Оглавление
George Acquaah. Principles of Plant Genetics and Breeding
Table of Contents
List of Tables
List of Illustrations
Guide
Pages
About the Companion Website
Principles of Plant Genetics and Breeding
Preface
Acknowledgments
Industry highlights boxes
Industry highlights boxes: Authors
Section 1 Overview and historical perspectives
1 Introduction. Purpose and expected outcomes
1.1 What is plant breeding?
1.2 The goals of plant breeding
1.3 The concept of genetic manipulation of plant attributes
1.4 Why breed plants?
1.4.1 Addressing world food and feed quality needs
1.4.2 Addressing food supply needs for a growing world population
1.4.3 Need to adapt plants to environmental stresses
1.4.4 Need to adapt crops to specific production systems
1.4.5 Developing new horticultural plant varieties
1.4.6 Satisfying industrial and other end‐use requirements
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
1.7.1 Art and the concept of the “breeder's eye”
1.7.2 The scientific disciplines and technologies of plant breeding
1.8 Training of plant breeders
1.9 The plant breeding industry
1.9.1 Private sector plant breeding
Industry highlights Box 1.1 Training game changers in plant breeding at the West Africa Centre for Crop Improvement (WACCI) in Africa for Africa
Genesis of WACCI
Overall goal and objectives
Student recruitment and PhD program structure
Quality assurance
Funding
Student research and breeding programs
WACCI graduates' research and breeding programs
Breeding programs at WACCI
WACCI maize breeding program
Visibility and impact of WACCI
Acknowledgments
1.9.2 Public sector plant breeding. The USA experience
The UK experience
Crop research and development in European Community (EC) countries
International plant breeding
1.9.3 Public sector versus private sector breeding
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
Key references and suggested reading
Internet resources for reference
Outcomes assessment. Part A
Part B
Part C
Note
2 History of plant breeding. Purpose and expected outcomes
2.1 Origins of agriculture and plant breeding
2.2 The “unknown breeder”
2.2.1 The “farmer‐breeder”
2.2.2 The “no name” breeder
2.3 Plant manipulation efforts by the 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
2.6.1 Technologies/techniques associated with creation of variation
Artificial pollination
Hybridization
Tissue culture/embryo culture
Chromosome doubling
Bridge cross
Protoplast fusion
Hybrid seed technology/technique
Seedlessness technique
Mutagenesis
rDNA technology
Important modern milestones associated with the creation of variation
2.6.2 Technologies/techniques for selection
Selection (breeding) schemes
Molecular marker technology
Gene mapping
Genomic selection
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
2.9.1 Changes in the science of breeding
2.9.2 Changes in laws and policies
2.9.3 Changes in breeding objectives
2.9.4 Changes in the creation of variability
2.9.5 Changes in identifying and evaluating genetic variability
2.9.6 Selecting and evaluating superior genotypes
2.10 Achievements of modern plant breeders
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
Section 2 Population and quantitative genetic principles
3 Introduction to concepts of population genetics. Purpose and expected outcomes
3.1 Concepts of a population and gene pool
3.1.1 Definitions
3.1.2 Mathematical model of a gene pool
Calculating gene frequency
Hardy‐Weinberg equilibrium
An example of a breeding application of Hardy‐Weinberg equilibrium
3.2 Issues arising from Hardy‐Weinberg equilibrium
3.2.1 Issue of population size
3.2.2 Issue of multiple loci
3.3 Factors affecting changes in gene frequency
3.3.1 Migration
3.3.2 Mutation
3.3.3 Selection
3.4 Frequency dependent selection
3.5 Summary of key plant breeding applications
3.6 Modes of selection
3.6.1 Stabilizing selection
3.6.2 Disruptive selection
3.6.3 Directional selection
3.7 Effect of mating system on selection
3.7.1 Random mating
3.7.2 Non‐random mating
Genetic assortative mating
Pheotypic assortative mating
Disassortative mating
3.8 Concept of inbreeding
3.9 Inbreeding and its implications in plant breeding
3.9.1 Consequences
3.9.2 Applications
3.9.3 Mating systems that promote inbreeding
3.10 Concept of population improvement
3.11 Types
3.11.1 Methods of population improvement
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
4 Introduction to quantitative genetics. Purpose and expected outcomes
4.1 What is quantitative genetics?
4.2 Quantitative traits
4.2.1 Qualitative genetics versus quantitative genetics
4.2.2 The environment and quantitative variation
4.2.3 Polygenes and polygenic inheritance
What are polygenes?
Number of genes controlling a quantitative trait
Modifying genes
4.2.4 Decision‐making in breeding based on biometrical genetics
What is the best cultivar to breed?
What selection method would be most effective for improvement of the trait?
Should selection be on single traits or multiple traits?
4.2.5 Gene action
Additive gene action
Dominance gene action
Overdominance gene action
Epistasis gene action
4.2.6 Gene action and plant breeding
4.2.7 Gene action and methods of breeding
Self‐pollinated species
Cross‐pollinated species
Impact of breeding method on genetic variance
Estimating gene action
Factors affecting gene action
4.2.8 Variance components of a quantitative trait
4.2.9 The concept of heritability
Definition
Types of heritability
Factors affecting heritability estimates
4.2.10 Methods of computation
Applications of heritability
Evaluating parental germplasm
4.2.11 Response to selection in breeding
Prediction of response in one generation – genetic advance due to selection
4.2.12 Concept of correlated response
4.2.13 Selection for multiple traits
Tandem selection
Independent curling
Index selection
4.2.14 Concept of intuitive index
4.2.15 The concept of general worth
4.2.16 Nature of breeding characteristics and their levels of expression
4.2.17 Early generation testing
4.2.18 Concept of combining ability
4.2.19 Mating designs
Hybrid crosses
Mating designs for random mating populations
Biparental mating (or pair crosses)
Polycross
North carolina design I
North carolina design II
North carolina design III
Diallele cross
Comparative evaluation of mating designs
4.3 The genetic architecture of quantitative traits
4.3.1 Effects of QTL on phenotype
4.3.2 Molecular basis of quantitative variation
4.4 Systems genetics
4.5 Predicting breeding value
4.6 Genomic selection (genome‐wide selection)
4.7 Mapping quantitative traits
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
Section 3 Reproductive systems
5 Introductionto reproduction. Purpose and expected outcomes
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
5.4.1 Sexual lifecycle of a plant (alternation of generation)
5.4.2 Duration of plant growth cycles
5.4.3 The flower structure
5.4.4 General reproductive morphology
5.4.5 Types of flowers
5.4.6 Gametogenesis
5.4.7 Pollination and fertilization
5.5 What is autogamy?
5.5.1 Mechanisms that promote autogamy
5.5.2 Mechanisms that prevent autogamy
Self‐incompatibility
Self‐incompatibility systems
Changing the incompatibility reaction
Plant breeding implications of self‐incompatibility
Male sterility
Exploiting male sterility in breeding
Dichogamy
5.5.3 Genetic and breeding implications of autogamy
Industry highlight boxes Introgression breeding on tomatoes for resistance to powdery mildew
