Advancement in Crop Improvement Techniques

Cover
Advancement in Crop
Improvement Techniques
Copyright
Dedication
	Dedicated to Ph.D. students and collaborators of Dr. Tuteja
Contributors
Editors biography
Foreword
Preface
Views and visions
	References
Views and visions
Combination of DNA markers and eQTL information for introgression of multiple salt-tolerance traits in rice
	Introduction
	DNA markers for rice breeding
		SSR markers
		SNP markers
		Fluorescent markers
			Illumina´s BeadArray platform
			Taqman
				TaqMan principle for SNP detection
			KASP technology: An efficient approach for breeding applications
				Chemistry of KASP technology
				Reaction mechanism
				KASP as a better choice
	Use of markers
		Mapping, QTL information, and use
			Mapping population
			Linkage mapping
			QTL detection
			Identified QTLs
			Candidate genes cosegregating with QTL regions
		RNAseq, eQTL information, and use
			Discovering the expression polymorphism
			Linking expression polymorphism to genetic polymorphism
			Significance of studying eQTLs
			Case studies on plant eQTLs
			Salt stress responsive eQTL study on Horkuch/IR29 cross population
			Challenges in studying eQTLs
		GWAS
		Breeding
	Computational analysis and technology advancement
		Mapping populations
		Phenotyping strategies
			High-throughput automated image-based phenotyping
		Genotyping strategies
			High-throughput DNA isolation methods
			Genotyping by sequencing
			Functional/diagnostic markers
		Computational tools for linkage and QTL mapping
		Breeding strategies
			GS is a way forward for MAS
			Rapid generation advance and transforming rice breeding
			Targeting induced local lesions in genome (TILLING)
			Marker-assisted gene pyramiding
	Conclusion and future perspectives
	References
The scope of transformation and genome editing for quantitative trait improvements in rice
	Introduction
	Transformation technologies
		Agrobacterium-mediated
		Biolistics
		In planta methods
		Genome editing
	Target quantitative traits
		Biotic and abiotic stress
			Conventional transformation
			Crop improvement through CRISPR-CAS
		Yield stability under stress
			Conventional transformation
			Crop improvement through CRISPR
	Computational analysis
	Technology advancement
	Conclusion and future perspectives
	References
Tweaking microRNA-mediated gene regulation for crop improvement
	Introduction
	Contribution of miRNA-mediated regulation in plant growth and development
		miRNA-mediated regulation of shoot meristem maintenance
		miRNA-mediated regulation of leaf growth and development
		miRNA-mediated regulation of root growth and development
		miRNA-mediated regulation of the vegetative-to-reproductive phase transition
		miRNA-mediated regulation of reproductive development and its improvement
		miRNA-mediated regulation of seed development and germination
		Role of miRNAs in improving crop yield and other agronomic traits
		miRNA-mediated regulation involved in plant architecture improvement
		Role of miRNAs in acclimatization of plant growth to diverse environmental stresses
		miRNA-mediated regulation of host-partner relationships in crop plants
		miRNA-mediated regulation of disease resistance in crop plants
	Use of computational biology in advancing plant miRNA research in crop plants
	Technology advancements
		Recent advancements in miRNA profiling and validation
		Applications of genome editing technology in miRNA-mediated crop improvement
	Conclusion and future perspectives
	References
Modern tools in improving rice production
	Introduction
	Bioinformatic tools
	Genome-wide association studies (GWAS)
	Use of molecular markers in rice yield improvement
	Genome editing tools
	Installing C4 photosynthetic pathways into C3 rice plants to enhance the crop yield
	Rice yield and MAPK signaling
	Conclusion and future perspectives
	References
Molecular aspects of seed priming as a means of progress in crop improvement
	Introduction
	Seed priming in the context of current challenges facing agriculture and crop production
		Priming agents and treatments: An overview
	Seed priming versus seed aging in the context of seed bank storage
		Seed priming as a tool to limit aging-associated damage
	The molecular know-how of seed priming and its implications in promoting new advances in the sectors of seed biology a ...
