Smart Plant Breeding for Field Crops in Post-genomics Era

Preface
Book Summary
Contents
Editors and Contributors
1: The Role of Epigenetic Transcriptional Regulation in Brassica Vegetables: A Potential Resource for Epigenetic Breeding
1.1 Introduction
1.2 DNA Methylation
1.3 Histone Modification
1.4 Epigenome Analysis
1.4.1 Whole Genome Bisulfite Sequencing (WGBS)
1.4.2 Chromatin Immunoprecipitation Sequencing (ChIP-seq)
1.4.3 Epigenetic States in Regions Encoding Long Noncoding RNAs
1.4.4 Epigenetic States in Transposable Elements
1.5 Epigenetic Regulation in Vernalization of Brassica Vegetables
1.6 Epigenetic Regulation Under Stress
1.7 Epigenetics in Hybrid Vigor/Heterosis
1.8 Dominance Relationship of S Haplotypes in Pollen Is Caused by De Novo DNA Methylation in the SP11 Promoter Region of a Rec...
1.9 A Perspective of Epigenetic Breeding in Brassica Vegetables
References
2: Melon (Cucumis melo L.): Genomics and Breeding
2.1 Introduction
2.2 Doubled-Haploid Technology
2.3 Breeding in the Genomics Era
2.3.1 Genomic Resources
2.3.2 The Melon Genome
2.3.3 Genomic Tools for Melon Breeding
2.3.4 Genomic Selection
2.3.4.1 MAS and FMs for Precision Breeding
2.3.4.2 R-Genes
2.3.4.3 Trait Mapping and Discovery of Candidate Genes
Disease Resistance
Fruit Quality
2.3.5 Genome Editing
2.3.5.1 Tilling
2.3.5.2 CRISPR/Cas9
2.4 Conclusion
References
3: Ash Gourd Genomics: Achievements, Challenges and Future Perspectives
3.1 Introduction
3.2 The Ash Gourd Genome
3.3 Beyond Ash Gourd to Family Cucurbitaceae
3.4 Molecular Markers in Ash Gourd Breeding
3.5 Gene and QTL Mapping
3.6 Transcriptomics in Ash Gourd
3.7 Role of Genomics in Detection of Viral Diseases
3.8 Summary and Future Perspectives
References
4: Understanding the Genetics and Genomics of Vegetable Grafting to Ensure Yield Stability
4.1 Introduction
4.2 Grafting, Its Purpose, Historical Background to Current Status
4.3 Genetic Basis of Vegetable Grafting
4.4 Crop Improvement via Vegetable Grafting
4.5 Epigenetics Basis of Vegetable Grafting
4.6 Methods of Vegetable Grafting
4.6.1 Cleft Grafting
4.6.2 Tongue Approach/Approach Grafting
4.6.3 Hole Insertion/Top Insertion Grafting
4.6.4 One Cotyledon/Slant/Splice Grafting
4.6.5 Pin Grafting
4.7 Diverse Applications of Vegetable Grafting
4.7.1 Grafting Improves Biotic Stresses
4.7.1.1 Vegetable Grafting to Induce Resistance Against Fungal Pathogens
4.7.1.2 Vegetable Grafting to Induce Resistance Against Bacteria Pathogens
4.7.1.3 Vegetable Grafting to Induce Résistance Against Nematode
4.7.1.4 Vegetable Grafting to Induce Resistance Against Virus
4.7.2 Grafting Improves Abiotic Stresses
4.7.3 Grafting Improving Yield Stability
4.7.4 Improving the Fruit Quality
4.8 Problems Associated with Vegetable Grafting
4.9 Conclusion and Future Prospects
References
5: Biotechnological Implications in Tomato for Drought Stress Tolerance
5.1 Introduction
5.2 Drought Stress Responses of Tomato
5.3 Molecular Mechanisms of Drought Tolerance in Tomato
5.4 Genome-Editing Approaches in Tomato for Drought Tolerance
5.5 Applications of Biotechnological Tool for Tomato Improvement
5.6 Tomato Genomics Approaches for Drought Stress Tolerance
5.7 Transgenic Tomato for Drought Tolerance
5.8 Conclusion
References