Tomato and its wild relatives
Introgression breeding
An example of introgression breeding
Search for resistance in wild relatives of tomato
Inheritance of the resistance
Generation of near isogenic lines
Releasing NILs to companies for production of resistant cultivars
References
5.6 Genotype conversion programs
5.7 Artificial pollination control techniques
5.8 What is allogamy?
5.8.1 Mechanisms that favor allogamy
Monoecy
Dioecy
5.8.2 Genetic and breeding implications of allogamy
Inbreeding depression
5.9 Mendelian concepts relating to the reproductive system
5.9.1 Mendelian postulates
5.9.2 Concept of genotype and phenotype
5.9.3 Predicting genotype and phenotype
5.9.4 Distinguishing between heterozygous and homozygous individuals
5.10 Complex inheritance
5.10.1 Incomplete dominance and codominance
5.10.2 Multiple alleles of the same gene
5.10.3 Multiple genes
5.10.4 Polygenic inheritance
5.10.5 Concept of gene interaction and modified Mendelian ratios
5.10.6 Pleiotropy
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
6 Hybridization. Purpose and expected outcomes
6.1 Concept of gene transfer and hybridization
6.2 Applications of crossing in plant breeding
6.3 Artificial hybridization
6.4 Artificial pollination control techniques
6.5 Flower and flowering issues in hybridization
6.5.1 Flower health and induction
6.5.2 Synchronization of flowering
6.5.3 Selecting female parents and suitable flowers
6.6 Emasculation
6.6.1 Factors to consider for success
6.6.2 Methods of emasculation
Direct anther emasculation
Indirect anther emasculation
6.7 Pollination
6.7.1 Pollen collection and storage
6.7.2 Application of pollen
6.7.3 Tagging after pollination
6.8 Number of F1 crosses to make
6.9 Genetic issues in hybridization
6.9.1 Immediate effect
6.9.2 Subsequent effect
6.9.3 Gene recombination in the F2
6.10 Types of populations generated through hybridization
6.10.1 Divergent crossing
6.10.2 Convergent crosses
6.11 Wide crosses
Industry highlights Maize and Tripsacum : experiments in intergeneric hybridization and the transfer of apomixis
A historical review
Generating maize × Tripsacum hybrids
Gene transfer from Tripsacum to maize
Potential pathways for Tripsacum introgression. The 28→38→20 Non‐apomictic pathway
The 28→38 apomictic transfer pathway
The 46→56→38 non‐apomictic pathway
The 46→56→38 apomictic transfer pathway
Transfer of apomixis from Tripsacum to maize
Pitfalls in the development of an apomictic maize. FDR in apomictic maize‐ Tripsacum hybrids
Potential advantages of apomictic hybrid corn
References
6.11.1 Objectives of wide crosses
6.11.2 Selected success with wide crosses
6.12 Issue of reproductive isolation barriers
6.13 Overcoming challenges of reproductive barriers
6.14 Bridge crosses
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
7 Clonal propagation and in vitro culture. Purpose and expected outcomes
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
7.9.1 Planned introduction
7.9.2 Clonal selection
Purifying an infected cultivar
Clonal selection for cultivar development
7.9.3 Crossing with clonal selection
7.9.4 Mutation breeding
7.9.5 Breeding implications, advantages, and limitations of clonal propagation
7.10 Natural propagation
7.11 In vitro culture
Industry highlights use of comparative molecular markers and plant tissue culture techniques for genetic diversity assessment and rapid production of Musa species at Bowie State University
Introduction
Genetic diversity and population structure of Musa species using CDDP, ISSR, and SCoT markers
Conserved DNA‐derived polymorphism (CDDP), inter‐simple sequence repeat (ISSR) and start codon targeted (SCoT) markers
Macropropagation and micropropagation of Musa accessions
References
7.12 Micropropagation
7.12.1 Axillary shoot production
7.12.2 Adventitious shoot production
7.12.3 Somatic adventitious embryogenesis
7.13 Concept of totipotency
7.14 Somaclonal variation
7.15 Apomixis
7.15.1 Occurrence in nature
7.15.2 Benefits of apomixis
Benefits to the plant breeder
Benefits to the producer
Impact on the environment
7.15.3 Mechanisms of apomixis
Apospory
Diplospory
Adventitious embryo
Parthenogenesis
7.16 Other tissue culture applications
7.16.1 Synthetic seed
7.16.2 Limitations to commercialization of synthetic seed technology
7.16.3 Production of virus‐free plants
7.16.4 Applications in wide crosses
Embryo rescue
Somatic hybridization
7.17 Production of haploids
7.17.1 Anther culture
Applications
Limitations
7.17.2 Ovule/Ovary culture
7.17.3 Haploids from wide crosses
7.17.4 Doubled haploids
Key features
Applications
Procedure
Advantages and disadvantages
Genetic issues
7.18 Germplasm preservation
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
Section 4 Germplasm for breeding
8 Variation: types, origin, and scale. Purpose and expected outcomes
8.1 Classifying plants
8.2 Rules of classification of plants
8.3 Operational classification systems
8.4 Types of variation among plants
8.4.1 Environmental variation
8.4.2 Genetic variability
8.5 Origins of genetic variability
8.5.1 Genetic recombination
8.5.2 Ploidy modifications
8.5.3 Mutation
8.5.4 Transposable elements
8.6 Biotechnology for creating genetic variability
8.6.1 Gene transfer
8.6.2 Somaclonal variation
8.7 Scale of variability
8.7.1 Qualitative variation
8.7.2 Quantitative variation
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
9 Plant domestication. Purpose and expected outcomes
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
Industry highlights: the use of the wild potato species, Solanum etuberosum, in developing virus and insect‐resistant potato varieties
