories of clonally propagated species based on economic use 7.4 Categories of clonally propagated species for breeding purposes 7.5 Types of clonal propagation 7.6 Importance of clonal propagation in plant breeding 7.7 Breeding implications of clonal propagation 7.8 Genetic issues in clonal breeding 7.9 Breeding approaches used in clonal species 7.10 Natural propagation 7.11 In vitro culture 7.12 Micropropagation 7.13 Concept of totipotency 7.14 Somaclonal variation 7.15 Apomixis 7.16 Other tissue culture applications 7.17 Production of haploids 7.18 Doubled haploids 7.19 Germplasm preservation SECTION 4 GERMPLASM FOR BREEDING CHAPTER 8 VARIATION: TYPES, ORIGIN AND SCALE 8.1 Classifying plants 8.2 Rules of classification of plants 8.3 Operational classification systems 8.4 Types of variation among plants 8.5. Origins of genetic variability 8.6 Biotechnology for creating genetic variability 8.7 Scale of variability CHAPTER 9 PLANT DOMESTICATION 9.1 The concept of evolution 9.2 What is domestication 9.3 Evolution versus domestication 9.4 Conscious selection versus unconscious selection 9.5 Patterns of plant domestication 9.6 Centers of plant domestication 9.7 Roll call of domesticated plants 9.8 Changes accompanying domestication 9.9 Genetic bottleneck 9.10 Tempo of domestication 9.11 Genetic architecture and domestication 9.12 Models of domestication 9.13 Modern breeding is a continuation of the domestication process CHAPTER 10 PLANT GENETIC RESOURCES 10.1 Importance of germplasm to plant breeding 10.2 Centers of diversity in plant breeding 10.3 Sources of germplasm for plant breeding 10.4 Concept of genetic vulnerability 10.5 What plant breeders can do to address crop vulnerability 10.6 Wild (exotic) germplasm in plant breeding 10.7 Plant genetic resources conservation 10.8 Nature of cultivated plant genetic resources 10.9 Approaches to germplasm conservation 10.10 Germplasm collection 10.11 Types of plant germplasm collection 10.12 Managing plant genetic resources 10.13 Issue of redundancy and the concept of core subsets 10.14 Germplasm storage technologies 10.15 Using genetic resources 10.16 Plant exploration and introduction and their impact on agriculture 10.17 international conservation efforts 10.18 An example of a national germplasm conservation system 10.19 Who owns biodiversity? 10.20 Understanding the genetic architecture of germplasm for crop improvement SECTION 5 BREEDING OBJECTIVES CHAPTER 11 YIELD AND MORPHOLOGICA TRAITS 11.1 Physiological traits 11.2 What is yield? 11.3 Biological versus economic yield 11.4 The ideotype concept 11.5 Improving the efficiency of dry matter partitioning 11.6 Harvest index as a selection criterion for yield 11.7 Selecting for yield per se 11.8 Biological pathway to economic yield 11.9 The concept of yield potential 11.10 The concept of yield plateau 11.11 Yield stability 11.12 Lodging resistance 11.13 Shattering resistance 11.14 Reduced plant height 11.15 Breeding determinancy 11.16 Photoperiod response 11.17 Early maturity CHAPTER 12 QUALITY TRAITS 12.1 Concept of quality 12.2 Nutritional quality of food crops 12.3 Brief history of breeding for improved nutritional quality of crops 12.4 Breeding for improved protein content 12.5 Improving protein content by genetic engineering 12.6 Breeding improved oil quality 12.7 Breeding low phytate cultivar 12.8 Breeding end use quality 12.9 Breeding seedlessness 12.10 Breeding for industrial uses 12.11 Breeding plants for novel traits 12.12 Breeding for enhanced bioavailability CHAPTER 13 ENVIRONMENTAL STRESS FACTORS 13.1 Environmental stress factors in crop production 13.2 Climate change and plant breeding 13.3 Crop production environment