George Acquaah - Principles of Plant Genetics and Breeding

16 Section 11: Computer‐aided applications in plant breeding 30 Bioinformatics, big data analytics, and computer simulations in plant breeding 30.1 What is bioinformatics? 30.2 Subdivisions of bioinformatics 30.3 Workflow for bioinformatics projects 30.4 General goals of bioinformatics 30.5 Data for bioinformatics 30.6 Data sources and how they are utilized in bioinformatics 30.7 Types of bioinformatics databases 30.8 Data management and 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 or model? 30.15 Applications of computer simulation in plant breeding 30.16 Ideotype breeding 30.17 Simulation models in plant breeding Key references and suggested reading Internet resources Outcomes Assessment

17 Section 12: Variety release process in plant breeding 31 Performance evaluation for crop 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 × environment interaction (GEI) 31.6 Models of G × E interaction 31.7 Measurement of GEI 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 Key references and suggested reading Internet Outcomes assessment 32 Seed certification and commercial seed release 32.1 The role of improved seed in agriculture 32.2 Role of the private sector in the seed industry 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 Key references and suggested reading Outcomes assessment 33 Regulatory andLegal Issues 33.1 The concept of intellectual property 33.2 Patents 33.3 Patents in plant breeding and biotechnology: unique issues and challenges 33.4 Protecting plant varieties 33.5 The concept of substantial equivalence in regulation of biotechnology 33.6 The issue 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 Labeling of biotechnology products 33.11 Economic impact of labeling and regulations 33.12 Legal risks that accompany adoption of GM crops 33.13 Overview of the regulation of the biotechnology industry in the US 33.14 The concept of biopiracy 33.15 The impact of IPRs on plant breeding Key references and suggested reading Internet resources Outcomes assessment

18 Section 13: Societal issues in plant breeding 34 Value‐driven concepts and social concerns 34.1 Concepts of ethics, morals, and values 34.2 Evolution of social debates on science‐based issues 34.3 Ethics in plant breeding 34.4 Risk analysis of biotechnology 34.5 Genetic use restriction technologies 34.6 Public perceptions and fears about biotechnology 34.7 Some concerns of plant breeders 34.8 GM foods and the issue of food allergy 34.9 The concept of organic plant breeding 34.10 Principles of organic plant breeding 34.11 Acceptable organic plant breeding techniques 34.12 Making agricultural biotechnology more acceptable to society 34.13 The “halo effect” of GM crops in the field 34.14 The rise of minor pests in GM fields 34.15 Who owns biodiversity? Key references and suggested reading Internet resources Outcomes assessment 35 International plant breeding efforts 35.1 International crop research centers 35.2 The CGIAR centers and their mission 35.3 Brief overview of plant breeding in developed countries 35.4 Plant breeding efforts in Sub‐Saharan Africa 35.5 Biotechnology efforts in developing countries 35.6 Participatory plant breeding (PPB) 35.7 Conventional plant breeding versus decentralized‐participatory plant breeding 35.8 The Green Revolution 35.9 The Green Revolution and the impact of international breeding efforts Key references and suggested reading Internet resources Outcomes assessment

19 Section 14: Breeding selected crops 36 Breeding wheat 36.1 Economic importance 36.2 Origin and history 36.3 Adaptation 36.4 History of breeding in the US 36.5 Commercial wheat classes 36.6 Germplasm resources 36.7 Cytogenetics 36.8 Genetics 36.9 General botany 36.10 Reproductive biology 36.11 Common breeding methods 36.12 Establishing a breeding nursery 36.13 Artificial pollination for hybridization 36.14 Natural pollination 36.15 Seed development 36.16 Breeding objectives Key references and suggested reading Outcomes assessment 37 Breeding corn 37.1 Economic importance 37.2 Origin and general history 37.3 Adaptation 37.4 History of corn breeding in the United States 37.5 Types of corn 37.6 Germplasm resources 37.7 Cytogenetics 37.8 Genetics 37.9 General botany 37.10 Reproductive biology 37.11 Genetic consequences of reproductive biology 37.12 Common breeding approaches 37.13 Establishing a breeding nursery 37.14 Other nurseries 37.15 Special environment 37.16 Artificial pollination for hybridization 37.17 Natural pollination for hybridization 37.18 Common breeding objectives Key references and suggested reading Outcomes assessment 38 Breeding rice 38.1 Economic importance 38.2 Origin and history 38.3 Adaptation 38.4 Commercial classes 38.5 Germplasm resources 38.6 Cytogenetics 38.7 Genetics 38.8 General botany 38.9 Reproductive biology 38.10 Common breeding methods 38.11 Establishing a breeding nursery 38.12 Common breeding objectives Key references and suggested further reading Outcomes assessment 39 Breeding sorghum 39.1 Economic importance 39.2 Origin 39.3 History of breeding in the US 39.4 Genetic resources 39.5 Cytogenetics 39.6 Genetics 39.7 General botany 39.8 Sorghum races 39.9 Grain sorghum groups 39.10 Reproductive biology 39.11 Pollination 39.12 Common breeding methods 39.13 Establishing a breeding nursery 39.14 Artificial pollination 39.15 Natural pollination 39.16 Seed development 39.17 Harvesting 39.18 Common breeding objectives Key references and suggested reading Outcomes assessment 40 Breeding soybean 40.1 Economic importance 40.2 History and origin 40.3 History of breeding 40.4 Genetic resources 40.5 Cytogenetics 40.6 Genetics 40.7 General botany 40.8 Cultivars 40.9 Reproductive biology 40.10 Common breeding methods 40.11 Establishing a field nursery 40.12 Artificial hybridization 40.13 Natural hybridization 40.14 Seed development 40.15 Harvesting 40.16 Breeding objectives Key references and suggested reading Internet resources Outcomes assessment 41 Breeding peanut 41.1 Economic importance 41.2 Origin and history 41.3 Market types 41.4 Genetic resources 41.5 Cytogenetics 41.6 General botany 41.7 Reproductive biology 41.8 Common breeding methods 41.9 Establishing a breeding nursery 41.10 Artificial pollination 41.11 Common breeding objectives Key references and suggested reading Internet resources Outcomes assessment 42 Breeding potato 42.1 Economic importance 42.2 Origin and history 42.3 Adaptation 42.4 Genetic resources 42.5 Cytogenetics 42.6 Genetics 42.7 General botany 42.8 Cultivars 42.9 Reproductive biology 42.10 Common breeding methods 42.11 Establishing a breeding nursery 42.12 Artificial pollination for hybridization 42.13 Natural pollination 42.14 Seed development 42.15 Breeding objectives Key references and suggested reading Internet resources Outcomes assessment 43 Breeding cotton 43.1 Economic importance 43.2 Origin and history 43.3 Germplasm resources 43.4 Cytogenetics 43.5 Genetics 43.6 Cultivars 43.7 American upland cotton 43.8 General botany 43.9 Reproductive biology 43.10 Common breeding methods 43.11 Establishing a breeding nursery 43.12 Artificial crossing 43.13 Natural pollination 43.14 Seed development 43.15 Breeding objectives Key references and suggested reading Outcomes assessment 44 Breeding tomato 44.1 Economic importance 44.2 Origin and history 44.3 Commercial market classes 44.4 Tomato types 44.5 Germplasm 44.6 Cytogenetics 44.7 Genetics 44.8 General botany 44.9 Brief history of tomato breeding 44.10 Breeding objectives 44.11 Common breeding methods Key references and suggested reading Outcomes assessment