Cotton Breeding and Biotechnology: Challenges and Opportunities

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Foreword
Editors
List of Contributors
Chapter 1: Role of Breeding and Biotechnology in Sustainable Cotton Production
	1.1 Introduction
	1.2 Challenges to Sustainable Cotton Production
	1.3 Genetic Improvement of Cotton through Breeding
	1.4 Genetic Improvement of Cotton through Biotechnology
	1.5 Genetic Improvement against Biotic Stress
	1.6 Genetic Improvement against Abiotic Stress
	1.7 Genetic Improvement for Fiber Yield and Quality
	1.8 Future Perspectives
	Bibliography
Chapter 2: Cotton Genetics and Genomics
	2.1 Introduction
	2.2 Evolution and History of Cotton Genus
	2.3 Worldwide Gene Pool of Gossypium and Its Improvement
	2.4 Cotton Genetic and Genomics Resources
	2.5 The Gossypium Transcriptomics
	2.6 Role of Genetics and Genomics in Cotton Improvement
	2.7 Summary
	References
Chapter 3: Conventional Breeding of Cotton
	3.1 Introduction
	3.2 Selection
		3.2.1 Criteria for Selection in a Cotton-Breeding Program
		3.2.2 Mass Selection
		3.2.3 Progeny Selection
	3.3 Hybridization
		3.3.1 Intraspecific Hybrids
		3.3.2 Interspecific Hybrid
			3.3.2.1 Field Techniques for Interspecific Hybrid
	3.4 Pedigree Method
	3.5 Backcrossing Method
	3.6 Bulk Method
	3.7 Multiple Cross or Composite Cross
	3.8 Single Seed Descent (SSD)
	3.9 Mutation Breeding in Cotton
	3.10 Summary
	References
Chapter 4: Molecular Cotton Breeding
	4.1 Introduction
		4.1.1 Classical Breeding Methods and Their Limitations
	4.2 Marker-Assisted Breeding (MAS)
		4.2.1 Restriction Fragment Length Polymorphism (RFLP)
		4.2.2 Random Amplified Polymorphic DNAs (RAPDs)
		4.2.3 Amplified Fragment Length Polymorphism (AFLP)
		4.2.4 Sequence-Characterized Amplified Region (SCAR)
		4.2.5 Simple Sequence Repeat (SSR)
		4.2.6 Inter-Simple Sequence Repeat (ISSR)
		4.2.7 Sequence-Tagged Sites (STS)
		4.2.8 Expressed Sequence Tags (ESTs)
		4.2.9 Cleaved Amplified Polymorphic Sequences (CAPS) and Derived Cleaved Amplified Polymorphic Sequences (dCAPS)
		4.2.10 Kompetitive Allele-Specific PCR Markers (Gel-Free Markers)
		4.2.11 Single Nucleotide Polymorphism (SNP)
	4.3 Genotyping by Sequencing (GBS)
	4.4 Targeting-Induced Local Lesions in Genomes (TILLING)
	4.5 Genome Editing for Cotton Breeding
	4.6 Conclusions
	Bibliography
Chapter 5: Gene Mapping in Cotton
	5.1 Introduction
	5.2 Genome Evolution of Cotton
	5.3 Genetic Diversity Estimation in Cotton
		5.3.1 Cotton in the Era of Genomics
		5.3.2 Population Development in Cotton for Genetic Mapping
		5.3.3 Association Mapping and Its Applications in Cotton
		5.3.4 Cotton Genome Scan for Different Quantitative Traits Loci (QTLs) Through Genetic Mapping
	5.4 Conclusion
	References
Chapter 6: Functional Genomics in Cotton
	6.1 Introduction
	6.2 Mutagenesis in Cotton
	6.3 Use of Physical and Chemical Mutagens
	6.4 TILLING and RNAi for Functional Genomic Studies
	6.5 Genetic Transformation in Cotton
	6.6 Modern Tools of Functional Genomics in Cotton
	6.7 Concluding Remarks
	Bibliography
Chapter 7: Cotton Transformation and Regeneration
	7.1 Introduction
	7.2 Tissue Culture and Regeneration System of Cotton
		7.2.1 Somatic Embryogenesis (SE)
	7.3 Factors Influencing Tissue Culture/Regeneration