Historical background of the potato
Potato viruses
Solanum etuberosum: its use in the genetic improvement of potato
Virus and green peach aphid resistances of somatic hybrids and their progeny
Wireworm resistance of backcross progeny derived from somatic hybrids
References
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
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
10 Plant genetic resources. Purpose and expected outcomes
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
10.4.1 What is genetic vulnerability?
10.4.2 Key factors in genetic vulnerability‐induced crop failure
10.5 What plant breeders can do to address crop vulnerability
10.5.1 Reality check
10.5.2 Use of wild germplasm
10.5.3 Paradigm shift
10.5.4 Use of biotechnology to create new variability
10.5.5 Gene pyramiding
10.6 Wild (exotic) germplasm in plant breeding
10.7 Plant genetic resources conservation
10.7.1 Why conserve plant genetic resources?
10.7.2 Genetic erosion
10.7.3 Selected impact of germplasm acquisition. Impact on North American agriculture
Other parts of the world
10.8 Nature of cultivated plant genetic resources
10.9 Approaches to germplasm conservation
Industry highlights plant genetic resources for breeding
Introduction
PGR conservation and monitoring of PGR
In situ conservation
Ex situ conservation
Characterization and evaluation of plant genetic resources
Germplasm enhancement
Examples of successful use of plant genetic resources
Conclusion
References
10.9.1 In situ conservation
10.9.2 Ex situ conservation
Industry highlights conservation and utilization of plant genetic resources
10.10 Germplasm collection
10.11 Types of plant germplasm collections
10.11.1 Base collections
10.11.2 Backup collections
10.11.3 Active collections
10.11.4 Working or breeders' collections
10.12 Managing plant genetic resources
10.12.1 Regeneration
10.12.2 Characterization
10.12.3 Evaluation
10.12.4 Monitoring seed viability and genetic integrity
10.12.5 Exchange
10.13 Issue of redundancy and the concept of core subsets
10.14 Germplasm storage technologies
10.14.1 Seed storage
10.14.2 Field growing
10.14.3 Cryopreservation
10.14.4 In vitro storage
10.14.5 Molecular conservation
10.15 Using genetic resources
10.15.1 Perceptions and challenges
10.15.2 Concept of pre‐breeding
10.16 Plant explorations and introductions and their impact on agriculture. 10.16.1 Plant explorations
US Historical Perspectives
Other efforts
10.16.2 Plant introductions
10.17 International conservation efforts
10.18 An example of a national germplasm conservation system
10.18.1 Plant introduction
10.18.2 Collections
10.18.3 Information
10.19 Who owns biodiversity?
10.20 Understanding the genetic architecture of germplasm for crop improvement
10.20.1 Established approaches for gene identification
10.20.2 Emerging approaches for gene identification
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
Section 5 Breeding objectives
11 Yield andmorphological traits. Purpose and expected outcomes
11.1 Physiological traits
11.2 What is yield?
11.3 Biological versus economic yield
11.3.1 Biological yield
11.3.2 Economic yield
11.4 The ideotype concept
Industry highlights Box 11.1 Barley breeding in the United Kingdom
Targets
Crossing to commercialization
The UK barley breeding community
The impact of molecular markers
Future prospects
Acknowledgments
References
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
11.12.1 Nature, types, and economic importance
11.12.2 Genetics and breeding
11.13 Shattering resistance
11.13.1 Nature, types, and economic importance
11.13.2 Breeding grain shattering resistance
11.14 Reduced plant height
11.14.1 Nature, types, and economic importance
11.14.2 Genetics and germplasm resources
11.15 Breeding determinacy
11.15.1 Nature, types, and economic importance
11.15.2 Genetics and germplasm resources
11.16 Photoperiod response
11.16.1 Nature, types, and economic importance
11.16.2 Genetics and germplasm
11.17 Early maturity
11.17.1 Nature, types, economic importance
11.17.2 Genetics and germplasm
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
12 Quality traits. Purpose and expected outcomes
12.1 Concept of quality
12.2 Nutritional quality of food crops
12.3 Brief history of breeding for improved nutritional quality of crops
Industry highlights Box 12.1 development of high pro‐vitamin a‐enriched hybrid maize varieties in Ghana
Introduction
Product target
Source germplasm
Development of three‐way cross maize hybrids
Multi‐location yield and on‐farm trials of promising hybrids
Varietal release
Future research and direction
References
12.4 Breeding for improved protein content
12.4.1 Breeding high lysine content of grain
12.4.2 Quality protein maize (QPM)
12.5 Improving protein content by genetic engineering
12.5.1 The making of “golden rice”
12.5.2 Matters arising from the development of golden rice
12.6 Breeding improved oil quality
12.6.1 Chemical composition of seed oil
12.6.2 Approaches to breeding oil quality
12.7 Breeding low phytate cultivar
12.8 Breeding end‐use quality
12.8.1 Extended shelf life
Delayed ripening
The FlavrSavr tomato
12.8.2 Breeding cooking and processing qualities
12.9 Breeding seedlessness
12.9.1 Selection of diploid lines for developing tetraploids
12.9.2 Tetraploid induction
12.9.3 Development of tetraploid lines
12.9.4 Evaluation of tetraploid lines
12.9.5 Development and evaluation of triploid lines
12.10 Breeding for industrial uses
12.11 Breeding plants for novel traits
12.12 Breeding for enhanced bioavailable micronutrients
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
13 Environmental stress factors and plant breeding. Purpose and expected outcomes
13.1 Environmental stress factors in crop production
13.2 Climate change and plant breeding
13.2.1 Climate vs weather
13.2.2 What is climate change?
13.2.3 The consequences of climate change
13.2.4 Implications for plant breeding
13.3 Crop production environment and stress
13.4 Abiotic environmental stress factors
13.5 Biotic environmental stress factors
13.6 Effects of combined stresses
13.7 Impact of environmental stress factors in crop production
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
14 Breeding for resistanceto diseases and insect pests. Purpose and expected outcomes
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. 14.6.1 The pathogen
14.6.2 The host
14.6.3 The concept of disease triangle
14.7 Mechanisms of defense in plants against pathogens and pests
14.7.1 Avoidance
14.7.2 Resistance
Pre‐existing defense mechanisms
Infection‐induced defense mechanisms
14.7.3 Tolerance
14.7.4 Host versus non‐host disease resistance
14.7.5 Specificity of defense mechanisms
14.7.6 Specificity of the pathogen
14.7.7 Gene‐for‐gene reaction (genetics of specificity)
14.8 Types of genetic host resistance and their breeding approaches
14.8.1 Vertical resistance
Industry highlights Box 14.1 Breeding for durable resistance against Downy Mildew in Lettuce
Background
Aim
Methods and results. F2 population strategy
Introgression lines as an infinite population strategy
Limitations
Future work
References
14.8.2 Horizontal resistance
14.8.3 Combining vertical and horizontal resistance
14.8.4 Durability and breakdown of resistance
14.9 Resistance breeding strategies
14.9.1 General considerations for breeding resistance to pathogens and pests
14.9.2 Planned deployment of resistance genes
14.9.3 Gene pyramiding
14.9.4 Multilines
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
14.12.1 Facilities
14.12.2 Factors affecting expression of disease and insect resistance
14.13 Applications of biotechnology in pest resistance breeding
14.13.1 Engineering insect resistance
Protein toxins from Bacillus thuringiensis (Bt)
14.13.2 Engineering viral resistance
14.14 Epidemics and plant breeding
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
15 Breeding for resistance to abiotic stresses. Purpose and expected outcomes
15.1 Importance of breeding for resistance to abiotic stresses
15.2 Resistance to abiotic stress and yield potential
Industry highlights Box 15.1 Introgressiomics for adapting crops to climate change
