Omics Approaches for Sugarcane Crop Improvement

Description

In this book, the information encompasses various researchable biotechnology aspects of sugarcane, its genomic structure, diversity, comparative and structural genomics, data mining, etc. This book explores both the theoretical and practical aspects of sugarcane crops, focusing on innovative processes. This book argues in favor of developing an integrated research and development system to strengthen the research and development capabilities of all the areas of sugarcane. Further, it covers the recent trends of sugarcane biotechnology, especially in the next-generation sequencing (NGS) era. This book will be very useful for professors and scientists who are working in the area of sugarcane crops by using molecular biology and bioinformatics. It is also useful for students to use as a reference for their classes or thesis projects. Key features • Discusses an integral part of molecular biology and pivotal tools for molecular breeding; enables breeders to design cost-effective and efficient breeding strategies for sugarcane • Discusses the harnessing genomics technologies for genetic engineering and pathogen characterization and diagnosis of sugarcane • Provides new examples and problems, added where needed • Provides insight from contributors drawn from around the globe Cover Half Title Title Page Copyright Page Contents Preface Editor Bio Contributors 1. Potential and Advanced Strategies for Sugarcane improvement 1.1 Introduction 1.2 Exploration, Conservation, and Utilization of Genetic Resources of Sugarcane Germplasm Bank Assisted by Molecular Markers 1.3 Molecular Techniques to Detect Systemic Diseases during Quarantine and Tissue Culture to Sanitize Diseased Plants 1.4 Genetic Variability Generation through Hybridization 1.4.1 Selection of Parents 1.4.2 Hybridity Determination and Progeny Test Assisted by Molecular Markers 1.5 Selecting Outstanding Clones: Molecular Markers Linked to Traits of Interest and Genomic Selection 1.6 Micropropagation Techniques to Provide with Healthy and True-to-type Seed Cane 1.7 Genetic Engineering: Genetic Transformation and Genome Editing 1.8 Remarked Conclusions 1.9 Future Prospects References 2. Role of Biotechnology for Improvement of Sugarcane 2.1 Introduction 2.2 Economic Importance of Sugarcane 2.3 Genetics of Sugarcane 2.4 Challenges for Sustainable Sugarcane Production 2.5 Strategy for Enhancing Sugarcane Productivity 2.5.1 Traditional Breeding 2.5.2 Role of Biotechnology in Improving Sugarcane Productivity 2.5.2.1 Marker-Assisted Breeding 2.5.2.2 Somaclonal Variations 2.5.3 Genome Editing (CRISPR/Cas9 Technology) 2.6 Role of Bioinformatics Tools and Functional Genomics in Sugarcane Productivity 2.7 Future Prospective References 3. Biotechnological Intervention in Sugarcane: Progress Made So Far 3.1 Introduction 3.2 Mutation Breeding 3.3 Genetic Transformation 3.4 Genome Editing 3.5 Application of Molecular Markers and Marker-assisted Selection 3.6 Genomics and Transcriptomics Approaches for Sugarcane Improvement 3.7 Conclusion References 4. Sugarcane Biotechnology: Developments and Opportunities 4.1 Introduction 4.2 Intervention of Biotechnology Tools for Sugarcane Improvement 4.3 Molecular Markers in Sugarcane 4.4 Genomics in Sugarcane 4.5 Sugarcane Transcriptomics 4.6 Proteomics for Sugarcane 4.7 Tissue Culture in Sugarcane 4.8 Genetic Engineering Approaches in Sugarcane 4.9 CRISPR-Cas System as a Genome Editing Tool for Sugarcane 4.10 