and stress 13.4 Abiotic environment stress factors 13.5 Biotic environmental stress factors 13.6 Effects of combined stresses 13.7 Impact of environmental stress factors in crop production CHAPTER 14 BREEDING FOR RESISTANCE TO DISEASES AND INSECT PESTS 14.1 Selected definitions 14.2 Groups of pathogens and pests targeted by plant breeders 14.3 Biological and economic effects of plant pathogens 14.4 Overview of the methods for control of plant pathogens and pests 14.5 Concepts of resistance in breeding 14.6 Concepts of pathogen and host 14.7 Mechanisms of defense in plant against pathogens and pests 14.8 Types of genetic host resistance and their breeding approaches 14.9 Resistance breeding strategies 14.10 Challenges of breeding for pest resistance 14.11 Role of wild germplasm in disease and pest resistance breeding 14.12 Screening techniques in disease and pest resistance breeding 14.13 Applications of biotechnology in pest resistance breeding 14.14 Epidemics and plant breeding CHAPTER 15 BREEDING FOR RESISTANCE TO ABIOTIC STRESSES 15.1 Importance of breeding for resistance to abiotic stresses 15.2 Resistance to abiotic stress and yield potential 15.3 Types of abiotic environmental stresses 15.4 Tolerance to stress or resistance to stress? 15.5 Screening for stress resistance 15.6 Drought stress 15.7 Breeding drought resistance 15.8 Approaches for breeding drought resistance 15.9 Cold stress 15.10 Mechanisms of resistance to low temperature 15.11 Selection for low-temperature tolerance 15.12 Breeding for tolerance to low-temperature stress 15.13 Salinity stress 15.14 Heat stress 15.15 Mineral toxicity stress 15.16 Mineral deficiency stress 15.17 Oxidative stress 15.18 Flood stress (water logging) SECTION 6 SELECTION METHODS CHAPTER 16 BREEDING SELF-POLINATED SPECIES 16.1 Types of cultivars 16.2 Genetic structure of cultivars and its implications in breeding 16.3 Types of self-pollinated cultivars 16.4 Common plant breeding notations 16.5 Mass selection 16.6 Pure-line selection 16.7 Pedigree selection 16.8 Bulk population breeding 16.9 Single seed descent 16.10 Backcross breeding 16.11 Special backcross procedures 16.12 Multiline breeding and cultivar blends 16.13 Composites 16.14 Recurrent selection CHAPTER 17 BREEDING CROSS-POLLINATED SPECIES 17.1 The concept of population improvement 17.2 Concept of recurrent selection 17.3 Genetic basis of recurrent selection 17.4 Types of recurrent selection 17.5 Intrapopulation improvement methods 17.6 Optimizing gain from selection in population improvement 17.7 Development of synthetic cultivars 17.8 Backcross breeding CHAPTER 18 BREEDING HYBRID CULTIVARS 18.1 What is a hybrid cultivar? 18.2 Brief historical perspective 18.3 The concept of hybrid vigor and inbreeding depression 18.4 Genetic basis of heterosis 18.5 Biometrics of heterosis 18.6 Concept of heterotic relationship 18.7 Types of hybrids 18.8 Germplasm procurement and development for hybrid production 18.9 Selection of parents (inbred lines) 18.10 Field establishment 18.11 Maintenance 18.12 Harvesting and processing 18.13 Hybrid seed production of maize 18.14 Hybrids in horticulture 18.15 Exploiting hybrid vigor in asexually reproducing species 18.16 Prerequisites for successful commercial hybrid seed production CHAPTER 19 BREEDING CLONALLY PROPAGATED SPECIES 19.1 Clones, inbred lines and pure lines 19.2 Categories of clonally propagated species for breeding purposes 19.3 Breeding implications of clonal propagation 19.4 Genetic issues in clonal breeding 19.5 Breeding approaches used in clonal crops 19.6 Advantages and limitations of clonal propagation 19.7 Breeding apomictic cultivars 19.8 In vitro selection SECTION 7 TECHNOLOGIES