Introduction
The introgressiomics approach
Conclusions
Acknowledgments
References
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
15.6.1 What is drought stress?
15.6.2 An overview of drought stress concepts
15.6.3 Managing drought stress
15.7 Breeding drought resistance
15.7.1 Underlying principles
15.7.2 Characterization of the drought environment
15.7.3 Plant traits affecting drought response
Phenology
Plant development and size
Plant root characteristics
Plant surface
Non‐senescence
Stem reservation utilization
15.7.4 Mechanisms of drought resistance
Escape
Avoidance
Tolerance
Recovery
15.8 Approaches for breeding drought resistance
15.8.1 Indirect breeding
15.8.2 Direct breeding
Field selection
Selection under managed stress environments
Selection based on yield per se
Selection based on developmental traits
Selection based on assessment of plant water status and plant function
15.9 Cold stress
15.9.1 An overview of cold stress concepts
15.9.2 Genetic basis of low‐temperature stress tolerance
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
15.13.1 Overview of salinity stress concepts
15.13.2 Breeding for salt tolerance
15.14 Heat stress
15.14.1 Overview of heat stress concepts
15.14.2 Breeding for resistance to heat stress
15.15 Mineral toxicity stress
15.15.1 Soil nutrient elements
15.15.2 Aluminum toxicity
15.15.3 Breeding aluminum tolerance
15.16 Mineral deficiency stress. 15.16.1 Concepts associated with mineral deficiency
15.16.2 Breeding efforts
15.17 Oxidative stress. 15.17.1 Concepts associated with oxidative stress
15.17.2 Applications and breeding efforts
15.18 Flood stress (waterlogging)
15.18.1 Concepts associated with waterlogging stress
15.18.2 Breeding efforts
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
Section 6 Selection methods
16 Breeding self‐pollinated species. Purpose and expected outcomes
16.1 Types of cultivars
16.1.1 Pure‐line cultivars
16.1.2 Open‐pollinated cultivars
16.1.3 Hybrid cultivars
16.1.4 Clonal cultivars
16.1.5 Apomictic cultivars
16.1.6 Multilines
16.2 Genetic structure of cultivars and its implications
16.2.1 Homozygous and homogeneous cultivars
16.2.2 Heterozygous and homogeneous cultivars
16.2.3 Heterozygous and heterogeneous cultivars
16.2.4 Homozygous and heterogeneous cultivars
16.2.5 Clonal cultivar
16.3 Types of self‐pollinated cultivars
16.4 Common plant breeding notations
16.4.1 Symbols for basic crosses
16.4.2 Symbols for inbred lines
16.4.3 Notation for pedigrees
16.5 Mass selection
16.5.1 Key features
Industry highlights Box 16.1 Recurrent selection with soybean
Selection using a restricted index
Selection procedure
Development of “Prolina” soybean
Recurrent selection using male sterility
Recurrent mass selection for seed size
References
16.5.2 Application
16.5.3 Procedure. Overview
Steps
16.5.4 Genetic issues
16.5.5 Advantages and disadvantages
Advantages
Disadvantages
16.5.6 Modification
16.6 Pure‐line selection
16.6.1 Key features
16.6.2 Application
16.6.3 Procedure. Overview
Steps
16.6.4 Genetic issues
16.6.5 Advantages and disadvantages
Advantages
Disadvantages
16.7 Pedigree selection
16.7.1 Key features
16.7.2 Application
16.7.3 General guides to selection following a cross
F 1 generation
F 2 generation
F 3 generation
F 4 generation
F 5 generation
F 6 generation
F 7 and subsequent generations
16.7.4 Procedure. Overview
Steps
Comments
16.7.5 Genetic issues
16.7.6 Advantages and disadvantages
Advantages
Disadvantages
16.7.7 Modifications
16.8 Bulk population breeding
16.8.1 Key features
16.8.2 Applications
16.8.3 Procedure. Overview
Steps
Comments
16.8.4 Genetic issues
16.8.5 Advantages and disadvantages
Advantages
Disadvantages
16.8.6 Modifications
16.9 Single‐seed descent
16.9.1 Key features
16.9.2 Applications
16.9.3 Procedures. Overview
Steps
Comments
16.9.4 Genetic issues
16.9.5 Advantages and disadvantages
Advantages
Disadvantages
16.9.6 Modifications
16.10 Backcross breeding
16.10.1 Key features
16.10.2 Application
16.10.3 Procedure. Overview
Steps
Comments
Comments
16.10.4 Genetic issues
16.10.5 Advantages and disadvantages
Advantages
Disadvantages
16.10.6 Modifications
16.11 Special backcross procedures. 16.11.1 Congruency backcross
16.11.2 Advanced backcross QTL
16.12 Multiline breeding and cultivar blends
16.12.1 Key features
16.12.2 Applications
16.12.3 Procedure
16.12.4 Genetic issues
16.12.5 Advantages and disadvantages
Advantages
Disadvantages
16.12.6 Modifications
16.13 Composites
16.14 Recurrent selection
16.14.1 Comments
16.14.2 Advantages and disadvantages
Advantages
Disadvantages
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
17 Breeding cross‐pollinated species. Purpose and expected outcomes
17.1 The concept of population improvement
Intrapopulation improvement
Interpopulation improvement
17.2 Concept of recurrent selection
17.2.1 Key features
17.2.2 Applications
17.3 Genetic basis of recurrent selection
17.4 Types of recurrent selection
17.5 Intrapopulation improvement methods
17.5.1 Individual plant selection methods. Mass selection
Key features
Genetic issues
Procedure
Advantages
Disadvantages
Modifications
17.5.2 Family selection methods
Steps
Genetic issues
Application
Modification
Steps
Genetic issues
Application
Steps
Genetic issues
Application
Steps
Genetic issues
Application
17.5.3 Family selection based on test cross
Key features
Applications
Procedure
Genetic issues
Modifications
Advantages and disadvantages
Key features
Application
Procedure
Advantages and disadvantages
Modification
Key features
Procedure
Genetic issues
Key features
Procedure
Advantages
Genetic issues
Application
17.6 Optimizing gain from selection in population improvement
17.7 Development of synthetic cultivars. 17.7.1 Synthetic cultivar versus germplasm composites
17.7.2 Desirable features of a synthetic cultivar
17.7.3 Application
17.7.4 Key features
Testers
Procedure
17.7.5 Genetic issues
17.7.6 Factors affecting performance of synthetic cultivars
17.7.7 Advantages and limitations of development of synthetics. Advantages
Disadvantages
17.8 Backcross breeding
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
18 Breeding hybrid cultivars. Purpose and expected outcomes
18.1 What is a hybrid cultivar?
18.2 Brief historical perspective
18.3 The concepts of hybrid vigor and inbreeding depression
18.3.1 Hybrid vigor
18.3.2 Inbreeding depression
18.4 Genetic basis of heterosis
18.4.1 Dominance theory
18.4.2 Overdominance theory
18.5 Biometrics of heterosis
18.6 Concept of heterotic relationship
18.6.1 Definition
18.6.2 Methods for developing heterotic groups
18.6.3 Heterotic groups and patterns in crops
18.6.4 Estimation of heterotic effects
18.7 Types of hybrids
18.8 Germplasm procurement and development for hybrid production
18.8.1 Development and maintenance of inbred lines
Inbred lines of inbreeding species
Inbred lines of cross‐pollinated species
Conventional or normal inbreds
Non‐conventional inbred lines
Genetically modified inbreds
18.8.2 Storage of seed
18.9 Selection of parents (inbred lines)
18.10 Field establishment
Box 18.1Calculating heat units. Heat units and degree‐days
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. 18.15.1 Plants with vegetative propagations
18.15.2 Apomixis
18.15.3 Monoecy and dioecy
18.16 Prerequisites for successful commercial hybrid seed production
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
19 Breeding clonally propagated species. Purpose and expected outcomes
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
19.5.1 Planned introduction
19.5.2 Clonal selection
Purifying an infected cultivar
Clonal selection for cultivar development
19.5.3 Hybridization with clonal selection
Industry highlights Box 1.1 The practice of yam breeding
Introduction
Genetic resources
Breeding goals and targets
Breeding methods and techniques
Box 19.2 Seed‐to‐tuber‐to‐seed process in yam breeding
Product delivery
Conclusion
References
19.5.4 Mutation breeding
19.6 Advantages and limitations of clonal propagation
Advantages
Disadvantages
19.7 Breeding apomictic cultivars
19.8 In vitro selection
19.8.1 Using whole plants or organs
19.8.2 Using undifferentiated tissue
19.8.3 Directed selection
Selection for disease resistance
Selection for herbicide tolerance
Selection for tolerance to abiotic stresses
Single‐cell selection system
Key references and suggested reading
Internet resources
Outcomes Assessment. Part A
Part B
Part C
Section 7 Technologies for linkinggenes to traits
20 Molecular markers. Purpose and expected outcomes
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
20.7.1 Restriction fragment length polymorphisms (RFLPs)
20.7.2 Minisatellites (SSRs)
20.7.3 Directed amplified minisatellite (DAMD)
20.7.4 Diversity arrays technology (DArT)
20.8 PCR‐based markers
Industry highlights Box 20.1 Molecular marker survey of genetic diversity in the genus Garcinia