		The redox context of the pregerminative metabolism and the harmful oxidative damage
		Active DNA repair during the pregerminative metabolism: a molecular know-how for seed priming
	Technology advancement
		Multilevel approaches to understand seed biology and assess seed quality
	Conclusion and future perspectives
	References
	Further Reading
Plant histidine kinases: Targets for crop improvement
	Introduction
	Plant histidine kinases (HKs) and the multistep phosphorelay (MSP)
	Histidine kinases for crop improvement in dicots
		Ethylene receptors
		Nonethylene receptors and cytokinin receptors
	Targeting histidine kinases to improve cereal productivity
	Genome-wide analysis: Histidine kinases from other plant species
	Technology advancement
	Conclusion and future perspectives
	References
Recent efforts in developing high-yield, drought-tolerant rice varieties
	Introduction
		Historical famines and food shortages in the world
		Food security and malnutrition
	Climate change and its effect on food production
	Drought
	Biology of drought tolerance
	Trait characterization and phenotyping as selection criteria
	Physiological, morphological, and biochemical response and derivations to tolerance
	Breeding strategies
		Population development and improvement
		Conventional breeding
		Marker-assisted breeding
		Fine mapping of identified genetic regions
		Deployment of genetic loci: QTL pyramiding
		Interaction among QTLs, and with background and environment
		Transgenic approaches
		High-throughput novel genotypic strategies and techniques
	Computational analysis
	Drought policies
	Conclusion and future perspectives
	References
	Further reading
Advances in genomics and molecular breeding for legume improvement
	Introduction
	Evolution of molecular marker technologies and genotyping assays
	Genetic resources and molecular mapping of agriculturally important traits
	Whole genome sequencing of the reference genotypes
	Resequencing multiple genomes to better understand genetic variation
		Genomics-assisted breeding in legume crops: From MAS to GS and sequence-based breeding
	Speed breeding in legume crops for accelerating genetic gains
	Genomic technologies to accelerate hybrid breeding
	Conclusion and perspectives
	References
Advancements in plant disease control strategies
	Introduction
	Plant immune system
	Marker-assisted breeding for crop improvement
	Genome editing approaches for disease-resistant plants
		Emergence of CRISPR technology
			CRISPR-Cas system: A brief overview
			Application of CRISPR/Cas9 for plant defense
				Resistance against viruses
				Resistance against fungi
				Resistance against bacteria
			Limitations of CRISPR/cas9 system
			Current status of CRISPR-Cas technology
		RNA interference as a tool for plant defense
			Mechanism of RNA silencing
			RNAi for plant resistance
		Exosome-like vesicle-mediated RNAi silencing: an emerging approach
	Biological control agents for efficient disease management
		Mechanisms of pathogen antagonism by BCA
			Hyperparasitism
			Predation
			Competition
			Metabolite production
			Induction of resistance
		Biological control of fungal pathogens
	Computational tools
	Conclusion and future perspectives
	References
How Crisp is CRISPR? CRISPR-Cas-mediated crop improvement with special focus on nutritional traits
	Overview of CRISPR-Cas technology
	An array of CRISPR-Cas-mediated genome editing systems
		Cas9
		Cpf1
		Cas13a
		Cas14a
	Advancements in genome editing for crop improvement: stress and nutritional traits
		Gene knockout
		Precise editing via gene targeting
		Base editing
		Prime editing
		Molecular farming
		Molecular domestication via CRISPR-Cas9-based breeding
		Editing for simple and complex traits
		Multiplex genome editing and applications
	Approaches in genome editing for crop improvement
	Strategies for reducing off-target effects of the CRISPR-Cas system
		Modulating Cas9 activity
		Optimization of sgRNA design
		Cas9 and Cpf1 variants
		DNA-free genome editing/Cas9 protein RNP complexes in vitro
		Enhancing HDR pathway efficiency by reducing the NHEJ pathway
		High-throughput screening of plant mutant libraries
		Chimeric fusion of catalytic domains
		Employing anti-CRISPR protein activities
		CRISPR-Cas9 mediated antiviral breeding approaches
		Employing differential CRISPR-Cas delivery systems
	CRISPR achievements in plants that cater to nutrition