FOR LINKING GENES TO TRAITS CHAPTER 20 MOLECULAR MARKERS 20.1 The concept of genetic markers 20.2 Use of genetic markers in plant breeding 20.3 Concept of polymorphism and the origin of molecular markers 20.4 Brief history of molecular markers 20.5 Classification of molecular markers 20.6 Enzyme-based markers 20.7 Hybridization-based markers 20.8 PCR-based markers 20.9 PCR based markers from RFLPs 20.10 DNA sequence-based markers 20.11 Comparison of selected molecular markers 20.12 Desirable properties of a molecular marker system 20.13 Readying markers for marker assisted selection CHAPTER 21 MAPPING OF GENES 21.1 Why map genes? 21.2 Types of gene maps 21.3 Principles of linkage mapping 21.4 Mapping populations 21.5 Modifications of polymorphic markers 21.6 Linkage analysis of markers 21.7 Rendering linkage maps 21.8 Mapping quantitative trait loci (QTLs) 21.9 High-resolution QTL mapping 21.10 Bulk segregant analysis 21.11 The value of multiple populations in mapping 21.12 Comparative genome mapping 21.13 Synteny 21.14 Genome wide association studies CHAPTER 22 GENE SEQUENCING and OMICs TECHNOLOGIES 22.1 What is gene sequencing 22.2 Types of sequencing technologies 22.3 Next generation sequencing (NGS) workflow 22.4 Genotyping-by-sequencing 22.5 What are the OMICs technologies? 22.6 Genomics 22.7 Transcriptomics 22.8 Proteomics 22.9 Metabolomics 22.10 Phenomics SECTION 8 APPLICATIONS OF GENETIC MARKERS IN BREEDING CHAPTER 23 MARKER ASSISTED SELECTION 23.1 The concept of molecular breeding 23.2 Choosing molecular markers for MAS 23.3 Advantages of MAS over conventional breeding protocols 23.4 MAS schemes 23.5 Marker assisted backcross breeding 23.6 Marker assisted recurrent selection 23.7 Backcross breeding for introgression of wild genes 23.8 Marker assisted "forward selection" 23.9 Marker assisted gene pyramiding 23.10 Marker assisted early generation selection 23.11 Limitations of MAS 23.12 Enhancing the potential of MAS in breeding CHAPTER 24 GENOMIC SELECTION AND GENOME WIDE ASSOCIATION STUDIES 24.1 Making the case for genomic selection 24.2 What is genomic or genome wide selection? 24.3 Overview of genomic selection procedure 24.4 Designing a training population 24.5 Markers of genomic selection 24.6 Statistical models for genomic selection 24.7 Applications of genomic selection 24.8 Genome wide association studies 24.9 MAS, MABC and GS compared 24.10 Haplotype 24.11 Linkage disequilibrium and haplotypes 24.12 Linkage disequilibrium mapping (Association mapping) 24.13 Breeding applications of association mapping SECTION 9 MUTATIONS AND PLOIDY IN PLANT BREEDING CHAPTER 25 MUTAGENESIS IN PLANT BREEDING 25.1 Brief historical perspective 25.2 Types of mutations 25.3 Mutagenic agents 25.4 Types of tissues used for mutagenesis 25.5 Factors affecting the success of mutagenesis 25.6 Mutation breeding of seed-bearing plants 25.7 Mutation breeding of clonally propagated species 25.8 Mutations from tissue culture systems 25.9 Using induced mutants 25.10 Limitations of mutagenesis as a plant breeding technique 25.12 Molecular techniques for enhancing efficiency of induced mutagenesis 25.13 Reverse genetics 25.14 Horticultural applications of mutagenesis 25.15 General effects of mutagenesis 25.16 Key successes of induced mutagenesis CHAPTER 26 POLYPLOIDY IN PLANT BREEDING 26.1 Terminology 26.2 Variation in chromosome number 26.3 General effects of polyploidy in plants 26.4 Origin of polyploids 26.5 Autoploidy 26.6 Breeding autoploids 26.7 Natural alloploids 26.8 Anueploidydd 26.9 General importance of polyploidy in plant improvement 26.10 Inducing polyploids 26.11 Use of 2n gametes for introgression breeding 26.12 Haploidy 26.13 Anther culture 26.14 Doubled haploids SECTION 10 MOLECULAR GENETIC MODIFICATION IN PLANT BREEDING CHAPTER 30 BREEDING GENETICALLY MODIFIED PLANTS 27.1 What is biotechnology? 