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