	Foods developed employing CRISPR as a means to revolutionize agriculture
	Inclusion of GWAS into the CRISPR domain for additive nutrition
	Value rendered by CRISPR toward the promotion of food security
	Technological influx and CRISPR-Cas technology
		Machine learning and CRISPR-Cas9 genome editing
	Social acceptance of genome-edited (GE) plants using CRISPR technology
	Policy and government perspectives on the regulation of GE crops
	Conclusion
	References
Targeted genome editing using CRISPR-Cas9: Applications in fruit quality and stress resilience
	Introduction
	Improvement of traits associated with fruit quality
	Mitigation of climate change effects on agricultural productivity
	Computational analysis
	Technology advancement
	Conclusions and future perspectives
	References
Chapter 13 - Systems biology of crop improvement: Drought tolerance as a model to integrate molecular biology, physiology, and breeding
	Introduction
	The complex physiological response to drought
		ROS production and antioxidants as a means for drought tolerance
		Phytohormones in drought stress response
	Connecting physiological and molecular responses to drought
		Drought-inducible proteins
		Transcription factors
		Kinases
		Micro-RNAs
		Role of epigenetic response to abiotic stress
		Novel molecular targets and processes for drought tolerance
	Breeding for drought tolerance
		The case of the QTL qDTY12.1
		Big data analytics for efficient breeding
	The WISH project: A case study
		Wonder Rice Initiative for Food Security and Health
		Addressing common breeding bottlenecks under the WISH program
			Speed and cost of varietal improvement
			Quality of improved rice cultivars
			Acceptability of improved varieties by farmers
	Conclusions
	References
The microbial symbionts: Potential for crop improvement in changing environments
	Introduction
	Diversity of soil- and plant-associated microorganisms isolated from environments
	The endophytic microbes associated with plant symbionts and their functions
		Rhizobium (Rhizobiaceae)
		Arbuscular mycorrhizal fungi
		Trichoderma
		Serendipita indica
		Significance of microorganisms for agriculture and inoculants in the future
	Technological advancement
	Conclusion and future perspectives
	References
Reactive oxygen species (ROS) management in engineered plants for abiotic stress tolerance
	Introduction
	Abiotic stresses
	Reactive oxygen species and its scavenging machinery
	Role of ion transporters
	Role of osmolytes/osmoprotectants
	Role of transcription factors
	Genetic engineering approaches to develop salinity tolerance
	To increase crop production
	To increase nutrition values
	Genomewide perspective of ROS scavenging machinery in plants
	References
	Further reading
Metabolomics-assisted crop improvement
	Plant metabolome and metabolic pathways
	Metabolomics
		Practical approaches in metabolomics
			Targeted metabolomics
			Nontargeted metabolomics
			Metabolomics at the cellular and subcellular levels
		Integration of metabolomics with other ``omics´´
			Integration of metabolomics with transcriptomics
			Integration of metabolomics with proteomics
	Metabolomics-assisted crop improvement
	Computational analysis
	Technological advancements and limitations
	Conclusion and future prospects
	References
Improving medicinal crops through phytochemical perspective: Withania somnifera (Ashwagandha)
	Introduction
	Diverse species of W. somnifera
	Ethnobotany of W. somnifera
	Withanolides: The signature molecules of W. somnifera
	Development of improved varieties of W. somnifera
		Improvement in W. somnifera by conventional approaches
		Improvement by nonconventional approaches
			Technical advancement of W. somnifera
			Application of metabolic engineering
				Functional characterization of enzymes involved in early biosynthetic steps
				Enzymes involved in the modification of the terpene backbone in withanolide biosynthesis
			Application of computational and in silico studies
			Computational analysis in W. somnifera
			Transcriptome-wide analysis to identify genes involved in withanolide biosynthesis
			EST and transcriptome analysis to identify genes involved in withanolide biosynthesis
		Application of in vitro methods
		Marker-based approaches
	Conclusions and future perspectives
	References
Approaches for conservation and improvement of Himalayan plant genetic resources
	Introduction
	Strategies for the conservation and improvement of plant genetic resources