Introduction
Study 1: RAPD marker. Materials and method
Results and discussion
Study 2: AFLP marker. Materials and methods
Results and discussion
Conclusion
20.8.1 Microsatellites
20.8.2 Inter‐simple sequence repeats (ISSR)
20.8.3 Random amplified microsatellite polymorphism (RAMP)
20.8.4 Random amplified polymorphic DNA (RAPD)
20.8.5 DNA amplification fingerprinting (DAF)
20.8.6 Sequence characterized amplified regions (SCAR) and sequence tagged sites (STS)
20.8.7 Amplified fragment length polymorphism (AFLP)
20.8.8 Start Codon Targeted (SCoT)
20.9 PCR‐based markers from RFLPs
20.10 DNA sequence‐based markers
20.10.1 Single nucleotide polymorphisms (SNPs)
20.10.2 Expressed sequence tags (ESTs)
20.11 Comparison of selected molecular markers
20.12 Desirable properties of a molecular marker system
20.13 Readying markers for marker assisted selection
20.13.1 Marker validation
20.13.2 Marker conversion
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
21 Mapping of genes. Purpose and expected outcomes
21.1 Why map genes?
21.2 Types of gene maps
21.3 Principles of linkage mapping
21.4 Mapping populations
21.4.1 Types of traditional 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)
21.8.1 Principles of QTL mapping
21.8.2 Steps in QTL mapping
21.8.3 Methods of QTL detection and localization
Single marker analysis
Simple interval mapping
Composite interval mapping
Multiple interval mapping
Presenting interval mapping results
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
21.12.1 MAGIC population mapping
21.12.2 NAM population mapping
21.13 Comparative genome mapping
21.14 Synteny
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
22 DNA sequencingand OMICs technologies. Purpose and expected outcomes
22.1 What is DNA sequencing?
22.2 Types of sequencing technologies
22.2.1 Sanger method
22.2.2 Toward high‐throughput sequencing
22.3 Next‐generation sequencing (NGS) workflow
22.4 Genotyping by sequencing
22.4.1 GBS workflow
22.4.2 Plant breeding applications
22.5 What are the “OMICs” technologies in plant breeding?
22.6 Genomics
22.6.1 Categories of genomics research
22.6.2 Genomics technologies and applications in breeding
22.6.3 Applications of genomics in plant breeding
22.7 Transcriptomics
22.7.1 Types and common technologies
22.7.2 Applications in plant breeding
22.8 Proteomics
22.8.1 Types of proteomics
22.8.2 Applications of proteomics
22.9 Metabolomics
Industry highlights: plant metabolomic and elicitation approaches enhance the plant metabolite level and play a complementary role in plant breeding
Targeted metabolomics approach aims to measure and profile metabolites with known chemical structures. Project 1: Timewise metabolic profiling of the effects of chemical elicitors on the production levels of α and β carotene in different carrot ( Daucus carota ) plants
Results
Project 2: Exogenous pre‐harvest treatment with methyl jasmonate and chitosan elicits lycopene biosynthesis in tomato plants
Non‐targeted metabolomics approaches
Metabolite profiling, usually includes a chromatographic separation step prior to analysis. Project 3: HPTLC (high‐performance thin‐layer chromatography) method development for classifying 23 different dried bean cultivars. (The work is done in collaboration with Dr. Davinand Luthria, USDA Laboratory.)
Results
Metabolic fingerprinting, where no chromatographic separation of the samples is done. Project 4: Analyzing the metabolites in passionfruits ( Passiflora edulis ) using spectral fingerprinting. (The work is done in collaboration with Dr. Davinand Luthria, USDA Laboratory.)
Results
References
22.9.1 Types and common technologies used
Untargeted approaches
Targeted approaches
Semi‐targeted approaches
22.9.2 Applications of metabolomics in plant breeding
22.10 Phenomics
22.10.1 Methodologies and breeding applications
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
Section 8 Applications of genetic markers in breeding
23 Marker‐assisted selection. Purpose and expected outcomes
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
23.4.1 Assessment of genetic diversity and selection of parents for crossing
23.4.2 Increasing favorable gene action
23.4.3 Increasing selection efficiency
23.4.4 Marker‐assisted backcrossing breeding
23.4.5 Marker‐assisted recurrent selection
23.4.6 Backcross breeding for introgression of wild genes
Advanced backcross breeding
Backcross inbred lines (BILs)
23.4.7 Marker‐assisted “forward selection”
23.4.8 Marker‐assisted gene pyramiding
23.4.9 Marker‐assisted early generation selection
23.5 Limitations of MAS
23.6 Enhancing the potential of MAS in breeding
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
24 Genomic selection and genome‐wide association studies. Purpose and expected outcomes
24.1 Making the case for genomic selection
24.2 What is genomic selection?
24.2.1 Overview of genomic selection procedure
24.2.2 Designing a training population
24.2.3 Markers for genomic selection
24.2.4 Statistical models for genomic selection
24.2.5 Applications of GS in plant breeding
24.3 Genome‐wide association studies
24.4 MAS, MABC, and GS compared
24.5 Haplotypes
Industry highlights Box 24.1 The use of haplotype information in QTL analysis
Introduction
Resolution into quantitative trait loci (QTL)
What are the most important lessons learned from these QTL studies?
The next step: resolution of QTL into trait alleles
The experimental design determines the number of different quantitative trait alleles (QTA) that can be analyzed
The binary information of molecular genetic methods
Why is marker development and validation not always successful?
Conclusion
References
24.5.1 Linkage disequilibrium and haplotypes
24.6 Linkage disequilibrium mapping (association mapping)
24.6.1 Breeding applications of association mapping
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
Section 9 Mutations and ploidy in plant breeding
25 Mutagenesis in plant breeding. Purpose and expected outcomes
25.1 Brief historical perspectives
25.2 Types of mutations
25.2.1 Induced mutations versus spontaneous mutations
25.2.2 Cell type: gametic mutations versus somatic mutations
25.2.3 Gene action: dominant versus recessive mutations
25.2.4 Structural changes at the chromosomal level
Gene mutation. Kind
Effect at the protein level
Frame shift mutation
Genomic mutation
Structural chromosomal changes (aberrations)
25.3 Mutagenic agents
25.3.1 Physical mutagens
25.3.2 Chemical mutagens
25.4 Types of tissues used for mutagenesis
25.5 Factors affecting the success of mutagenesis
25.6 Mutation breeding of seed‐bearing plants. 25.6.1 Objectives
25.6.2 Genotypes and source of material
25.6.3 Treatment
25.6.4 Field planting and evaluation
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. 25.10.1 Associated side effects
25.10.2 Large number of segregating populations needed
25.10.3 Recessivity of mutants
25.10.4 Limited pre‐existing genome
25.10.5 Mutations are generally random events
25.11 Selected significant successes of mutation breeding
25.12 Molecular techniques for enhancing efficiency of induced mutagenesis
25.12.1 Reverse genetics
25.12.2 Targeted induced local lesions in genomes (TILLING)
25.12.3 T‐DNA mutagenesis
25.13 Horticultural applications of mutagenesis
25.14 General effects of mutagenesis
25.14.1 Disadvantages of induced mutagenesis for breeding vegetatively propagated species
25.14.2 Overcoming drawbacks
25.15 Key successes of induced mutagenesis
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
26 Ploidy in plantbreeding. Purpose and expected outcomes
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
26.5.1 Natural autoploids of commercial importance
26.5.2 Cytology of autoploids
26.5.3 Genetics of autoploids
26.5.4 Induction of autoploids
26.6 Breeding autoploids
26.6.1 Autotetraploids and autotriploids
26.7 Natural alloploids
26.7.1 Genetics of alloploids
26.7.2 Breeding alloploids
26.8 Aneuploidy
26.8.1 Cytogenetics of autoploids
26.8.2 Applications of aneuploidy
Chromosome additions
Chromosome deletions
Chromosome substitution
Supernumerary chromosomes
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
Industry highlights Box 26.1 utilizing a dihaploid‐gamete selection strategy for tall fescue development
Introduction
Methods
Conclusions
References
26.12.1 Application of haploids in plant breeding
26.13 Anther culture
Applications
Limitations
26.13.1 Ovule/ovary culture
26.13.2 Haploids from wide crosses
26.13.3 Haploid breeding versus conventional methods
26.14 Doubled haploids
Industry highlights Box 20.2 haploids and doubled haploids: their generation and application in plant Breeding
What are haploids?
