George Acquaah - Principles of Plant Genetics and Breeding

6 Effects of combined stresses 13.7 Impact of environmental stress factors in crop production Key references and suggested reading Outcomes assessment 14 Breeding for resistanceto 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 and pests 14.4 Overview of the methods of 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 plants 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 Key references and suggested reading Outcomes assessment 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 (waterlogging) Key references and suggested reading Outcomes assessment

11 Section 6: Selection methods 16 Breeding self‐pollinated species 16.1 Types of cultivars 16.2 Genetic structure of cultivars and its implications 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 Key references and suggested reading Outcomes assessment 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 Key references and suggested reading Outcomes assessment 18 Breeding hybrid cultivars 18.1 What is a hybrid cultivar? 18.2 Brief historical perspective 18.3 The concepts 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 Key references and suggested reading Internet resources Outcomes assessment 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 Key references and suggested reading Internet resources Outcomes Assessment

12 Section 7: Technologies for linkinggenes to traits 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 Key references and suggested reading Outcomes assessment 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 Identification of polymorphic markers 21.6 Linkage analysis of markers 21.7 Rendering linkage maps 21.8 Mapping quantitative trait loci (QTL) 21.9 High‐resolution QTL mapping 21.10 Bulk segregant analysis (BSA) 21.11 The value of multiple parent populations in mapping 21.12 Creating MAGIC and NAM populations for QTL mapping 21.13 Comparative genome mapping 21.14 Synteny Key references and suggested reading Outcomes assessment 22 DNA sequencingand OMICs technologies 22.1 What is DNA 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 in plant breeding? 22.6 Genomics 22.7 Transcriptomics 22.8 Proteomics 22.9 Metabolomics 22.10 Phenomics Key references and suggested reading Outcomes assessment

13 Section 8: Applications of genetic markers in breeding 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 The MAS schemes 23.5 Limitations of MAS 23.6 Enhancing the potential of MAS in breeding Key references and suggested reading Outcomes assessment 24 Genomic selection and genome‐wide association studies 24.1 Making the case for genomic selection 24.2 What is genomic selection? 24.3 Genome‐wide association studies 24.4 MAS, MABC, and GS compared 24.5 Haplotypes 24.6 Linkage disequilibrium mapping (association mapping) Key references and suggested reading Outcomes assessment

14 Section 9: Mutations and ploidy in plant breeding 25 Mutagenesis in plant breeding 25.1 Brief historical perspectives 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 25.11 Selected significant successes of mutation breeding 25.12 Molecular techniques for enhancing efficiency of induced mutagenesis 25.13 Horticultural applications of mutagenesis 25.14 General effects of mutagenesis 25.15 Key successes of induced mutagenesis Key references and suggested reading Internet resources Outcomes assessment 26 Ploidy in plantbreeding 26.1 Terminology 26.2 Variations in chromosome number 26.3 General effects of polyploidy of plants 26.4 Origin of polyploids 26.5 Autoploidy 26.6 Breeding autoploids 26.7 Natural alloploids 26.8 Aneuploidy 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 Key references and suggested reading Internet resources Outcomes assessment

15 Section 10: Genetic molecular modifications in plant breeding 27 Breeding genetically modified crops 27.1 What is biotechnology? 27.2 Antisense technology 27.3 Restriction enzymes 27.4 Vectors 27.5 Categories of vectors by functions 27.6 Cloning 27.7 Breeding genetically modified (GM) cultivars 27.8 Engineering pest resistance 27.9 Trends in adoption of GM cultivars Key references and suggested reading Internet resources Outcomes assessment 28 Genome editing and other modification 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 Key references and suggested reading Outcomes assessment 29 Paradigm shifts in plantbreeding and other non‐GM technologies 29.1 The way 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 29.11 Techniques for shortening the plant generation cycle for faster breeding Key references and suggested reading Internet resources Outcomes assessment

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