Conclusions and Perspectives References 5. Augmenting Sugar Accumulation Potential in Sugarcane: Conventional and Molecular Approaches 5.1 Introduction 5.2 Sugarcane Improvement: the Initial Phase 5.3 Improving Sugar Content: Conventional and Modern Tools 5.3.1 Genetic Resources and Their Utilization 5.3.2 Varietal Breeding for Improving Sugar Content 5.3.2.1 Varietal Breeding for Sugar Content: R&D Set up in India 5.3.3 Pre-Breeding for Sugar Content 5.4 Biotechnological Tools for Improving Sugar Content 5.4.1 Molecular Marker Applications for Sugar Improvement 5.4.2 Functional Genomics 5.4.3 Bioinformatics 5.5 Future Research Thrusts References 6. Omics Applications to Decipher Host-Pathogen Interactions and to Understand Pathogens in Sugarcane 6.1 Introduction 6.2 Sugarcane-Colletotrichum Falcatum Interaction 6.2.1 Accomplishments Made in Pre-Genomics Era 6.2.2 Early Phase of Omics Era 6.2.3 Application of NGS Tools 6.2.4 C. falcatum Genome Characterization 6.2.5 Characterization of Pathogenicity Gene Homologs/Proteins in C. falcatum 6.2.6 Functional Analysis of Pathogenicity-related Genes 6.2.7 Candidate Genes for Fungicidal Targets 6.3 Sugarcane S. scitamineum Interaction 6.4 Pokkah Boeng Disease 6.5 Rust 6.6 Sugarcane Viruses 6.6.1 Sugarcane Bacilliform Virus 6.6.1.1 SCBV Genomics 6.6.2 Sugarcane Mosaic 6.6.2.1 Genomics of Mosaic Associated Viruses 6.6.2.2 Sugarcane Mosaic Transcriptomics 6.6.3 Sugarcane Yellow Leaf Disease 6.6.3.1 ScYLV Genomics 6.6.4 Sugarcane Viral Metagenomics 6.7 Sugarcane Grassy Shoot Disease 6.8 Conclusion References 7. Genomics-Assisted Precision Breeding for Drought Tolerance in Sugarcane 7.1 Introduction 7.2 Origin, Taxonomy, and Cultivation of Sugarcane 7.3 Physiological and Biochemical Response to Drought Stress 7.4 Varietal Screening for Drought Tolerance 7.5 Genetic and Biochemical Basis of Drought Tolerance 7.6 Genomics and Bioinformatics Resources 7.7 Genome Complexity 7.8 Genomic Tools for Precision Breeding 7.8.1 High Throughput Genotyping Platforms 7.8.2 Transcriptome Analysis 7.8.3 Marker-assisted Breeding 7.8.3.1 Candidate Gene Approach 7.8.3.2 Marker-Trait Association(MTA) 7.8.4 In vitro Mutagenesis 7.8.5 Genome Engineering 7.8.5.1 Transgenic Breeding 7.8.5.2 Cisgenic Approach 7.8.5.3 Genome Editing 7.9 Conclusion References 8. Enhancing Abiotic Stress Tolerance of Sugarcane: Genome-Editing Approach 8.1 Introduction 8.2 Drought Stress 8.3 Heat and Cold Stress 8.4 Nutrition-related Stresses 8.5 Conclusions and Future Prospects References 9. Techniques Used for the Identification of Defense-related Protein in Sugarcane in Response to Biotic Stress 9.1 Introduction 9.2 Different Techniques Used in Identification of Expressed Proteins in Sugarcane against Infection 9.3 In Sugarcane Crop identification of Induced Proteins in Response to Infection by Sporisorium scitamineum by Quantitative Proteomics 9.3.1 Liquid Chromatography Orbitrap Mass Spectrometry Analysis 9.3.2 Protein Identification and Data Processing 9.3.3 Real-Time PCR (qRT-PCR) 9.3.4 Bioinformatics Analysis of DEPs in Sugarcane 9.4 Identification of Defense Proteins in Sugarcane in Response to Xanthomonas albineans 9.4.1 Proteomic Profiling 9.5 Detection of Expressed Proteins against X. albilineans 9.5.1 (PPIs) Protein-Protein Interactions Network 9.5.2 Detection of Defense Genes Triggered by X. albilineans in Sugarcane 9.5.3 Transcript Profiling by qRT-PCR 9.6 Transcriptomic Analysis of Sugarcane against Leifsonia xyli 9.7 Proteomic Analysis: Acidovorax