Advantages in the utilization of haploids
Generation of haploids and doubled haploids. Chromosome elimination
In vitro androgenesis
In vivo androgenesis
Induction of maternal haploids in maize
Generating doubled haploids
Application of haploids and doubled haploids in plant breeding
References
26.14.1 Key features
26.14.2 Applications
26.14.3 Procedure
Natural sources
Artificial sources
Advantages and disadvantages
Genetic issues
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
Section 10 Genetic molecular modifications in plant breeding
27 Breeding genetically modified crops. Purpose and expected outcomes
27.1 What is biotechnology?
27.2 Antisense technology
27.3 Restriction enzymes
27.4 Vectors
27.5 Categories of vectors by functions
27.5.1 Cloning vectors
27.5.2 Transcription vectors
27.5.3 Expression vectors
27.6 Cloning
27.7 Breeding genetically modified (GM) cultivars
Clearance
Conduct research
Hybridize (cross)
Backcross
Evaluation
Field testing
Commercialization
27.8 Engineering pest resistance
27.8.1 Engineering insect pest resistance (Bt)
27.8.2 Engineering herbicide resistance
Why engineer herbicide‐resistant crops?
Modes of action and herbicide resistance mechanisms
27.8.3 Concerns with the deployment of GM cultivars. Environmental impact
Pest resistance
27.9 Trends in adoption of GM cultivars
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
28 Genome editing and other modification technologies. Purpose and expected outcomes
28.1 General steps in genome editing
28.2 Types of editing systems
28.2.1 Site‐directed nuclease technologies
28.2.2 Meganucleases (homing endonucleases)
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. Part A
Part B
Pact C
29 Paradigm shifts in plantbreeding and other non‐GM technologies. Purpose and expected outcomes
29.1 The way breeders manipulate the plant genome
29.2 Paradigm shifts in plant breeding
29.2.1 Shifts in creation of novel variation
29.2.2 Selection criteria
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
29.8.1 Applications in plant breeding
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. Part A
Part B
Part C
Section 11 Computer‐aided applications in plant breeding
30 Bioinformatics, big data analytics, and computer simulations in plant breeding. Purpose and expected outcomes
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
Box 30.1 Industry highlights bioinformatics and its applicability in plant breeding
Applicability of bioinformatics through various databases. Databases for searches
Types of bioinformatics databases
Primary databases
Secondary databases
Specialized databases
Protein family databases
GenBank and sequence format
Retrieval of sequence information through basic alignment search tool (BLAST)
Sequence alignment for identification of variations within the sequence data
Phylogenomics
Different types of phylogenetic trees and uses
References
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
30.17.1 QU‐GENE
30.17.2 QU‐LinePlus
Key references and suggested reading
Internet resources
Outcomes Assessment. Part A
Part B
Part C
Section 12 Variety release process in plant breeding
31 Performance evaluation for crop cultivar release. Purpose and expected outcomes
31.1 Purpose of performance trials
31.2 Kinds of field trials
31.2.1 Breeder's trials
Researcher‐managed
Farmer‐managed
31.2.2 Official trial
Industry highlights Public release and registration of “prolina” soybean and nitrogen fixation research unit
