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OMICS-Based Approaches in Plant Biotechnology
Rintu Banerjee (Edited by), Garlapati Vijay Kumar (Edited by), S.P. Jeevan Kumar (Edited by)
9781119509936, Wiley
Hardback, published 5 March 2019
348 pages
1 x 1 x 1 cm, 0.454 kg
Burgeoning world population, decreased water supply and land resources, coupled with climate change, result in severe stress conditions and a great threat to the global food supply. To meet these challenges, exploring Omics Technologies could lead to improved yields of cereals, tubers and grasses that may ensure food security. Improvement of yields through crop improvement and biotechnological means are the need-of-the-hour, and the current book “OMICS-Based Approaches in Plant Biotechnology”, reviews the advanced concepts on breeding strategies, OMICS technologies (genomics, transcriptomics and metabolomics) and bioinformatics that help to glean the potential candidate genes/molecules to address unsolved problems related to plant and agricultural crops. The first six chapters of the book are focused on genomics and cover sequencing, functional genomics with examples on insecticide resistant genes, mutation breeding and miRNA technologies. Recent advances in metabolomics studies are elucidated in the next 3 chapters followed by 5 chapters on bioinformatics and advanced techniques in plant biotechnology and crop breeding. The information contained in the volume will help plant breeders, plant biotechnologists, plant biochemists, agriculture scientists and researchers in using this applied research to focus on better crop breeding and stress adaptation strategies.
Introduction xiii Part 1: Genomics 1 1 Exploring Genomics Research in the Context of Some Underutilized Legumes—A Review 3 1.1 Introduction 3 1.2 Velvet Bean [Mucuna pruriens (L.) DC. var. utilis (Wall. ex Wight)] Baker ex Burck 4 1.3 Psophocarpus tetragonolobus (L.) DC. 7 1.4 Vigna umbellata (Thunb.) Ohwiet. Ohashi 8 1.5 Lablab purpureus (L.) Sweet 9 1.6 Avenues for Future Research 10 1.7 Conclusions 12 Acknowledgments 12 References 12 2 Overview of Insecticidal Genes Used in Crop Improvement Program 19 2.1 Introduction 19 2.2 Insect-Resistant Transgenic Model Plant 21 2.3 Insect-Resistant Transgenic Dicot Plants 27 2.4 Insect-Resistant Transgenic Monocot Plants 34 2.5 Working Principle of Insecticidal Genes Used in Transgenic Plant Preparation 39 2.6 Discussion 41 References 42 3 Advances in Crop Improvement: Use of miRNA Technologies for Crop Improvement 55 3.1 Introduction 56 3.2 Discovery of miRNAs 56 3.3 Evolution and Organization of Plant miRNAs 57 3.4 Identification of Plant miRNAs 58 3.5 miRNA vs. siRNA 59 3.6 Biogenesis of miRNAs and Their Regulatory Action in Plants 60 3.7 Application of miRNA for Crop Improvement 61 3.8 Concluding Remarks 62 References 70 4 Gene Discovery by Forward Genetic Approach in the Era of High-Throughput Sequencing 75 4.1 Introduction 75 4.2 Mutagens Differ for Type and Density of Induced Mutations 76 4.3 High-Throughput Sequencing is Getting Better and Cheaper 77 4.4 Mapping-by-Sequencing 77 4.5 Different Mapping Populations for Specific Need 81 4.6 Effect of Mutagen Type on Mapping 83 4.7 Effect of Bulk Size and Sequencing Coverage on Mapping 83 4.8 Challenges in Variant Calling 85 4.9 Cases Where Genome Sequence is either Unavailable or Highly Diverged 85 4.10 Bioinformatics Tools for Mapping-by-Sequencing Analysis 86 Acknowledgments 87 References 87 5 Functional Genomics of Thermotolerant Plants 91 5.1 Introduction 91 5.2 Functional Genomics in Plants 93 5.3 Thermotolerant Plants 94 5.4 Studies on Functional Genomics of Thermotolerant Plants 98 5.5 Concluding Remarks 99 Abbreviations 100 References 100 Part 2: Metabolomics 