		7.3.1 Genotype Dependency
		7.3.2 Explant
		7.3.3 Plant Growth Hormones
	7.4 Genetic Transformation of Cotton
		7.4.1 Agrobacterium - Mediated Transformation
		7.4.2 Biolistic Transformation
		7.4.3 Pollen Tube Pathway-Mediated Transformation
	References
Chapter 8: Breeding Cotton for Heat Tolerance
	8.1 Introduction
	8.2 Heat Stress in Cotton
		8.2.1 Impacts of Heat Stress on Root Development
		8.2.2 Heat Stress Effects on Photosynthesis
	8.3 Effects of Elevated Temperature on Plant’s Morphology
		8.3.1 High Temperature Causes Impaired Reproduction
		8.3.2 Pollen Infertility Due to Impact of Heat Stress
		8.3.3 Number of Pollens Decrease with Increase in Temperature
		8.3.4 Final Yield Affected by High Temperature in Cotton Crop
	8.4 Mode of Action at Molecular Level in Response to Heat Stresses
		8.4.1 Role of miRNAs
		8.4.2 Role of Calcium under Elevated Temperatures
		8.4.3 Heat Shock Proteins (HSPs) Activity under Heat Stress
		8.4.4 Heat Stress Impacts on Signaling Pathways
		8.4.5 Epigenetic Response during Heat Stress
		8.4.6 eRNAs Role under Heat Stress
	8.5 Breeding Strategies to Cope with Heat Stress
		8.5.1 Conventional Breeding
		8.5.2 Stomatal Conductance
		8.5.3 Canopy Temperature
		8.5.4 Photosynthesis Activity
		8.5.5 Cell Membrane Thermostability (CMT)
		8.5.6 Limitations of Conventional Breeding
		8.5.7 Mutation Breeding
	8.6 Molecular Approaches for Developing Tolerance to Heat Stress
		8.6.1 Marker-Assisted Selection and Identification of QTLs
		8.6.2 QTL Mapping
		8.6.3 Genotyping by Sequencing (GBS)
		8.6.4 Genome-Wide Association Study
		8.6.5 Novel Breeding Approaches to Develop Tolerance against Heat Stress
	8.7 Future Trends
	Acknowledgements
	References
Chapter 9: Breeding Cotton for Drought Tolerance
	9.1 Introduction
		9.1.1 Morpho-Physiological Mechanism in Response to Drought Stress
			9.1.1.1 Root Development
			9.1.1.2 Fiber Quality
			9.1.1.3 Photosynthesis
			9.1.1.4 Stomatal Regulation
			9.1.1.5 Osmotic Adjustment
			9.1.1.6 Seed Cotton Yield
		9.1.2 Strategies to Promote Tolerance against Moisture Stress in Cotton
			9.1.2.1 A. Marker-Assisted Selection (MAS) based on Drought-Related QTLs/Genes
			9.1.2.2 Transgenic Approach
			9.1.2.3 Micro RNAs (miRNAs)
			9.1.2.4 Functional Genomics for Stress Tolerance
			Conclusions and Future Research Directions
	Bibliography
Chapter 10: Breeding Cotton for Salt Tolerance
	10.1 Introduction
		10.1.1 Classification of Salt-Affected Soils
		10.1.2 Salinity in Cotton
		10.1.3 Salinity Leads to Drought
	10.2 Morpho-Physiological Features in Cotton to Combat Salt Stresses
		10.2.1 Osmoregulation—A Mechanism of Salt Tolerance
	10.3 Strategies to Promote Tolerance against Salinity Stress in Cotton
		10.3.1 Breeding Strategies
		10.3.2 Marker-Assisted Selection (MAS) based on Salinity-Related Quantitative Trait Loci (QTLs)/Genes
		10.3.3 Transgenic Approach
		10.3.4 GenEd Tools
		10.3.5 Regulating TFs
	Bibliography
Chapter 11: Breeding Cotton for Cotton Leaf Curl Disease Resistance
	11.1 Introduction
	11.2 History and Biology of Cotton Leaf Curl Disease in South Asia
		11.2.1 Geminiviral Pathogens of Cotton
		11.2.2 Geminivirus Diversification and Whitefly Vector Differentiation – Major Challenges to Developing Durable Resistance