avenae Causing Red Stripe in Sugarcane 9.8 Conclusion References 10. Physiological and Molecular Stress Responses in Sugarcane 10.1 Introduction 10.2 Morphological and Physiological Responses of Sugarcane to Water Stress 10.3 Sugarcane Defense Mechanism to Drought 10.4 Drought Stress-regulated Genes and Protein 10.5 Proteomics Studies on Sugarcane Response to Salinity Stress 10.6 Transcriptomics Studies on Sugarcane Response to Abiotic Stresses References 11. Avoidance and Tolerance Strategy of Sugarcane in Drought Stress: Response Mechanism 11.1 Introduction 11.2 Strategies of Drought Tolerance in Sugarcane 11.2.1 Protective Mechanisms of Drought-Avoidance Strategy 11.2.2 Response of Stomatal Conductance and Its Mechanism under Drought Stress 11.2.2.1 Hydropassive Mechanism 11.2.2.2 Hydroactive Mechanism 11.2.3 Response of Leaf Rolling and Its Mechanism under Drought Stress 11.2.4 Response of Leaf Senescence and Its Mechanism under Drought Stress 11.2.5 Response of Photosynthesis and Their Role under Drought Stress 11.2.5.1 Sugarcane Drought-Tolerance Accustomed Strategy 11.2.5.2 Accumulation of Solutes, Secondary Metabolites, and Antioxidant Activity as Response to Drought Tolerance in Sugarcane 11.3 Drought Tolerance Metabolism 11.4 ABA-Mediated Signaling and Production in Canes under Drought Stress 11.5 Gene Expression in Sugarcane under Drought-Stress Tolerance 11.6 Conclusion References 12. High-Throughput Sequencing and SNP Markers-based Identification of Sugarcane Cultivars for Parentage Determination and Intellectual Property Protection 12.1 Introduction 12.2 Parentage Determination and IPRs 12.3 High Throughput Sequencing Applications and their Role in Genotyping 12.3.1 Whole-Genome Sequencing (WGS) 12.3.2 Exome Sequencing 12.3.3 RNA Sequencing 12.3.4 Genotyping by Sequencing (GBS) 12.4 SNP Arrays and Their Role in Genotyping 12.5 SNP Markers 12.5.1 SNP Markers Validation by KASP Assay 12.6 Summary References 13. Recent Advancements in Diagnostics and Management of Phytoplasma-infecting Sugarcane 13.1 Introduction 13.2 Phytoplasma Diseases of Sugarcane 13.2.1 Grassy Shoot Disease (GSD) 13.2.2 White Leaf Disease (WLD) 13.2.3 Yellow Leaf Disease (YLD) 13.3 Disease Transmission and Insect Vectors 13.4 Diagnosis of Phytoplasmas 13.5 Host Range of Sugarcane Phytoplasmas 13.6 Integrated Disease Management Approaches 13.7 Conclusion References 14. The Improvement of Sugarcane (Saccharum officinarum L.) for Sugar, Ethanol and Biofuel Production Through Innovative Biotechnology: A Perspective View on its Scope, Importance & Challenges 14.1 Introduction 14.2 Scope and Importance of Biotechnology Applications in the Improvement of Sugarcane for Sugar Production 14.3 Scope and Importance of Biotechnology Applications in the Improvement of Sugarcane for Ethanol and Biofuel Production 14.4 Challenges in the Genetic Improvement of Sugarcane 14.5 Conclusion References 15. Industrial Biotechnology Applied to Sugarcane 15.1 Introduction 15.2 Fructooligosaccharides (FOS) Production 15.3 Ethanol Production 15.4 Production of fodder yeast or torula yeast (candida utilis yeast) 15.4.1 Obtaining Biogas from Sugar Agribusiness Waste 15.5 Organic Biofertilizer or Compost 15.6 Cellulosic Ethanol 15.7 Edible Mushrooms 15.8 Production of Biofertilizers, Biopesticides, and Biostimulators of Plant Growth from Fermentation Processes Using Sugar Substrates 15.8.1 Biofertilization 15.8.2 Biocontrol 15.9 Direct Growth Promotion of the Plants 15.10 Conclusions References