27.2 Antisense technology 27.3 Restriction enzymes 27.4 Vectors 27.5 Categories of vectors by function 27.6 Cloning 27.7 Breeding genetically modified (GM) cultivars 27.8 Engineering pest resistance 27.9 Trends in adoption of GM cultivars CHAPTER 28 GENOME EDITING TECHNOLOGIES 28.1 General steps in genome editing 28.2 Types of editing systems 28.3 Zinc-finger nucleases (ZFNs) 28.4 Transcription activator-like effector nucleases (TALENs) 28.5 Clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) 28.6 Comparison of gene editing systems 28.7 RNA interference (RNAi) 28.8 Oligonucleotide-directed mutagenesis CHAPTER 29 PARADIGM SHIFT IN PLANT BREEDING and OTHER NEW BREEDING TECHNOLOGIES 29.1 The way plant breeders manipulate the plant genome 29.2 Paradigm shifts in plant breeding 29.3 Cisgenesis 29.4 Intragenesis 29.5 Reverse breeding 29.6 Grafting non-GM scion on GM-rootstock 29.7 Agroinfiltration 29.8 Epigenetics 29.9 RNA-directed DNA methylation 29.10 DNA barcoding SECTION 11 COMPUTER-AIDED APPLICATIONS IN PLANT BREEDING CHAPTER 30 BIOINFORMATICS IN PLANT BREEDING 30.1 What is bioinformatics? 30.2 Subdivisions of bioinformatics 30.3 Workflow of a bioinformatics project 30.4 General goals of bioinformatics 30.5 Data for bioinformatics 30.6 Data sources and how they are used in bioinformatics 30.7 Types of bioinformatics databases 30.8 Data management in integration 30.9 Data mining 30.10 Applications of bioinformatics in plant breeding 30.11 What is big data? 30.12 Big data workflow in plant breeding 30.13 Plant breeding applications 30.14 What is a computer simulation of model 30.15 Applications of computer simulation in plant breeding 30.16 Ideotype breeding 30.17 Simulation models in plant breeding SECTION 12 VARIETY RELEASE PROCESS IN BREEDING CHAPTER 31 PERFORMANCE EVALUATION FOR CULTIVAR RELEASE 31.1 Purpose of performance trials 31.2 Kinds of field trials 31.3 Designing field trials 31.4 The role of the environment in field trials 31.5 Genotype x environment interaction (GEI) 31.6 Models of GxE interaction 31.7 Measurement of GxE interaction using ANOVA 31.8 Importance and applications of GEI in plant breeding 31.9 Stability analysis models 31.10 Adaptation 31.11 Field plot technique in plant breeding 31.12 Field plot designs 31.13 Materials, equipment, and machinery for field evaluation of genotypes CHAPTER 32 SEED CERTIFICATION AND COMMERCIAL SEED RELEASE 32.1 The role of improved seed in agriculture 32.2 The role of the private sector in seed breeding 32.3 General steps of operation of the seed industry 32.4 The cultivar release process 32.5 Multiplication of pedigree seed 32.6 Concept of seed certification 32.7 The seed certification process 32.8 Seed testing 32.9 Tagging commercial seed 32.10 International role in seed certification 32.11 Production of conventional seed 32.12 Production of hybrid seed 32.13 Crop registration 32.14 Variety protection CHAPTER 33 REGULATORY AND LEGAL ISSUES IN PLANT BREEDING 33.1 The concept of intellectual property 33.2 Patents 33.3 Patents in plant breeding biotechnology; unique issues and challenges 33.4 Protecting plant varieties 33.5 The concept of substantial equivalence in regulation of biotechnology products 33.6 The issues of "novel traits" 33.7 The concept of the precautionary principle 33.8 Regulation and the issue of public trust 33.9 Biosafety regulation at the international level 33.10 Labelling of biotechnology products 33.11 Economic impact

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