6: Spinach (Spinacia oleracea L.) Breeding: From Classical to Genomics-Centric Approach
6.1 Introduction
6.2 Botanical Overview of the Genus Spinacia
6.3 Gene Pool and Genetic Resources of the Crop
6.4 Origin and Genomic Basis of Spinach Domestication
6.5 Genomic Resources of Spinach
6.6 Genetics and Epigenetic Regulation on Flower-Sex Expression
6.7 Genomics-aided Breeding for Quality Traits and Stress Resistance
6.7.1 Breeding for Improvement of Quality Traits
6.7.2 Breeding for Biotic Stress Resistance
6.7.2.1 Downy Mildew
6.7.2.2 White Rust (WR)
6.7.2.3 Leaf Spot
6.7.2.4 Anthracnose
6.7.2.5 Wilt
6.7.2.6 Leaf Miner
6.7.3 Breeding for Abiotic Stress Resistance
6.8 Transcriptomes-Based Approach for Functional Characterization of Genes
6.9 Future Prospects
References
7: Impact of Biotic and Abiotic Stresses on Onion Production: Potential Mitigation Approaches in Modern Era
7.1 Introduction
7.2 Climate Change and Overview of Major Biotic and Abiotic Stresses
7.3 Biotic Stress Factors Affecting Onion Growth
7.3.1 Onion Thrips (Thrips tabaci)
7.3.2 Leek Moth (Acrolepiopsis assectella)
7.3.3 Onion Maggot (Delia antiqua)
7.3.4 Weeds
7.4 Abiotic Stress Factors Affecting Onion Growth
7.4.1 Physio-biochemical Changes in Onion
7.4.2 Abiotic Stresses and Photosynthesis
7.4.3 Production of Oxidative Stress
7.4.4 Role of Antioxidant Enzymes for ROS Mitigation
7.5 Molecular Approaches for Stress Tolerance in Onion
7.5.1 Stress Signaling and Positive Role of Sensors
7.5.2 Role of Transcription Factors
7.5.3 Role of Transporters
7.6 Modern Plant Breeding Approaches in Onion
7.7 Potential of Smart Agriculture in Onion Production
References
8: Advances in Summer Squash (Cucurbita pepo L.) Molecular Breeding Strategies
8.1 Introduction
8.2 Origin and Distribution
8.3 Botanical and Distribution
8.4 Economic Importance, Uses and Health Benefits
8.5 Photochemistry
8.6 Nutritional and Genetic Studies
8.7 Cultivation and Conventional Breeding
8.7.1 Recent Cultivation Procedures of the Summer Squash
8.7.2 Current Agricultural Challenges
8.7.3 Tolerance for Environmental Stress
8.7.4 Genetic Improvement Objectives
8.8 Germplasm Diversity and Conservation
8.8.1 Plant Germplasm Conservation
8.8.2 In-situ Conservation
8.8.3 Ex-situ Preservation
8.8.4 Cryopreservation
8.8.5 Cytogenetics
8.9 Traditional Breeding of Summer Squash
8.9.1 Inbreeding Depression and Selection
8.9.2 Heritability
8.9.3 Genotypic and Phenotypic Correlation
8.10 Molecular Breeding
8.10.1 SDS-PAGE Electrophoresis
8.10.2 Molecular Marker-assisted Breeding
8.10.3 Genomic Resources
8.11 Tissue Culture Applications
8.12 Genetic Engineering and Gene Editing
8.13 Mutation Breeding in Summer Squash
8.13.1 Conventional Mutagenesis (Seeds)
8.13.2 Enhanced Traits and Improved Cultivars
8.14 Hybridization
8.14.1 Conventional Hybridization
8.14.2 Heterosis and Hybrid Vigor
8.14.3 Genetic Parameters and Nature of Gene Action
8.14.3.1 Complete Diallel Mating Design
8.14.3.2 Half Diallel Mating Design
8.14.3.3 Factorial (Line x Tester) Mating Design
8.14.3.4 Homogeneity Test
8.15 Conclusions and Prospects
References
9: Enhancing Spinacia oleracea L. Breeding in the Post Genomics Era
9.1 Introduction
9.1.1 Taxonomy
9.1.2 Origin and Distribution
9.1.3 Spinach Nutritional Value
