Plant Genomics for Sustainable Agriculture

This book collates the basic and advanced concepts of plant biotechnology and genomics along with the future trends. It discusses the combination of conventional breeding techniques with genomic tools and approaches leading to a new genomics-based plant breeding technology supporting crop plants that respond better to biotic and abiotic stress, and pathogen attacks. Plant genomics play an important role in developing more efficient plant cultivars which are essential for the neo green revolution needed to feed the world’s rapidly growing population. Plant genomic data is being utilized in genetic engineering to ensure that better and resilient varieties of crops are available ensuring food security. This book is of immense interest to teachers, researchers, crop scientists, capacity builders, and policy makers. Also, the book serves as additional reading material for undergraduate and graduate students of agriculture, biotechnology, genomics, soil science, and environmental sciences. National and International agricultural scientists and policy makers will also find this to be a useful read. Preface Organization of the Book Acknowledgements Contents Contributors 1: Introduction, Scope, and Applications of Biotechnology and Genomics for Sustainable Agricultural Production 1.1 Introduction 1.2 Crop Improvement and Plant Genetic Resources 1.3 Biotechnological Interventions 1.4 Genomics for Crop Improvement 1.4.1 Whole Genome Sequencing 1.4.2 Marker Assisted Selection and QTL Mapping 1.4.3 High Throughput Phenotyping 1.4.4 Bioinformatics for Next-Generation Plant Breeding in Plant Genomics 1.5 Advances in Genomics 1.6 Conclusion and Future Perspective References 2: Structure and Organization of Plant Nuclear Genome 2.1 Introduction Box 2.1: Genome Size or Nuclear DNA Content (C-Value) 2.2 Evolution of Plant Nuclear Genome 2.3 Composition of Plant Nuclear Genome 2.3.1 Nuclear DNA 2.3.1.1 Coding and Non-coding Sequences 2.3.1.2 Regulatory Elements 2.3.1.3 Repetitive DNA 2.4 Structure of Plant Nuclear Genome 2.4.1 Overview of Nucleus (Site of Plant Nuclear Genome) 2.4.1.1 Nuclear Membrane/Nuclear Envelope 2.4.1.2 Nucleoplasm 2.4.1.3 Nucleolus 2.4.1.4 Chromosomes 2.4.2 Structure of Plant Nuclear DNA 2.4.3 Organization of Plant Nuclear Genome 2.4.3.1 Chromatin Structure and DNA Packaging 2.4.3.2 Nucleosome 2.5 Genome Sequencing in Plants 2.5.1 First Generation DNA Sequencing 2.5.1.1 The Maxam and Gilbert Technique (Also Known as the Chemical Cleavage Method) 2.5.1.2 Sanger ́s Plus and Minus Technique 2.5.1.3 Chain-Termination or Dideoxy Technique 2.5.2 Second Generation DNA Sequencing 2.5.2.1 Roche (454) Sequencing 2.5.2.2 Illumina Sequencing 2.5.2.3 SOLid Sequencing 2.5.2.4 Ion Torrent Semiconductor Sequencing 2.5.3 Third Generation DNA Sequencing 2.5.3.1 Heliscope Single Molecule Sequencing 2.5.3.2 Single Molecule Real-Time (SMRT) Sequencing 2.5.3.3 Nanopore Sequencing 2.6 Concluding Remarks References 3: Transgenesis in Plants: Principle and Methods 3.1 Introduction 3.2 Development of Transgenic Crops 3.3 Transformation Techniques 3.3.1 Vector Mediated Gene Transfer 3.3.1.1 Agrobacterium Mediated Gene Transfer 3.3.1.1.1 Ti Plasmid 3.3.1.1.2 Induction of Tumour 3.3.1.1.3 The Biology of Agrobacterium Infection 3.3.1.1.4 The T-DNA 3.3.1.1.5 The Vir Region 3.3.1.1.6 Genes Necessary for Transfer of T-DNA 3.3.1.1.7 The Process of T-DNA Transfer and Integration 3.3.1.2 The co-Integrative Vector 3.3.1.3 The Binary Vector 3.3.1.4 Plant Viral Vectors 3.3.1.4.1 Geminiviruses 3.3.1.4.2 Tobacco Rattle Virus (TRV) 3.3.1.4.3 Cucumovirus 3.3.1.4.4 Cowpea Mosaic Virus 3.3.2 Direct Gene Transfer 