Omics Approaches for Sugarcane Crop Improvement

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