		11.2.3 Begomoviruses are Transmitted by the Bemisia tabaci Cryptic Species
	11.3 Management Strategies for Developing Genetic Resistance to Cotton Leaf Curl Disease
	11.4 Conventional Breeding Approaches for Developing Resistance to Leaf Curl Disease
		11.4.1 Genetics of Cotton Leaf Curl Disease Resistance
		11.4.2 Breeding Approaches
	11.5 Screening Methods to Select for Cotton Leaf Curl Disease Resistance
		11.5.1 Greenhouse Screening by Graft Inoculation
	11.6 Interspecific Hybridization
		11.6.1 Paraphyletic Introgression
		11.6.2 Pseudophyletic Introgression
		11.6.3 Aphyletic Introgression
	11.7 Biotechnological Approaches and Tools for Developing Leaf Curl-Resistant Cotton
		11.7.1 Genetically Engineered Resistance to Combat Cotton Leaf Curl Disease
		11.7.2 Antiviral Strategies in Plant Breeding
	11.8 Transgenic Approaches for Developing Resistance to Begomoviruses
		11.8.1 Pathogen-Derived Resistance
	11.9 Non-Pathogen-Derived Resistance against Cotton Leaf Curl Disease
	11.10 ‘New generation’ Approaches: Genome Editing toward Virus Resistance
	11.11 Comparison of Breeding Approaches and Limitations
	References
Chapter 12: Breeding Cotton for Insect/Pests Resistance
	12.1 Background
	12.2 Mechanisms and Traits in Cotton Regarding Resistance to Insects
		12.2.1 Non-Preference/Antixenosis
		12.2.2 Antibiosis
		12.2.3 Tolerance
	12.3 R-Genes-Mediated Resistance to Insects
	12.4 Mechanisms of Insect Resistance to Plants
		12.4.1 Categorization of Insecticide Resistance
		12.4.2 Insect Resistance Based on Inheritance Pattern
		12.4.3 Insecticide Tolerance, Cross-Resistance, and Multiple Resistance
	12.5 Sources of Resistance
		12.5.1 Wild Relatives and Landraces
		12.5.2 Bt and Non-Bt Transgenics
	12.6 Potential Targets to Counter Control Insect Resistance
		12.6.1 ABC Transporters
		12.6.2 Proteases
		12.6.3 Proteases that Target the Cuticle
		12.6.4 Proteases That Target the Basement Membrane
		12.6.5 Potential Use of Cadherin Fragments
	12.7 Alternative Strategies to Control Insect Resistance to Bt Cotton
		12.7.1 Refuge Planting
		12.7.2 High Dose along with Refuge Strategy
		12.7.3 Gene Pyramiding
		12.7.4 RNA Interference
	12.8 Mode of Inheritance of Physical and Biochemical Traits in Cotton Related to Insect Resistant
		12.8.1 Plant Pubescence
		12.8.2 Nectariless
		12.8.3 Frego Bract
		12.8.4 Okra Leaf
		12.8.5 Red Pigmentation
		12.8.6 Gossypol Glands
	12.9 Breeding Cotton for Insect Resistance
		12.9.1 Screening and Evaluation of Germplasm
		12.9.2 Conventional Breeding Methods
		12.9.3 Transgenic Cotton Breeding
	12.10 Success Stories in Bt Cotton Production and Adoption
	12.11 A Logical Approach in Insect Control – the CRISPR/Cas9 System
	12.12 Crop Protection and CRISPR/Cas9-Based Gene Drive for Insect Control
	12.13 Conclusion
	References
Chapter 13: Breeding Cotton for Herbicide Resistance
	13.1 Introduction
	13.2 History of Chemical and Transgenic Control of Weeds
	13.3 Types of Herbicides
	13.4 Mode of Action of Herbicides
	13.5 Conventional Breeding Strategies for Herbicide-Resistant Cotton
	13.6 Role of Transgenic Technology for Herbicide-Resistant Cotton
	13.7 Future Options for Use of Herbicides in Cotton
	13.8 Summary
	References
Chapter 14: Breeding Cotton for Fiber Traits
	14.1 Introduction
	14.2 Cotton Fiber Market
	14.3 Applications of Cotton Fiber
	14.4 Fiber Quality Parameters
	14.5 Biochemical Composition of Cotton Fibers
	14.6 Cotton Fiber Development
	14.7 Cotton Fiber Elongation Mechanism
	14.8 Cotton Fiber Genes
		14.8.1 Expansins
		14.8.2 Sucrose Phosphate Synthase (SPS)
		14.8.3 Sucrose Synthase (SS)
		14.8.4 Lipid Transfer Proteins (LTPs)
		14.8.5 Cytoskeleton Genes
		14.8.6 Carbohydrate Metabolism Genes
		14.8.7 Transcription Factor Genes
		14.8.8 Phosphoenol Pyruvate Carboxylase (PEPc)
		14.8.9 Reactive Oxygen Species (ROS) Scavenger Genes
		14.8.10 Xyloglycan Endotransglycosylase (XTH)
		14.8.11 Fatty Acid Metabolism Genes
	14.9 Cotton Fiber Promoters
	14.10 Transcriptomic Studies of Fiber Genes
	14.11 Mapping for Fiber-Related Traits in Cotton
	14.12 Improvement of Cotton through Combined Use of Conventional Breeding and Genetic Engineering
	14.13 Summary
	References