3.3.2.1 Physical Methods 3.3.2.1.1 Electroporation 3.3.2.1.2 Microinjection 3.3.2.1.3 Particle Bombardment 3.3.2.1.4 Fibre Mediated DNA Delivery 3.3.2.1.5 Laser Induced DNA Delivery 3.3.2.2 Chemical Methods 3.3.2.2.1 Polyethylene Glycol (PEG) Mediated 3.3.2.2.2 Liposome Fusion 3.3.2.2.3 Diethylaminoethyl (DEAE) Dextran Mediated 3.4 Analysis and Confirmation of Transgene Integration 3.5 Advantages of Transgenic Plants 3.5.1 Herbicide Resistant 3.5.2 Insect and Pest Resistant 3.5.3 Therapeutic Proteins from Transgenic Plants 3.5.4 Nutritional Benefits 3.5.5 Salt Tolerance 3.6 Global Status of Transgenic Crops 3.7 Major Concerns of Transgenic Crops 3.7.1 Environmental Concerns 3.7.2 Transgenesis and Human Health 3.7.2.1 Allergenicity 3.7.2.2 Horizontal Transfer and Antibiotic Resistance 3.8 Conclusions and Future Prospective References 4: Genetically Modified Crops and Their Applications 4.1 Introduction 4.2 Transgenic Methods to Produce Genetically Modified Crops 4.2.1 Agrobacterium Tumefaciens Mediated Transformation 4.2.2 Microinjection 4.2.3 Electroporation 4.2.4 Chemical Methods 4.3 Benefits of GM Crops 4.3.1 Herbicide and Insect-Tolerant Transgenic Plants 4.3.2 Abiotic Stress Tolerant GM Crops 4.3.3 GM Crops Expressing Therapeutic Molecules 4.3.4 Biofortification of Crops with Nutrients by Transgenic Approaches 4.3.4.1 Cereals and Oil Rich Crops 4.3.4.2 Legumes and Pulses 4.3.4.3 Vegetables and Fruits 4.4 Public Acceptance of GM Crops 4.4.1 Global Acceptance of GM Crops Among Farmers 4.4.2 Consumers ́ Attitudes Towards GM Crops 4.5 Conclusion References 5: Transcriptomics in Plant 5.1 Introduction 5.2 Historical Development 5.3 Pipeline for Transcriptome Analysis in Plants 5.3.1 Transcriptomic Study Design 5.3.2 RNA Isolation and Processing 5.3.3 Library Preparation 5.3.4 Library Sequencing 5.3.4.1 Roche (454) FLX 5.3.4.2 Illumina/Solexa 5.3.4.3 ABI SOLiD 5.3.4.4 Ion Torrent (Semiconductor-Based Life Technologies) 5.3.4.5 Pacific Biosciences 5.3.4.6 Oxford Nanopore Technologies 5.3.5 Quality Control 5.3.6 Read mapping, assembly and annotation 5.4 Bioinformatics Software for Transcriptome Analysis 5.4.1 Filtering 5.4.2 Assembly 5.4.3 Annotation 5.4.4 Differential Gene Expression 5.4.5 Pathway and Gene Ontology Mapping 5.5 Transcriptomics of Plants 5.5.1 Arabidopsis thaliana 5.5.2 Current Status of Transcriptomics in Crop Plants 5.6 Transcriptomics in Jute: An Overview 5.6.1 Transcriptome Assembly 5.6.2 Gene Discovery from Transcriptome Data 5.6.3 Orthologous Group Identification and Gene Ontology 5.6.4 Identification of Novel genes 5.6.5 Metabolic Pathway Identification 5.6.6 DEG Analysis 5.6.7 Marker Development 5.6.7.1 SSR 5.6.7.2 SNP and InDel 5.7 Conclusion References 6: Molecular Breeding and Marker-Assisted Selection for Crop Improvement 6.1 Introduction 6.2 Conventional Plant Breeding 6.3 Molecular Markers and Genotyping Methodologies 6.3.1 Molecular Marker 6.3.2 Genetic Markers 6.3.3 Classification of Molecular Markers 6.3.4 Application of Molecular Markers in Crop Science 6.3.4.1 Evolution and Phylogeny 6.3.4.2 Investigation of Heterosis 6.3.4.3 Identification of Haploid Plants and Cultivars Genotyping 6.3.4.4 Genetic Diversity Assessment 6.3.4.5 Utilization of Molecular Markers in Backcrossing 6.3.4.6 Linkage Map Construction 6.3.4.7 Varietal and Hybrid Identification 6.4 QTL Mapping and Applications 6.4.1 QTL Mapping 6.4.2 Mapping Population 6.4.3 Methods for QTL Detection and Mapping 6.4.3.1 Composite Interval mapping 6.4.3.2 Multiple Interval Mapping 6.4.3.3 Bayesian Multiple QTL Mapping. 