		Geospatial and imaging technologies
			Geographic information system technologies
			Remote sensing technologies
			Thermal imaging for species discrimination
		Functional trait-based approach for conservation of threatened species
		Micropropagation as a method for sustainable resource generation
		Importance of adventitious roots and hairy roots in conservation
		In vitro production of quality medicinal and aromatic plant ingredients
		Hydroponic and aeroponic cultivation of medicinal plants
			Picrorhiza kurroa Royle ex Benth: A case study
		Importance of genetic diversity in conservation of biodiversity
			Genomic resource creation and genetic diversity analysis in Himalayan plants
		Gene banks, captive cultivation, and varietal improvement of threatened medicinal plants
		Metabolic engineering for modulating primary and secondary metabolisms
		Technological advancements
	Conclusion
	References
Molecular markers as tools to improve date palms
	Introduction
	Role of molecular markers in the assessment of genetic diversity
	DNA markers
		Restriction fragment length polymorphism (RFLP)
		Amplified fragment length polymorphism (AFLP)
		Random amplified polymorphic DNA (RAPD)
		Microsatellites
		Intersimple sequence repeats (ISSR)
		Expressed sequence tags (EST)
		Single nucleotide polymorphisms (SNPs)
	Combined methods
	Molecular markers linked to sex in the date palm
	Computational analysis
	Conclusion and future perspectives
	References
Transgenic approach in crop improvement
	Introduction
	Classification of crop improvement methods
		Plant breeding
		Transgenic approach
		Genetically modification via genetic tools
	Journey of plant transformation
	Plant transformation methods
		Agrobacterium-mediated transformation
		Microinjection
		Agro-infection
		Chloroplast transformation
		Electroporation
		Biolistic (gene gun) method
		Chemical method of gene transfer
			PEG-mediated gene transfer
			Calcium-phosphate coprecipitation-mediated transfer
			DEAE dextran-mediated transfer
		Pollen transformation
		Direct DNA uptake by mature zygotic embryos
	Need for transgenic approach in crop improvement
	Acceptance of transgenic crops
		Transgenic cotton
		Transgenic brinjal
	Transgenic Approval Committee in India
	Risk assessment of GM crops
	Role of transgenics in crop improvement
		Abiotic stress
		Biotic stress
		Role of transgenics in phytoremediation
	Conclusion
	References
In planta transformation: A smart way of crop improvement
	Introduction
	Methods of plant transformation
		Non-biological transformation methods
		Biological transformation method
			Tissue culture-based transformation
			In planta transformation
			In planta transformation: a general scenario
	Methods for in planta transformation
		Vacuum infiltration method
			Floral dip method
			Floral drop method
			Embryo transformation
		Rice transformation: in planta method
	Importance of in planta transformation in crop improvement
	Conclusion
	References
Fiber crop, jute improvement by using genomics and genetic engineering
	Introduction
	Genomic studies of jute
		Phylogenetic study
		Cytological study
		Molecular maps of jute
		Genome sequencing of jute
		Studies on genes and expressed sequence tags (EST) of jute
	Genetic engineering of jute: An immediate necessity
	Useful techniques for modification of the jute genome
		Conventional breeding
		Mutagenesis
		RNAi technology
		T-DNA transformation
		CRISPR/Cas9
	Genetic transformation of jute
	Agronomic trait development
		Insect-resistant (IR) jute
		Fungus-resistant (FR) jute
		Herbicide-tolerant (HT) jute
	Jute improvement-Future possibilities
		Exploring the unique qualities of wild jute
		Better genetic transformation system for jute
		Low lignin jute for industrial application
		Development of multitrait transgenic jute
	Commercialization of transgenic jute
	References
Harnessing protein posttranslational modifications for plant improvement
	Introduction
	Protein posttranslational modifications and their roles in gene regulatory networks
		Phosphorylation
		Ubiquitination
		SUMOylation
		S-Nitrosylation
		Lipid modification
			N-Myristoylation
			S-Acylation/S-palmitoylation
			Prenylation
		Methylation
		Acetylation
		Glycosylation
	Modeling kinetics and improving cellular system efficiencies through gene editing
	Conclusions
	References
Index
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