31.3 Designing field trials
31.4 The role of the environment in field trials
31.4.1 Types of environmental variables
Predictable factors
Unpredictable factors
31.4.2 Scale
Microenvironment
Macroenvironment
31.5 Genotype × environment interaction (GEI)
31.5.1 What is GEI?
31.5.2 Classification of G × E interaction
31.5.3 Non‐crossover interaction
31.5.4 Crossover interaction
31.6 Models of G × E interaction
31.6.1 Additive main effects and multiplicative interaction model (AMMI)
31.6.2 Sites regression model (SREG) or GGE model
31.6.3 Partial least squares regression (PLS)
31.6.4 Factorial regression (FR)
31.6.5 Linear‐bilinear mixed models
31.7 Measurement of GEI using ANOVA
31.7.1 Analysis of variance (ANOVA)
31.7.2 Breeding implications of ANOVA results
31.8 Importance and Applications of GEI in Plant Breeding
31.9 Stability analysis models
31.9.1 General concepts
Conventional models
Regression coefficient model
31.9.2 Plot of means versus coefficient of variation
31.9.3 Nonparametric methods
31.10 Adaptation
31.11 Field plot technique in plant breeding
31.11.1 Sources of experimental error
Soil (Site) Variability
Tactics for reducing experimental error
31.11.2 Principles of experimental design
31.12 Field plot designs
31.12.1 Evaluating single plants. No design arrangement
Modifications
Use of experimental designs. Grid design
Honeycomb (hexagonal) design
31.12.2 Evaluating multiple plants. Unreplicated tests
Replicated tests
Complete block designs
Incomplete block designs
31.13 Materials, equipment, and machinery for field evaluation of genotypes
31.13.1 Materials
31.13.2 Equipment
Key references and suggested reading
Internet
Outcomes assessment. Part A
Part B
Part C
32 Seed certification and commercial seed release. Purpose and expected outcomes
32.1 The role of improved seed in agriculture
32.1.1 Yield gains
32.1.2 Seed market
32.1.3 Regulations in the seed industry
32.2 Role of the private sector in the seed industry. 32.2.1 Early history
32.2.2 The growth of 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
32.5.1 Classes of seed in a certification system
32.5.1.1 Breeder seed
32.5.1.2 Foundation seed
32.5.1.3 Registered seed
32.5.1.4 Certified seed
32.5.2 Maintaining genetic identity of the breeder seed. 32.5.2.1 Properties of the breeder seed
32.5.2.2 Causes of loss of genetic purity of seed
32.5.2.3 Prevention of loss of genetic purity
32.6 Concept of seed certification
32.7 The seed certification process
32.7.1 Application for certification
32.7.2 Source of seed
32.7.3 Site selection (land)
32.7.4 Management in the field
32.7.5 Field inspection
32.7.6 Harvesting and processing
32.8 Seed testing
32.9 Tagging commercial seed
32.10 International role in seed certification
Industry highlights 32.1 Plant breeding research at ICRISAT
Introduction
Breeding objectives
Breeding methods and techniques
Major accomplishments. Chickpea
Pigeonpea
Groundnut
Sorghum
Pearl millet
Finger millet
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. Part A
Part B
Part C
33 Regulatory andLegal Issues. Purpose and expected outcomes
33.1 The concept of intellectual property
33.2 Patents. 33.2.1 Definition
33.2.2 The importance of patents to society
33.2.3 What can be patented?
33.2.4 Types of patents
Utility patent
Design patent
Plant patent
33.2.5 National and international patents
33.2.6 Scope of protection of a patent
33.2.7 Criteria for patentability
33.2.8 Applying for a patent
33.2.9 Exploiting intellectual property
Assignment
License
Freedom of use
33.3 Patents in plant breeding and biotechnology: unique issues and challenges. 33.3.1 Patenting organisms
33.3.2 Patenting the hereditary material
33.3.3 Patenting proteins
33.3.4 Patenting products of nature
33.3.5 Moral issues in patenting
33.3.6 International issues in patenting
33.4 Protecting plant varieties
33.4.1 International efforts
Distinctness
Uniformity
Stability
Novelty
Scope of plant breeders' rights
Breeders' exemption
Essentially derived variety
Farmers' privilege
Territorial limitations on plant protection
33.4.2 US efforts
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
33.12.1 Tort liability versus regulatory approval
33.12.2 Damage to property. Trespass
Strict liability
Negligence
Private nuisance
33.12.3 Damage to person
33.12.4 Damage to economic interest (market)
33.13 Overview of the regulation of the biotechnology industry in the US
33.13.1 USDA‐APHIS
33.13.2 FDA
33.13.3 EPA
33.14 The concept of biopiracy
33.15 The impact of IPRs on plant breeding
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
Section 13 Societal issues in plant breeding
34 Value‐driven concepts and social concerns. Purpose and expected outcomes
34.1 Concepts of ethics, morals, and values
34.2 Evolution of social debates on science‐based issues
34.3 Ethics in plant breeding
34.3.1 The biotechnology debate
34.3.2 Plant biotechnology: ethical and value issues
34.4 Risk analysis of biotechnology
34.5 Genetic use restriction technologies
34.5.1 How the TPS works
34.5.2 The current status of GURTs
34.6 Public perceptions and fears about biotechnology
34.6.1 The techniques of biotechnology are alien, unnatural, and too radical
34.6.2 Genetic engineering is an exact science
34.6.3 Pesticide resistance in the agroecosystem as a result of the use of biotech crops is unavoidable
34.6.4 Biotechnology products are unnatural and unsafe
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
34.9.1 The issue of “naturalness”
34.9.2 Need for 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. Part A
Part B
Part C
35 International plant breeding efforts. Purpose and expected outcomes
35.1 International crop research centers
35.2 The CGIAR centers and their mission
35.2.1 Structural organization and mission
35.2.2 Location and mandate of the CGIAR centers
35.2.3 Research emphasis
35.2.4 The Alliance
35.2.5 Mandate crops
Wheat
Maize
Rice
Barley
Sorghum
Soybean
Potato
35.2.6 Selected accomplishments
35.2.7 Education, training, and technical assistance
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
35.5.1 Overview of world food issues
35.5.2 Barriers to commercializing biotechnology in developing countries
35.5.3 The role of international initiatives in biotechnology
35.6 Participatory plant breeding (PPB)
Industry highlight Box 35.1 An example of participatory plant breeding: barley at ICARDA
References
Other publications
35.6.1 Concept of centralized breeding
35.6.2 Decentralized‐participatory plant breeding
35.7 Conventional plant breeding versus decentralized‐participatory plant breeding
35.7.1 Key features of conventional breeding
Advantages
Disadvantages
35.7.2 Key features of decentralized‐participatory breeding
Advantages
Disadvantages
35.7.3 Efficiency of plant breeding programs
35.8 The Green Revolution
Industry highlight Box 35.2 Norman Ernest Borlaug: the man and his passion
References
35.8.1 Key strategies of the green revolution
35.9 The Green Revolution and the impact of international breeding efforts
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
Section 14 Breeding selected crops
36 Breeding wheat. Taxonomy
36.1 Economic importance
36.2 Origin and history
36.3 Adaptation
36.3.1 Winter wheat
36.3.2 Spring wheat
36.4 History of breeding in the US
36.5 Commercial wheat classes
36.5.1 Hard red winter wheat
36.5.2 Hard red spring wheat
36.5.3 Soft red winter wheat
36.5.4 White wheat
36.5.5 Durum wheat
36.6 Germplasm resources
36.7 Cytogenetics
36.8 Genetics
36.9 General botany
36.10 Reproductive biology. 36.10.1 Floral biology
36.10.2 Pollination
36.11 Common breeding methods
36.12 Establishing a breeding nursery. 36.12.1 Field nursery. Layout
Planting
36.12.2 Greenhouse nursery
36.13 Artificial pollination for hybridization. 36.13.1 Materials and equipment
36.13.2 Emasculation
36.13.3 Pollination
36.14 Natural pollination
36.15 Seed development
36.16 Breeding objectives
36.16.1 Yield potential
36.16.2 Yield stability
36.16.3 Agromorphological traits
36.16.4 Adaptation. Winter hardiness
Drought resistance
Aluminum tolerance
36.16.5 Disease resistance
Rusts
Smuts
Powdery mildew
36.16.6 Insect resistance. Hessian fly
Greenbug
36.16.7 End‐use quality
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
37 Breeding corn. Taxonomy
37.1 Economic importance
37.2 Origin and general history
37.3 Adaptation
37.4 History of corn breeding in the United States
Industry highlights Hybrid breeding in maize
Source breeding populations
Development of parental inbreds. Inbreeding and inbreeding depression
Breeding methods to develop inbreds
Breeding methodologies
Development of hybrids. Heterotic groups
Correlation between inbred and hybrids, and hybrid prediction
Hybrid testing and screening
Modern maize hybrid breeding
References
37.5 Types of corn
37.6 Germplasm resources
37.7 Cytogenetics
37.8 Genetics
37.9 General botany
37.10 Reproductive biology. 37.10.1 Floral morphology. Staminate flower
Pollen
Pistillate flower
Receptivity of the stigma
37.11 Genetic consequences of reproductive biology
37.12 Common breeding approaches
37.12.1 Hybrid corn production. Development of inbred lines
37.13 Establishing a breeding nursery
37.14 Other nurseries
37.15 Special environment