Chapter 15: Breeding Cotton for Value-Added Traits
	15.1 Introduction
	15.2 Improving Oil and Protein Contents
	15.3 Organic Cotton
		15.3.1 Breeding Methods for Organic Cotton Farming
	15.4 Colored Cotton
		15.4.1 Pros and Cons of Colored Cotton
	15.5 Adaptation of Cotton for Mechanical Picking in Developing Countries
	15.6 Breeding Cotton for Flooding Conditions
	Literature Cited
Chapter 16: Genetically Modified Cotton: Boom or Dust
	16.1 Introduction
	16.2 Important Commercialized GM Crops and Traits
	16.3 Future Considerations for the Success of GM Crops
	16.4 Success of Transgenic Cotton
	16.5 Evolution of Transgenic Cotton
	16.6 Global Impact of Bt Cotton
	16.7 Traits of Interest
	16.8 Concerns Related to Transgenic Cotton
	16.9 Allergenicity
	16.10 Antibiotic Resistance
	16.11 Degradation Kinetics of Bt Proteins
	16.12 Vertical and Horizontal Gene Flow
	16.13 Effects of GM on Non-Target Insects
	16.14 Other Unidentified and Unpredictable Effects of GMOs
	16.15 Regulatory Concerns of GM Cotton
	16.16 Conclusions
	References
Chapter 17: Cotton Seed System
	17.1 Introduction
	17.2 What Is a Seed System?
	17.3 Formal Seed System
	17.4 Seed Certification
	17.5 Seed Certification System in Pakistan
		17.5.1 Crop Inspection
		17.5.2 Seed Testing
			17.5.2.1 Application Submission for Sampling
			17.5.2.2 Prerequisite for Seed Lots to be Sampled
		17.5.3 Seed Analysis
		17.5.4 Certificates of Seed Analysis and Temporary Labels
		17.5.5 Issuance of Final Labels and Seals
		17.5.6 Re-Testing of Seed Lots
		17.5.7 Checking of Seed Lot during Marketing and Import or Export
	17.6 Seed Laws and Rulemaking
	17.7 Seed Marketing
	17.8 Informal Seed System
	17.9 Cottonseed Production
	17.10 Seed Moisture Content and Storage
	17.11 Seed Quality
	17.12 Quality Cottonseed Production and Challenges in Pakistan
		17.12.1 Poor Seed Quality and Certification
		17.12.2 Uncertainty in Cotton Price Fixation
		17.12.3 Pests and Diseases
		17.12.4 Abiotic Stresses
	17.13 Summary
	References
Chapter 18: Cotton Breeding and Entrepreneurship: Challenges and Opportunities
	18.1 Introduction
		18.1.1 Understanding Entrepreneurship
		18.1.2 The Need for Entrepreneurial Development
	18.2 Entrepreneurship and Economic Development
		18.2.1 Agriculture and Entrepreneurship
	18.3 Contemporary Issues in Cotton Industry
	18.4 Status of Breeding Facilities and Its Commercialization in Pakistan
	18.5 Cotton Breeding and Entrepreneurship in Pakistan
		18.5.1 Economic Prospects
		18.5.2 Environmental Prospects
	18.6 Way Forward
		18.6.1 Change in Attitude
		18.6.2 Progression from Attitude to Action
		18.6.3 Action to Achievement
	18.7 Conclusion
	References
Chapter 19: Breeding Cotton for International Trade
	19.1 Introduction
	19.2 Types of Cotton Traded Internationally
		19.2.1 Cultivated Species of Cotton
			19.2.1.1 Sea Island Cotton
			19.2.1.2 Egyptian Cotton
			19.2.1.3 Pima Cotton
			19.2.1.4 Supima Cotton
			19.2.1.5 Extra-Long Staple Cotton
			19.2.1.6 Upland Cotton
			19.2.1.7 Natural-Colored Cotton
			19.2.1.8 Identity Cotton
			19.2.1.9 Organic Cotton
		19.2.2 Cotton Made in Africa (CmiA)
		19.2.3 Better Cotton Initiative (BCI)
		19.2.4 Fairtrade
	19.3 Pakistan’s Cotton Production and Trade Scenario
		19.3.1 Economic Importance
		19.3.2 Cotton Production
		19.3.3 Cotton Research and Development
			19.3.3.1 Pakistan Central Cotton Committee
			19.3.3.2 Other Breeding Institutions
			19.3.3.3 Private Sector Breeding Programs
		19.3.4 Breeding for International Trade
			19.3.4.1 Organic Cotton
			19.3.4.2 Colored Cotton
	19.4 Cotton Marketing and Trade
		19.4.1 Domestic Scenario
		19.4.2 Cotton Ginning Sector
		19.4.3 Spinning Sector
		19.4.4 Textile Sector
	19.5 Cotton-Related Associations Involved in Trade and Production
		19.5.1 All Pakistan Textile Mills Association (APTMA)
		19.5.2 Pakistan Cotton Ginners Association (PCGA)
		19.5.3 Karachi Cotton Association (KCA)
		19.5.4 Pakistan Crop Protection Association (PCPA)
		19.5.5 CropLife
		19.5.6 Seed Association of Pakistan (SAP)
	19.6 Market-Stabilizing Factors
		19.6.1 Crop Insurance Program
		19.6.2 Public Support in Cotton Prices
		19.6.3 Cotton Hedge Trading
	References
Index