Genetics, Genomics and Breeding of Bamboos

Cover
Series Page
Title Page
Copyright Page
Preface to the Series
Preface
Foreword
Table of Contents
Unit 1
1. Introduction
2. Taxonomy, Diversity, Distribution, and Use of Bamboos: Special Importance to Selected Four Northeast States of India
2.1 Introduction
2.2 Taxonomy
2.3 Distribution and Diversity
2.3.1 Diversity of Edible Bamboo Species
2.3.2 Diversity of Commercial Bamboo Species
2.4 Area and Resource Stock
2.5 Uses of Bamboo
2.5.1 Bamboo as Food
2.5.2 Bamboo in Medicinal, Cosmetic, and Agricultural Uses
2.5.3 Bamboo in Environmental Conservation and Carbon Sequestration
2.6 Conclusion
3. Germplasm Resources of Bamboos
3.1 Introduction
3.2 Bamboo Gardens and Their Coordinating Organizations
3.3 Botanic Gardens having Living Bamboo Collections
3.4 Earliest Living Bamboo Collections
3.5 Largest Living Bamboo Collections
3.6 Bamboos Conserved in Botanic Gardens and Bambuseta
3.7 Dominant Bamboo Genera under Living Collections
3.8 What are the Benefits of Bamboo Conservation?
3.9 How Should a Modern Bambusetum Function?
3.10 Seed and Rhizome Banks
3.11 Summary and Conclusion
4. Genetic Diversity Assessment and Molecular Markers in Bamboos
4.1 Introduction
4.2 Molecular Markers Used to Infer Phylogenetic Relationships in Bamboos
4.2.1 Bambusoideae
4.2.2 Arundinarieae
4.2.3 Bambuseae
4.2.4 Paleotropical Woody Bamboos
4.2.5 Neotropical Woody Bamboos
4.2.6 Olyreae
4.3 Molecular Markers Used to Analyze Genetic Diversity in Bamboos
4.3.1 AFLP Markers
4.3.2 ISSR Markers
4.3.3 RAPD Markers
4.3.4 SSR Markers
4.3.5 SNP (Single Nucleotide Polymorphism) Markers
4.4 Transcriptomes
5. Genetic Diversity Assessment and Molecular Markers in African Bamboos
5.1 Introduction
5.2 Bamboo Cytogenetics, Ploidy Level, and Genome Size
5.3 Geographical Distribution and Area Coverage of Bamboo
5.4 Importance of Genetic Diversity and Population Structure Study
5.5 Molecular Markers Used for the Genetic Diversity and Population Structure Study of Bamboos Found in Africa
5.6 Simple Sequence Repeat (SSR) Markers for the Genetic Diversity and Population Structure Study of Arundinaria alpina (K. Schum)
5.7 Inter Simple Sequence Repeat (ISSR) Markers for the Genetic Diversity and Population Structure Study of Oxytenanthera abyssinica (A. Rich.)
5.8 Chloroplast (cpDNA) Genes for the Population Genetic Diversity and Structure Study of Oxytenanthera abyssinica (A. Rich.)