105 6 A Workflow in Single Cell-Type Metabolomics: From Data Pre-Processing and Statistical Analysis to Biological Insights 107 6.1 Introduction 108 6.2 Methods and Data 109 6.3 Results 110 6.4 Discussion 122 6.5 Conclusion 124 Conflicts of Interest 124 Acknowledgment 125 References 125 7 Metabolite Profiling and Metabolomics of Plant Systems Using 1H NMR and GC-MS 129 7.1 Introduction 129 7.2 Materials and Methods 131 7.3 Selected Applications of Metabolomics and Metabolite Profiling 139 Acknowledgments 140 Competing Interests 140 References 140 8 OMICS-Based Approaches for Elucidation of Picrosides Biosynthesis in Picrorhiza kurroa 145 8.1 Introduction 146 8.2 Cross-Talk of Picrosides Biosynthesis Among Different Tissues of P. kurroa 148 8.3 Strategies Used for the Elucidation of Picrosides Biosynthetic Route in P. kurroa 148 8.4 Strategies Used for Shortlisting Key/Candidate Genes Involved in Picrosides Biosynthesis 151 8.5 Complete Architecture of Picrosides Biosynthetic Pathway 153 8.6 Challenges and Future Perspectives 161 Abbreviations 162 References 163 9 Relevance of Poly-Omics in System Biology Studies of Industrial Crops 167 9.1 Introduction 167 9.2 System Biology of Crops 169 9.3 Industrial Crops 171 9.4 Poly-Omics Application in System Biology Studies of Industrial Crops 176 9.5 Concluding Remarks 177 Abbreviations 177 References 178 Part 3: Bioinformatics 183 10 Emerging Advances in Computational Omics Tools for Systems Analysis of Gramineae Family Grass Species and Their Abiotic Stress Responsive Functions 185 10.1 Introduction 186 10.2 Gramineae Family Grass Species 187 10.3 Abiotic Stress 188 10.4 Emerging Sequencing Technologies 198 10.5 Omics Resource in Poaceae Species 202 10.6 Role of Functional Omics in Dissecting the Stress Physiology of Gramineae Members 203 10.7 Systems Analysis in Gramineae Plant Species 204 10.8 Nutritional Omics of Gramineae Species 205 10.9 Future Prospects 205 10.10 Conclusion 206 Acknowledgments 207 References 207 11 OMIC Technologies in Bioethanol Production: An Indian Context 217 11.1 Introduction 217 11.2 Indian Scenario 219 11.3 Cellulolytic Enzymes Producing Bacterial Strains Isolated from India 220 11.4 Biomass Sources Native to India 230 11.5 Omics Data and Its Application to Bioethanol Production 233 11.6 Conclusion 239 References 239 Part 4: Advances in Crop Improvement: Emerging Technologies 245 12 Genome Editing: New Breeding Technologies in Plants 247 12.1 Introduction: Genome Editing 248 12.2 GE: The Basics 249 12.3 Engineered Nucleases: The Key Players in GE 251 12.4 Targeted Mutations and Practical Considerations 259 12.5 New Era: CRISPR/Cas9 264 12.6 GE for Improving Economic Traits 269 12.7 Biosafety of GE Plants 273 12.8 What’s Next: Prospects 276 References 276 13 Regulation of Gene Expression by Global Methylation Pattern in Plants Development 287 13.1 Introduction 288 13.2 Nucleic Acid Methylation Targets in the Genome 289 13.3 Nucleic Acid Methyl Transferase (DNMtase) 290 13.4 Genomic DNA Methylation and Expression Pattern 291 13.5 Pattern of DNA Methylation in Early Plant Life 292 13.6 DNA Methylation Pattern in Mushroom 293 13.7 Methylation Pattern in Tumor 294 13.8 DNA Methylation Analysis Approaches 294 References 297 14 High-Throughput Phenotyping: Potential Tool for Genomics 303 14.1 Introduction 304 14.2 Relation of Phenotype, Genotype, and Environment 304 14.3 Features of HTP 306 14.4 HTP Pipeline and Platforms 310 14.5 Controlled Environment-Based Phenotyping 311 14.6 Field-Based High-Throughput Plant Phenotyping (Fb-HTPP) 311 14.7 Applications of HTP 313 14.8 Conclusion and Future Thrust 316 References 316 Index 323
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Subject Areas: Agriculture & farming [TV]
