Contents

Series list

Acknowledgements

Introduction

Part 1 Plant physiology and breeding

Chapter 1 Sugarcane genome sequencing and genetic mapping,2

1 Introduction

2 Sequencing sugarcane genomes

3 Genetic linkage mapping

4 Mapping simply inherited and complex traits

5 Applications of the Bru1 marker

6 Conclusion and future trends

7 Where to look for further information

8 References

Chapter 2 Advances in understanding of sugarcane plant growth and physiology

1 Introduction

2 The importance of plant physiology

3 Carbon fixation, partitioning and biomass of sugarcane

4 Flowering of sugarcane

5 Crop and metabolic modelling of sugarcane

6 Conclusion and future trends

7 Abbreviations

8 Where to look for further information

9 References

Chapter 3 Ensuring and exploiting the genetic diversity of sugarcane

1 Introduction

2 Germplasm collections

3 Introgression of Saccharum spontaneum

4 Introgression of Erianthus

5 Introgression of other genera and species

6 Conclusions and future trends

7 Where to look for further information

8 References

Chapter 4 Advances in conventional sugarcane breeding programmes

1 Introduction

2 Historical context

3 Advances in breeding and selection systems

4 Current concerns

5 Future trends and conclusion

6 References

Chapter 5 Advances in marker-assisted breeding of sugarcane

1 Introduction

2 Sugarcane fingerprinting and variety identification

3 Sugarcane diversity analysis

4 Linkage mapping and QTL analysis

5 GWAS/SNP-based mapping and QTL analysis

6 Genomic selection

7 Future trends and conclusion

8 Where to look for further information

9 References

Chapter 6 Genetic improvement of sugarcane by transgenic, intragenic and genome editing technologies

1 Introduction

2 Tissue culture, gene transfer and selectable marker systems

3 Transgene expression for the improvement of agronomic traits

4 Case study: transgenic, intragenic and genome editing approaches to improve bioethanol production from sugarcane

5 Metabolic engineering to elevate sucrose yields and produce alternative sugars or value-added biomaterials

6 Future perspectives

7 Where to look for further information

8 References

Part 2 Progress in understanding and managing diseases, pests and we

Chapter 7 Ensuring biosecurity in sugarcane cultivation

1 Introduction

2 The National Plant Protection Organisation

3 Risk analysis of sugarcane biosecurity

4 Surveying

5 Effective quarantine arrangements

6 Dealing with disease/pest incursions: a case study

7 Future trends and conclusion

8 Where to look for further information

9 Appendix

10 References

Chapter 8 Viral metagenomics and sugarcane pathogens

1 Introduction

2 Detecting the multi-segmented Ramu stunt virus

3 Discovery of a new sugarcane mastrevirus using viral metagenomics

4 Study of the genetic diversity of Sugarcane yellow leaf virus

5 Computational identification of plant viruses from metagenomics-based datasets

6 Challenges of metagenomics research

7 Future application of metagenomics to plant diagnostics, myth or reality?

8 Acknowledgements

9 References

Chapter 9 Progress in understanding fungal diseases affecting sugarcane: red rot

1 Introduction

2 Symptoms and economic impact

3 Disease transmission

4 Diagnosis and disease management

5 Understanding host–pathogen interactions

6 Summary and future trends

7 Where to look for further information

8 Acknowledgements

9 References

Chapter 10 Progress in understanding fungal diseases affecting sugarcane

1 Introduction

2 Characteristics of the disease

3 Disease control and pathogen detection

4 Pathogenic and molecular variability of Sporisorium scitamineum

5 Insights into Sporisorium scitamineum biology based on genomic and transcriptomic data

6 Sugarcane responses to pathogen invasiveness and development

7 Conclusion

8 Future trends

9 Acknowledgements

10 References

Chapter 11 Progress in understanding fungal diseases affecting sugarcane

1 Introduction

2 Biology of rusts

3 Host plant resistance

4 Control of rusts

5 Brown rust

6 Orange rust

7 Tawny rust

8 Conclusion

9 References

Chapter 12 Progress in understanding viruses affecting sugarcane

1 Introduction

2 Progress in viral discovery

3 Progress in detecting strain variation

4 Progress in viral diagnostics

5 Progress in controlling viruses

6 Case studies

7 Conclusion and future trends

8 Where to look for further information

9 Acknowledgements

10 References

Chapter 13 Recent progress in understanding three major bacterial diseas

1 Introduction

2 Bacterial pathogens of sugarcane

3 Genomic features of bacterial pathogens of sugarcane

4 Transposon mutagenesis studies to identify genes for pathogenicity

5 Genomic features indicating spreading strategies

6 Bacterial invasion of xylem vessels and non-vascular tissues of sugarcane

7 Genomics-based hypotheses on the origin and adaptation of bacterial pathogens of sugarcane

8 Conclusion and future trends

9 Where to look for further information

10 References

Chapter 14 Managing the soil biological community to improve soil health

1 Introduction

2 Nematode pests of sugarcane

3 Economic importance of plant-parasitic nematodes

4 Nematode control measures

5 Nematode management from a systems perspective

6 Nematode pests: only one component of the soil biological community

7 Integrated soil biology management

8 Improving soil health and reducing losses from nematode pests

9 Sugarcane farming systems to improve soil health and enhance sustainability

10 The impact of improved farming systems on nematode pests

11 Future challenges

12 Conclusions

13 Where to look for further information

14 References

Chapter 15 Progress in understanding and managing insect pests affecting

1 Introduction

2 Categories of sugarcane pests

3 Estimating sugarcane crop losses from pests

4 Biological control and habitat management of sugarcane pests

5 Cultural control of sugarcane pests

6 Insecticides

7 Remote sensing, GIS and population modelling of sugarcane pests

8 Biosecurity

9 Conclusion and future trends

10 Where to look for further information

11 References

Chapter 16 Integrated disease management strategies in sugarcane cultiva

1 Introduction

2 Integrated disease management (IDM)

3 Managing diseases by controlling the pathogens

4 Managing diseases through the host

5 Managing diseases by controlling environment

6 Factors considered in integrated disease management strategies

7 Future trends

8 Where to look for further information

9 References

Chapter 17 Integrated weed management in sugarcane cultivation

1 Introduction

2 Integrated weed management: overview and cultural control

3 Integrated weed management: mechanical weed control

4 Chemical weed control as part of integrated weed management: overview and preplant and pre-emergence herbicides

5 Chemical weed control as part of integrated weed management: post-emergence herbicides

6 Conclusion

7 Where to look for further information

8 References

Index