5.9 Conclusions
Unit 2
6. Breeding System, Molecular Genetic Map, and Artificial Hybridization in Woody Bamboos
6.1 Introduction
6.2 The Breeding System of Woody Bamboo
6.2.1 Flowering and Fruiting Phenomena of Woody Bamboos
6.2.1.1 Flowering Cycle
6.2.1.2 Flowering Types
6.2.2 Breeding System of Woody Bamboos
6.2.2.1 Inflorescence
6.2.2.2 Floret
6.2.2.3 Pollen
6.2.2.4 Pollination
6.2.2.5 Mating System
6.2.2.6 Fruits or Seeds
6.2.2.7 Seeds Setting Rate
6.3 Genetic Map of Woody Bamboo
6.4 Artificial Hybridization and Application to Woody Bamboo
6.5 Research Prospects
7. Circadian Clock Genes and their Role in Bamboo Flowering
7.1 Introduction
7.2 Bamboo Flowering: Types and their Ecological Impact
7.3 Photoperiodism in Flowering: What is Known about Bamboo?
7.4 Early Background on Important Photoreceptors Involved in Flowering
7.4.1 Red Light Photoreceptors
7.4.2 Blue Light Photoreceptors
7.5 Early Background on Molecular Mechanisms Controlling the Circadian Clock Regulation of Flowering
7.5.1 The Central Loop
7.5.2 The Morning Loop
7.5.3 The Evening Loop
7.6 LHY/CCA1, TOC1/PRR, ZTL, GI Gene Homologs Identified from Diverse Angiosperm Plants
7.7 Circadian Clock in Bamboo Flowering
7.8 Circadian Clock Integrator Gene CONSTANS (CO) in Bamboo and other Plants
7.9 Transcriptional Regulation of CO: Model Plants vs. Bamboo
7.10 Post Translational Regulation of CO: What is Happening in Bamboo?
7.11 Conclusions and Future Perspective
8. Genetics of Abiotic Stress Resistance in Bamboos
8.1 Introduction
8.2 Bamboo and the Environment
8.3 Bamboo Genome
8.4 Development of Abiotic Stress Resistance in Bamboo
8.5 Stress and Bamboo Shoot Organogenesis
8.6 Abiotic Stresses
8.6.1 Drought and High Temperature
8.6.2 Salinity
8.6.3 Cold/Chilling
8.7 Transgenic Approaches for Enhancing Abiotic Stress Tolerance in Bamboos
8.8 Role of Transcription Factors in Abiotic Stress Response
8.9 Effect of Abiotic Stresses on Physiology of Transgenic Lines with Bamboo Originated Genes
8.10 Conclusions
9. Current Understanding on Major Bamboo Diseases, Pathogenicity, and Resistance Genes
9.1 Introduction
9.2 Distribution of Major Bamboo Diseases and Pests in Asia
9.3 Bamboo Diseases Caused by Fungi
9.4 Bamboo Diseases Caused by Bacteria
9.5 Bamboo Diseases Caused by Virus
9.6 Bamboo Diseases Caused by Insects
9.7 Physical and Chemical Methods of Bamboo Preservation
9.8 Biochemical and Genetic Defence in Bamboo
9.9 The Bamboo Resistance (R)-gene Family and their Potential in Marker Assisted Selection
9.10 Conclusion and Future Perspective
10. Genome Annotation, In silico Tools and Databases with Special Reference to Moso Bamboo
10.1 Introduction
10.2 Genome Annotation
10.2.1 Evaluation of Genome Assembly Quality
10.2.2 Genome Structure Annotation
10.2.2.1 Repetition Sequence Identification
10.2.2.2 Annotation of the Coding Gene
10.2.2.3 Release of Data
10.2.3 Annotation of Gene Functions
10.3 Moso Bamboo Genome Annotation
11. Functional Genomics Study of Bamboo Shoot and Rhizome Development An Overview
11.1 Introduction
11.2 The Rapid Growth of Bamboo Culms
11.3 The Characteristics of Rapid Growth in Bamboos
11.3.1 Rapid-growth Stages
11.3.2 Cell Division or Cell Elongation
11.3.3 Dynamics of Cell Division and Cell Elongation
11.4 Transcriptional Regulation of Rapid Growth in Bamboos
11.4.1 Auxin and BR Responses
11.4.2 Hormones in SAM Region
11.4.3 Crosstalk Between Hormones
11.4.4 Transcription Factors
11.4.5 Crosstalk Between TF and Hormones