9.1.4 Primary and Secondary Metabolites
9.2 Pharmacological Activities
9.2.1 Protection Against Gamma Radiation
9.2.2 Antioxidant Activity
9.2.3 Hepatoprotective Activity
9.2.4 Anticancer Activity
9.3 Cytogenetics
9.4 Traditional Breeding
9.4.1 Spinach Breeding History
9.4.2 Crop Breeding
9.4.3 Methodologies and Limitations of Traditional Breeding
9.4.4 Examples for Breeding
9.5 Breeding and Climate
9.6 Molecular Breeding
9.6.1 Molecular Marker-Assisted Breeding
9.6.2 Functional Genomics
9.6.3 Quantitative Trait Locus (QTL)
9.7 Bioinformatics and Gene Bank
9.8 Tissue Culture
9.9 Conclusions
Appendix 9.1: Genetic Variability in Spinach
References
10: Breeding Strategies of Beetroot and a Future Vision in the Post-genomic Era´
10.1 Introduction
10.1.1 Taxonomy, Origin and Distribution
10.1.2 Beetroot Nutritional Value and metabolites
10.2 Pharmacological Activities
10.3 Cytogenetics
10.4 Traditional Breeding
10.4.1 Beetroot Breeding History
10.4.2 Crop Breeding
10.4.3 Methodologies and Limitations of Traditional Breeding
10.4.4 Examples for Breeding (Domestication and Selection)
10.5 Breeding and Climate
10.6 Molecular Breeding
10.6.1 Molecular Marker-Assisted Breeding and Quantitative Trait Locus
10.7 Bioinformatics and Gene Bank
10.8 Tissue Culture
10.9 Conclusions
References
11: Advances in Lettuce (Lactuca spp.) Molecular Breeding Strategies
11.1 Introduction
11.2 Origin, Classification and Distribution
11.3 Economic Importance
11.4 Genetic Diversity and Conservation
11.4.1 Genetic Diversity
11.5 Conventional Breeding
11.5.1 Improvement Strategies
11.5.2 Conventional Breeding Methods and Limitations
11.5.3 Biotechnology Role
11.6 Molecular Breeding
11.6.1 Marker-Assisted Selection
11.6.2 Functional Genomics
11.6.3 Bioinformatics
11.7 Genetic Engineering and Gene Editing
11.7.1 Improved Methods and Features
11.7.2 Genetically Modified Lettuce Varieties
11.8 Spread of Mutation Breeding
11.8.1 Traditional Mutagenesis
11.8.2 Induced Mutagenesis In Vitro
11.8.3 Mutation Molecular Analysis
11.8.4 Improved Traits and Varieties
11.9 Hybridization
11.9.1 Classical Hybridization
11.9.2 Somatic Hybridization
11.9.3 Hybrid Varieties
11.10 Conclusion and Prospects
References
12: Integrated Use of Molecular and Omics Approaches for Breeding High Yield and Stress Resistance Chili Peppers
12.1 Introduction
12.2 Economic Importance of Capsicum
12.2.1 Unique Properties of Chili and Their Economic and Pharmaceutical Uses
12.3 Diversity of Capsicum Species
12.3.1 Morphological and Genetic Diversity Among Different Capsicum Species
12.3.2 Characterization of Different Capsicum Species Based on Metabolic Diversity
12.4 Development of Molecular Markers in Capsicum
12.5 Development of Genetic Maps in Capsicum
12.6 QTL Mapping for Economically Important Traits
12.6.1 Plant Architecture
12.6.2 Fruit-Related Traits
12.6.2.1 Fruit Morphology
12.6.3 Pungency
12.6.4 Disease Resistance
12.7 Genome Sequencing and Identification of Genes/Genetic Loci Governing Important Traits
12.8 Application of Molecular and Omics Approaches for Breeding High Yielding and Stress Resistant Chili Peppers
12.8.1 Transcriptomic Analysis to Identify Gene(s) for Stress Resilient Capsicum Breeding
12.8.2 Sequencing of Non-coding RNAs in Capsicum