6.4.4 Factors Affecting the QTL Detection 6.4.5 QTL Validation 6.4.6 Software for QTL Mapping 6.5 Molecular Breeding 6.5.1 Marker-Assisted Selection or Marker-Aided Selection (MAS) 6.5.1.1 Prerequisites for Marker-Assisted Breeding Program 6.5.1.2 Important MAS Schemes 6.5.2 Advantages of MAB Over Conventional Breeding 6.5.3 Drawbacks of MAB 6.6 Association Mapping 6.6.1 Populations Used for Association Mapping 6.6.2 Types of Association Mapping 6.7 Conclusion 6.8 Future Thrust References 7: Bioinformatics in Plant Genomics for Next-Generation Plant Breeding 7.1 Introduction 7.1.1 Traditional Breeding to Next-Generation Breeding 7.1.2 IT (Information Technology) in Plant Breeding 7.2 Genomics in Plant Breeding 7.3 Next-Generation Breeding 7.3.1 Next-Generation Sequencing 7.3.1.1 RNA Sequencing 7.3.1.2 Chromatin Immunoprecipitation Sequencing (ChIP-Seq) 7.3.2 Genome Editing 7.3.3 Restriction-Site Associated DNA Sequencing (RAD-Seq) and Genotyping-by-Sequencing (GBS) 7.3.4 TILLING and EcoTILLING 7.3.5 SNP Discovery 7.3.6 Speed Breeding 7.4 Conclusion References 8: Whole-Genome Sequencing of Plants: Past, Present, and Future 8.1 Introduction 8.2 Plant Genome Research 8.2.1 The History and Research During Pre-genomic Era 8.2.2 Current Research in Field of Plant Genomic Studies 8.2.2.1 Introduction to Current Research 8.2.2.2 Sequencing, Assembly/Reassembly, Annotation 8.2.2.2.1 Sanger ́s Chain Termination Method 8.2.2.2.2 Pyrosequencing 8.2.2.2.3 Reversible Terminator Sequencing 8.2.2.2.4 Ligation-Based Approaches 8.2.2.2.5 Proton Detection 8.2.2.2.6 Sequencers Based on Single-Molecule Detection 8.2.2.2.7 Nanopore 8.3 Advances in Plant Genomics 8.3.1 Plant Genome Assembly from 3rd Generation Genomic Technologies 8.3.2 Machine Learning Aided Crop Plant Genomics 8.3.3 Accelerate the Development of New Crops via Speed Breeding 8.3.4 High-Throughput Phenotyping 8.4 Role of Genomic Studies in Plant Research 8.4.1 Using Genomics to Improve Crop Plant Diversity and Resilience 8.4.2 Tracing Our Steps Back to CWRs for Genetic Diversity 8.4.3 De novo Crop Domestication 8.4.4 Engineering Polyploid Plants 8.4.5 Boosting Agriculture Through Better Understanding of Plant-Microbe Interactions 8.4.6 Genome Editing for Nutritionally Enhanced Crop Production 8.5 Completeness of Functional Annotation for Better Candidate Gene Identification 8.5.1 New Breeding Targets from Non-coding Part of Genome 8.5.2 The Pan-Genome Approach 8.6 The Sequenced Angiosperm Genomes 8.7 Databases for Plant Genomics/Popular Genome Databases 8.7.1 The National Center for Biotechnology Information-Genome Browser 8.7.2 Plant Genome DataBase Japan (PGDBj) 8.7.3 EnsemblPlants 8.7.4 Genome Size in Asteraceae Database (GSAD): 8.7.5 Phytozome 8.7.6 Plant DNA C-Values Database 8.7.7 Plant rDNA Database 8.7.8 PlantGDB Genome Browser: 8.8 Further Remarks 8.9 Closing Note? References 9: Model Plants in Genomics 9.1 Introduction 9.2 Classical Model Plants in Biology 9.2.1 Maize (Zea mays) 9.2.2 Mouse-Ear Cress (Arabidopsis thaliana) 9.2.3 Rice (Oryza sativa) 9.3 Redefining `Model System ́ Concept 9.3.1 Phylogenetics, Comparative Genomics, and Model Plant Selection 9.3.2 Model Species for Lower Plants 9.3.3 Model Species for Higher Plants 9.4 Concluding Remarks References 10: RNA Interference Technology in Plants: Mechanisms and Applications in Crop Improvement 10.1 Introduction 10.2 RNAi: Discovery and Basic Mechanism of Action 10.3 Application of RNAi in Plant Improvement 10.3.1 Abiotic Stress Resistance 10.3.2 Biotic Stress Tolerance 10.3.2.1 Bacterial Disease Resistance 10.3.2.2 Viral Disease Resistance 10.3.2.3 Fungal Diseases 10.3.2.4 Nematode Resistance 10.3.2.5 Parasitic Weed Resistance 10.3.3 Increasing Nutritional Value 10.3.4 Development of Male Sterile Lines 10.3.5 