11.5 Post-transcriptional Regulation of Rapid Growth in Bamboos
11.5.1 Kinase
11.5.2 Small RNAs
11.5.3 Alternative Splicing, cis-NATs, and Circular RNAs
11.6 Rhizome Development of Bamboos
11.6.1 Characteristics of Bamboo Rhizome
11.6.2 Transcriptional and Post-transcriptional Regulation of Rhizome Development
11.6.2.1 Transcriptional Regulation
11.6.2.2 Post-transcriptional Regulation
11.7 Nitrate Signaling in Bamboo Development
Unit 3
12. In vitro Propagation and Genetic Transformation in Bamboo: Present Status and Future Prospective
12.1 Introduction
12.2 Micropropagation
12.2.1 Explant Selection and Disinfection
12.2.2 Nutrient Medium
12.2.3 Regeneration Process
12.2.3.1 Direct Organogenesis
12.2.3.2 Indirect Organogenesis
12.2.4 Somatic Embryogenesis
12.2.5 Acclimatization and Field Transfer
12.3 Genetic Transformation and Editing of the Genome in Bamboos
12.4 Conclusion and Future Prospective
13. Current Status of Bamboo Tissue Culture and Genetic Transformation Technology
13.1 Introduction
13.2 Propagation
13.2.1 Vegetative Propagation
13.2.2 Micropropagation
13.3 Limitations
13.3.1 Tissue Browning
13.3.2 Microbial Contamination
13.4 Conventional Strategies for Control of Contamination
13.5 Latent Contamination
13.6 Systemic Acquired Resistance to Control Latent Contamination
13.7 Rooting
13.8 In vitro Rhizome Induction
13.9 In vitro Flowering
13.10 Application of Modern Technology
13.11 Potential for Photoautotrophic Micropropagation (PAM)
13.12 Liquid Cultures/Bioreactors
13.13 Genetic Transformation for Bamboo Improvement
13.14 Conclusions
14. CRISPR/Cas Based Genome Editing and its Possible Implication in Bamboo Research
14.1 Introduction
14.2 Different Genome Editing Techniques and Advantages of CRISPR/Cas9
14.2.1 Zinc Finger Nuclease (ZFN)
14.2.2 Transcription Activator-like Effector Nucleases (TALEN)
14.2.3 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Protein (CRISPR/Cas)
14.3 Different Methods in CRISPR-mediated Gene Editing
14.3.1 Base Editing through CRISPR
14.3.2 Prime Editing
14.3.3 Gene Knock-out using CRISPR
14.3.4 Gene Knock-in using CRISPR
14.3.5 Transcriptional Control Models
14.3.6 CRISPR interference (CRISPRi)
14.3.7 CRISPR activation (CRISPRa)
14.4 Applications of CRISPR/Cas System in Bamboo Improvement
14.5 Challenges in Employing CRISPR/Cas System in Bamboo
14.6 Conclusion
15. Genome Editing and Future Scope in Bamboos
15.1 Introduction
15.1.1 ZFNs
15.1.2 TALENs
15.1.3 CRISPR/Cas
15.2 Mechanism and Classifications of CRISPR/Cas System
15.3 Characterization of Various Genes by CRISPR/Cas9 System
15.4 Genome Editing and Future Scope in Bamboo
16. Production of Quality Planting Material in Bamboo
16.1 Introduction
16.2 Flowering Behavior of Bamboo
16.3 Bamboo Propagation
16.3.1 Natural Propagation in Bamboo
16.3.2 Vegetative Propagation Methods
16.3.3 Micropropagation
16.4 Limitations to Conventional Breeding in Bamboo
16.5 Genetic Improvement in Bamboo
16.6 Hurdles in Species and Clonal Identification
16.7 DNA Barcoding
16.8 DNA Fingerprinting
16.9 Modern Analytical Techniques
16.10 Certification of Quality Planting Material in Bamboo
16.11 Identification of Species and Origin of Planting Material
16.12 Large Scale Multiplication of Planting Material
16.13 Traceability
16.14 Morphological and Plant Health Indicators of Planting Stock Quality
16.15 Accreditation of Bamboo Nurseries
16.15.1 Criteria for Accreditation of Bamboo Nurseries
16.16 Quality Parameters
16.17 Conclusions
Index