12.8.3 Epigenomic or Whole Genome Bisulfite Sequencing
12.8.4 Proteomics
12.9 Candidate Genes for Capsicum Breeding
12.10 Breeding for Stress Resistance in Capsicum
12.10.1 Biotic Stress Resistance
12.10.2 Abiotic Stress Resistance
12.10.2.1 Temperature Stress
12.10.2.2 Water Stress
12.10.2.3 Salinity Stress
12.11 Genetic Engineering for Improvement of Capsicum Crop
12.12 Capsicum Genomic Database Resources
12.13 Conclusions and Future Perspectives
References
13: Smart Plant Breeding for Potato in the Post-genomics Era
13.1 Introduction
13.2 VIGS
13.3 RNAi
13.4 SIGS
13.5 Mutagenesis
13.6 TILLING
13.7 Genome Editing
13.7.1 ZFNs
13.7.2 TALENs
13.7.3 CRISPR
13.8 Activation Tagging
13.9 Conclusion and Future Prospects
References
14: Current Overview of Breeding and Genomic Studies of White Button Mushroom (Agaricus bisporus)
14.1 Introduction
14.2 Genome Sequencing of Agaricus bisporus
14.3 Expression of Genes and Their Linkage with White Button Mushroom
14.4 Pangenome Genes of Agaricus bisporus
14.5 Gene Editing in Agaricus bisporus
14.6 Molecular Markers Developed from Genome Sequences
14.7 Conclusion
References
15: Insight into Carrot Carotenoids in Post-genomic World for Higher Nutrition
15.1 Introduction
15.2 Understanding Carotenoid Biosynthetic Pathway in Carrot
15.3 Factors Influencing Carotenoid Profile in Carrot
15.4 Genetics and Mapping of Carotenoids
15.4.1 Fate of Genome Editing in Carrot Carotenoids
15.5 Conclusion and Future Perspectives
References
16: Advances in Potato Breeding for Abiotic Stress Tolerance
16.1 Research on Salt and Alkali-Tolerant Breeding of Potato
16.1.1 Overview
16.2 Salt and Alkali Resistance Evaluation
16.3 Physiological Response to Saline Alkali Stress
16.3.1 Affecting Endogenous Hormones
16.3.2 Interference Ion Steady State
16.3.3 Causing Osmotic Stress
16.3.4 Weakening Photosynthesis
16.3.5 Leading to oxidative stress
16.4 Salt Tolerance Gene
16.5 Methods of Improving Salt and Alkaline Tolerance of Potato
16.5.1 Using Plant Growth-Promoting Rhizobacteria (PGPR)
16.5.2 Application of Exogenous Substances
16.6 Research on Drought-Tolerant Breeding of Potato
16.6.1 Overview
16.7 Drought Tolerance Evaluation
16.7.1 Morphological Yield Index
16.7.2 Physiological and Biochemical Indexes
16.7.3 Comprehensive Index (Membership Function Method)
16.8 Physiological Response to Drought Stress
16.9 Drought Tolerance Gene
16.10 Cold-Tolerant Breeding of Potato
16.10.1 Overview
16.10.2 Cold Resistance Evaluation
16.10.2.1 Identification Method
16.10.2.2 Cold-Tolerant Potato Varieties
16.10.2.3 Physiological Response to Low-Temperature Stress
16.10.2.4 Cold Tolerance Gene
16.11 Heavy Metal Tolerance Breeding of Potato
16.11.1 Overview
16.11.2 Evaluation of Heavy Metal Resistance
16.11.3 Physiological Response to Heavy Metal Stress
16.11.4 Heavy Metal Tolerance Gene
References
17: Genomics-Assisted Breeding for Abiotic Stress in Pisum Crop
17.1 Introduction
17.2 Genomics-Assisted Breeding in Crops
17.3 Germplasm Selection and Enhancement
17.4 Why GWAS (Genome-Wide Association Mapping)?
17.5 QTL Mapping for Abiotic Stress in Pisum
17.6 Importance and Future Perspectives of QTL Mapping in Various Crops
17.7 GWAS for Abiotic Stress in Pisum
17.8 Genomic Selection
17.9 Conclusion
References