Modification of Flower Color and Scent by RNAi-Mediated Gene Silencing 10.3.6 Enhanced Fruit Shelf Life 10.3.7 Manipulation of Secondary Metabolite 10.3.8 Seedless Fruit Development 10.3.9 Deletion of Allergens from Food Crops 10.3.10 Change in Plant Architecture 10.4 Conclusion References 11: Use of Genomics to Improve Stress Tolerance 11.1 Introduction 11.2 Abiotic Stresses 11.2.1 Drought Stress 11.2.2 Salinity Stress 11.2.3 Heat Stress 11.2.4 Cold Stress 11.2.5 Metal Stress 11.3 Biotic Stress 11.4 Role of Transcription Factors against Biotic Stress 11.5 Effect of Gene Targeting on Abiotic and Biotic Stress 11.6 Conclusion and Future Prospects References 12: Genetics of Plant Organelles: Plastid and Mitochondrial Genomes 12.1 Introduction 12.2 Organelles Genome 12.3 Plant Mitochondrial Genome 12.4 Structure of the Chloroplast Genome 12.5 Mitochondrial Genome Diversity in Angiosperm Plants 12.6 Mitochondrial Genome Stability 12.7 Chloroplast Genetic Engineering 12.7.1 Agronomic Trait Enhancement Via Chloroplast Modulation 12.7.2 Engineering of the Metabolic Pathway in Chloroplast for the Beneficial Product 12.7.3 Enhancement in Photosynthesis Efficiency Via Plastid Engineering 12.7.4 Chloroplast Genome Engineering for Insect Resistance 12.8 Evolution of Organelle Genome 12.8.1 Mitochondria Genome for Phylogeny Analysis 12.8.2 Evolution of Chloroplast Genome and Its Use in Phylogeny Analysis 12.8.2.1 rbcL Gene 12.8.2.2 MatK Gene 12.8.2.3 ndhF Gene 12.9 Conclusion References 13: DNA Barcoding in Plants: Past, Present, and Future 13.1 Introduction 13.2 The Genesis of Concept 13.3 Technical Know-How of DNA Barcoding 13.3.1 Sampling 13.3.2 DNA Extraction, PCR Amplification, and Sequencing 13.3.3 Analysis and Interpretation 13.4 Promising Plant DNA Barcoding Loci 13.5 Utility of Plant DNA Barcoding 13.6 Challenges of Plant Barcodes 13.7 Prospect of DNA Barcoding 13.8 Next-Generation Sequencing and DNA Barcoding 13.9 DNA Barcode-Based High-Resolution Melting Curve Analysis (Bar-HRM) 13.10 High-Throughput Plant DNA Barcoding Using Microfluidic Enrichment Barcoding (ME Barcoding) 13.11 Full-Length Multi-Barcoding (FLMB) 13.12 Genome Skimming Based Barcoding 13.13 Restriction Site-Associated DNA Sequencing (RAD) 13.14 Conclusion References 14: Advances in Epigenetics for Crop Improvement and Sustainable Agriculture 14.1 Introduction 14.1.1 Epigenetics 14.1.2 RNAs-miRNA, ShRNA, si RNA, Non-coding RNA 14.1.3 Small RNAs Can Trigger DNA Methylation and Chromatin Modification 14.1.4 Chromatin Remodeling/Condensation 14.1.5 Polycomb Proteins 14.1.6 Fungal Prions and Epigenetics 14.1.7 Global Hunger and Crop Production 14.2 Plant Epigenetics 14.3 Epigenetics to Increase the Crop Yield and Sustained Agriculture 14.4 Epigenetics for Crop Growth 14.5 Epigenetic Modifications to Sustain Agriculture for Crops Growing in Deserts 14.6 Epigenome Engineering Novel Techniques for Crop Improvement 14.7 Epigenetics in Agricultural Sector Patents 14.8 Challenges and Opportunities in Phyto-Epigenetics 14.9 Conclusion References 15: Ethical Aspects and Public Perception on Plant Genomics 15.1 Introduction 15.2 Plant Genomics 15.3 Ethical Aspects of Plant Genomics 15.4 Transgenic Plants Regulation in India 15.4.1 Framework for Implementation of Regulations for Handling with GMOs 15.5 International Regulations of Transgenic Plants 15.5.1 Regulation of European Union 15.5.2 Regulation of Non-European Union 15.5.2.1 North America 15.5.2.2 Latin America 15.5.2.3 Africa 15.5.2.4 Asia and the Pacific 15.5.2.5 Regulatory Updates for Gene Editing in Asia-Pacific 15.6 Plant Genome Databases 15.7 Public Perception on Plant Genomics 15.8 Conclusion References