37.16 Artificial pollination for hybridization. 37.16.1 Materials and equipment
37.16.2 Preparing the female flower
37.16.3 Pollination
37.17 Natural pollination for hybridization
37.18 Common breeding objectives
37.18.1 Grain yield
37.18.2 Yield stability
37.18.3 Agromorphological traits. Lodging resistance
Resistance to ear dropping
Husk covering
Dry‐down
37.18.4 Adaptation. Early maturity
Drought resistance
Cold tolerance
37.18.5 Disease resistance
Seed rots and seedling blights
Root, stalk, and ear rots
Leaf blight or spots
Smuts
37.18.6 Insect resistance
Soil‐inhabiting insects
Leaf, stalk, and ear insects
Stored corn grain insects
37.18.7 Product quality
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
38 Breeding rice. Taxonomy
38.1 Economic importance
38.2 Origin and history
38.3 Adaptation
38.3.1 Rainfed lowland rice ecosystem
38.3.2 Upland rice ecosystem
38.3.3 Flood‐prone rice ecosystem
38.3.4 Irrigated rice ecosystem
38.3.5 Other classification
38.4 Commercial classes
38.5 Germplasm resources
Industry highlights Breeding rice
Introduction
Timeline for development of saber rice. 1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
References
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. 38.11.1 Field establishment
38.11.2 Greenhouse and growth chamber
38.11.3 Artificial pollination for hybridization. Materials and equipment
Preparation of the female flower
Pollination
Natural cross‐pollination
Seed development and harvesting
38.12 Common breeding objectives. 38.12.1 Grain yield
38.12.2 Grain quality
38.12.3 Disease resistance
38.12.4 Resistance to environmental stresses
Key references and suggested further reading
Outcomes assessment. Part A
Part B
Part C
39 Breeding sorghum. Taxonomy
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
Box 39–1 Industry highlights Sorghum breeding
Overview
Private and public research
Methodology of the TAES sorghum breeding program at College Station
References
39.13 Establishing a breeding nursery
39.14 Artificial pollination. 39.14.1 Equipment
39.14.2 Preparing the female
39.14.3 Pollination
39.15 Natural pollination
39.16 Seed development
39.17 Harvesting
39.18 Common breeding objectives. 39.18.1 Grain yield
39.18.2 Yield stability
39.18.3 Agromorphological traits. Lodging resistance
Short stature
39.18.4 Adaptation. Early maturity
Photoperiod insensitivity
Drought resistance
Tolerance of aluminum
39.18.5 Disease resistance
Rots
Blights
Smuts
Rust
Viral diseases
39.18.6 Insect resistance
Greenbug
Sorghum midge
Stalk borers
Shoot fly
39.18.7 Product quality
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
40 Breeding soybean. Taxonomy
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. 40.9.1 Floral morphology
40.9.2 Pollination
40.10 Common breeding methods
40.11 Establishing a field nursery. 40.11.1 Field layout
40.11.2 Greenhouse nursery
40.12 Artificial hybridization. 40.12.1 Equipment and materials
40.12.2 Emasculation
40.12.3 Artificial pollinations
40.13 Natural hybridization
40.14 Seed development
40.15 Harvesting
40.16 Breeding objectives. 40.16.1 Grain yield
40.16.2 Agromorphological traits. Lodging resistance
Shattering resistance
40.16.3 Adaptation. Maturity
Drought and other environmental stresses
Herbicide resistance
40.16.4 Disease resistance
Bacterial blight
Rots
Box 40‐1 Industry highlights estimating inheritance factors and developing cultivars for tolerance to charcoal rot in soybean
References
Viral disease
Nematodes
40.16.5 Insect resistance
40.16.6 Seed compositional traits and quality. Oil quality
Seed protein
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
41 Breeding peanut. Taxonomy
41.1 Economic importance
41.2 Origin and history
41.3 Market types
41.3.1 Runner
41.3.2 Virginia
41.3.3 Spanish
41.3.4 Valencia
41.4 Genetic resources
41.5 Cytogenetics
41.6 General botany
41.7 Reproductive biology. 41.7.1 Floral morphology
41.7.2 Pollination
41.8 Common breeding methods
41.9 Establishing a breeding nursery. 41.9.1 Greenhouse establishment
41.10 Artificial pollination. 41.10.1 Materials and equipment
41.10.2 Preparation of female plant
41.10.3 Pollination
41.10.4 Seed development and harvesting
41.11 Common breeding objectives
Breeding Peanut (Arachis hypogaea L.) and Root‐knot Nematode Resistance
The Program
Introgression
Literature cited
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
42 Breeding potato. Taxonomy
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. 42.9.1 Floral biology
42.9.2 Pollination
42.10 Common breeding methods
Box 42‐1 Industry highlights The breeding of potato
Evolution of the modern potato crop
Potato breeding and the need for new cultivars. Potato breeding
Need for new cultivars
Breeding finished cultivars. Parents and crossing
Clonal generations
Genetic knowledge and molecular marker‐assisted selection
Widening the genetic base for future potato breeding
References
42.11 Establishing a breeding nursery. 42.11.1 Field nursery
42.11.2 Greenhouse nursery
42.12 Artificial pollination for hybridization. 42.12.1 Materials and equipment
42.12.2 Emasculation
42.12.3 Pollination
42.13 Natural pollination
42.14 Seed development
42.15 Breeding objectives
42.15.1 Tuber yield
42.15.2 Adaptation
42.15.3 Insect resistance
42.15.4 Potato tuber quality improvement
Key references and suggested reading
Internet resources
Outcomes assessment. Part A
Part B
Part C
43 Breeding cotton. Taxonomy
43.1 Economic importance
43.2 Origin and history
43.3 Germplasm resources
43.4 Cytogenetics
43.5 Genetics
43.6 Cultivars
43.6.1 G. hirsutum
43.6.2 G. barbadense
43.6.3 G. aboreum
43.6.4 G. herbaceum
43.7 American upland cotton
43.8 General botany
Box 43.1 Industry highlights Cotton breeding
Breeding program
Transgene introgression program
Program successes
Future
Further Reading
43.9 Reproductive biology. 43.9.1 Floral biology
43.9.2 Pollination
43.10 Common breeding methods
43.11 Establishing a breeding nursery
43.12 Artificial crossing. 43.12.1 Materials and equipment
43.12.2 Emasculation
43.12.3 Pollination
43.13 Natural pollination
43.14 Seed development
43.15 Breeding objectives
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
44 Breeding tomato. Taxonomy
44.1 Economic importance
44.2 Origin and history
44.3 Commercial market classes
44.3.1 Processing tomato
44.3.2 Fresh market tomato
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
Box 44.1 Industry highlights The breeding of tomato
Taxonomy, origin, and domestication
Breeding. Heirloom and hybrid
Hybrid breeding
Classification of tomato cultivars
Breeding goals
Exploitation of wild tomato relatives in breeding
Tomato, a model plant for genetics and genomics
References
44.11 Common breeding methods. 44.11.1 Use of wild germplasm
44.11.2 Transgenic tomato breeding (the FlavrSavr tomato)
44.11.3 Breeding hybrid tomato
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
S1 Plant cellular organization and genetic structure: an overview. S1.1 The unit of organization of living things
S1.2 Levels of eukaryotic organization
S1.3 The plant cell and tissue
S1.4 Plant genome
S1.5 Chromosomes and nuclear division
S1.5.1 Mitosis
S1.5.2 Meiosis
S1.6 Genetic linkage and its implications
S1.7 Chromosome mapping
S1.8 Penetrance and expressivity
S1.9 Nucleic acids: structure and function
S1.9.1 Structure of DNA
S1.9.2 Structure of RNA
Messenger RNA structure
Transfer RNA (tRNA) structure
Ribosomal structure
S1.10 Central dogma of molecular biology
S1.11 Expression of genetic information
S1.11.1 The genetic code
S1.11.2 Transcription: RNA synthesis
S1.11.3 Translation: protein synthesis
S1.12 Protein structure
S1.13 Regulation of gene expression
S1.14 Synteny and plant breeding
b
b
S2 Common statistical methods in plantbreeding. S2.1 Role of statistics in plant breeding
S2.2 Population versus sample
S2.3 The issue of causality
S2.4 Statistical hypothesis
S2.5 Concept of statistical error
S2.6 Principles of experimental design
S2.7 Probability
S2.8 Measures of central tendency
S2.9 Measures of dispersion
S2.10 Standard deviation
S2.11 The normal distribution
S2.12 Coefficient of variation
S2.13 Standard error of the mean
S2.14 Simple linear correlation
S2.15 Simple linear regression
S2.16 Chi‐square test
S2.17 t‐test
S2.18 Analysis of variance
S2.19 Multivariate statistics in plant breeding
Industry highlights Box S2.1Multivariate methods: applications in plant genetics, breeding, and agronomy
Introduction
Research questions of multivariate nature
Classification of MVAs
Exploratory MVAs. Visual classification and analysis
Cluster analysis (CA )
Factor analysis (FA)
Principal components analysis (PCA)
Multidimensional scaling (MDS)
Decisional MVAs. Canonical correlation
Multiple correspondence analysis (MCA)
Canonical discriminant analysis (CDA)
Multivariate variance (MANOVA) and covariance (MANCOVA) analysis
Partial least squares regression (PLSR)
Structural equation models (SEM)
References
S2.19.1 Factor analysis
S2.19.2 Principal component analysis
S2.19.3 Discriminant analysis
S2.19.4 Cluster analysis
S2.19.5 Canonical correlation analysis
S2.20 Path analysis
Key references and suggested reading
Outcomes assessment. Part A
Part B
Part C
Glossary of terms
Index
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