Per McCord, USDA-ARS, USA

© Burleigh Dodds Science Publishing Limited, 2018. All rights reserved.

ContentsSeries list xi

Acknowledgements xv

Introduction xvii

Part 1 Plant physiology and breeding

1 Sugarcane genome sequencing and genetic mapping 3

Xiping Yang and Ramkrishna Kandel, University of Florida (Gainesville), USA; Jian Song, University of Florida (Gainesville), USA and Dezhou University, China; Qian You, University of Florida (Gainesville), USA and Fujian Agriculture and Forestry University, China; Mengjuan Wang, Fujian Agriculture and Forestry University, China; Jianping Wang, University of Florida (Gainesville), USA and Fujian Agriculture and Forestry University, China

1 Introduction 32 Sequencing sugarcane genomes 53 Genetic linkage mapping 104 Mapping simply inherited and complex traits 185 Applications of the Bru1 marker 236 Conclusion and future trends 247 Where to look for further information 258 References 25

2 Advances in understanding of sugarcane plant growth and physiology 35Frederik C. Botha, Sugar Research Australia and the University of Queensland, Australia

1 Introduction 352 The importance of plant physiology 363 Carbon fixation, partitioning and biomass of sugarcane 374 Flowering of sugarcane 495 Crop and metabolic modelling of sugarcane 516 Conclusion and future trends 527 Abbreviations 538 Where to look for further information 549 References 54

3 Ensuring and exploiting the genetic diversity of sugarcane 59Anna L. Hale, USDA-ARS, USA; Phillip Jackson, CSIRO, Australia; and James R. Todd, USDA-ARS, USA

1 Introduction 592 Germplasm collections 613 Introgression of Saccharum spontaneum 624 Introgression of Erianthus 645 Introgression of other genera and species 66

vi Contents


6 Conclusions and future trends 677 Where to look for further information 688 References 68

4 Advances in conventional sugarcane breeding programmes 75Phillip Jackson, CSIRO, Australia

1 Introduction 752 Historical context 763 Advances in breeding and selection systems 814 Current concerns 945 Future trends and conclusion 976 References 98

5 Advances in marker-assisted breeding of sugarcane 109Per McCord, USDA-ARS, USA

1 Introduction 1092 Sugarcane fingerprinting and variety identification 1103 Sugarcane diversity analysis 1114 Linkage mapping and QTL analysis 1135 GWAS/SNP-based mapping and QTL analysis 1216 Genomic selection 1237 Future trends and conclusion 1278 Where to look for further information 1289 References 128

6 Genetic improvement of sugarcane by transgenic, intragenic and genome editing technologies 133Fredy Altpeter and Ratna Karan, University of Florida, USA

1 Introduction 1332 Tissue culture, gene transfer and selectable marker systems 1343 Transgene expression for the improvement of agronomic traits 1364 Case study: transgenic, intragenic and genome editing approaches to

improve bioethanol production from sugarcane 1395 Metabolic engineering to elevate sucrose yields and produce

alternative sugars or value-added biomaterials 1426 Future perspectives 1457 Where to look for further information 1458 References 146

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

7 Ensuring biosecurity in sugarcane cultivation 157Nicole Thompson, Sugar Research Australia, Australia

1 Introduction 1572 The National Plant Protection Organisation 1583 Risk analysis of sugarcane biosecurity 1584 Surveying 1625 Effective quarantine arrangements 164


Contents vii

6 Dealing with disease/pest incursions: a case study 1707 Future trends and conclusion 1748 Where to look for further information 1749 Appendix 175

10 References 178

8 Viral metagenomics and sugarcane pathogens 183Philippe Roumagnac, CIRAD, France; Dimitre Mollov, USDA-ARS, USA; and Jean-Heinrich Daugrois and Denis Filloux, CIRAD, France

1 Introduction 1832 Detecting the multi-segmented Ramu stunt virus 1863 Discovery of a new sugarcane mastrevirus using viral metagenomics 1874 Study of the genetic diversity of Sugarcane yellow leaf virus 1875 Computational identification of plant viruses from metagenomics-based

datasets 1916 Challenges of metagenomics research 1917 Future application of metagenomics to plant diagnostics, myth or reality? 1958 Acknowledgements 1969 References 196

9 Progress in understanding fungal diseases affecting sugarcane: red rot 201R. Viswanathan, A. Ramesh Sundar, R. Selvakumar and P. Malathi, ICAR-Sugarcane Breeding Institute, India

1 Introduction 2012 Symptoms and economic impact 2023 Disease transmission 2064 Diagnosis and disease management 2075 Understanding host–pathogen interactions 2126 Summary and future trends 2157 Where to look for further information 2168 Acknowledgements 2169 References 216

10 Progress in understanding fungal diseases affecting sugarcane: smut 221Claudia B. Monteiro Vitorello, Patricia Dayane Carvalho Schaker, Juliana Benevenuto, Natália de Sousa Teixeira e Silva and Sintia Silva de Almeida, University of São Paulo, Brazil

1 Introduction 2212 Characteristics of the disease 2233 Disease control and pathogen detection 2254 Pathogenic and molecular variability of Sporisorium scitamineum 2265 Insights into Sporisorium scitamineum biology based on genomic and

transcriptomic data 2296 Sugarcane responses to pathogen invasiveness and development 2317 Conclusion 2348 Future trends 2359 Acknowledgements 236

10 References 236

viii Contents


11 Progress in understanding fungal diseases affecting sugarcane: rusts 245R. Stuart Rutherford, South African Sugarcane Research Institute (SASRI) and University of KwaZulu-Natal, South Africa

1 Introduction 2452 Biology of rusts 2463 Host plant resistance 2494 Control of rusts 2545 Brown rust 2566 Orange rust 2647 Tawny rust 2688 Conclusion 2729 References 273

12 Progress in understanding viruses affecting sugarcane 285Kathy Braithwaite, Sugar Research Australia, Australia

1 Introduction 2852 Progress in viral discovery 2863 Progress in detecting strain variation 2884 Progress in viral diagnostics 2895 Progress in controlling viruses 2916 Case studies 2937 Conclusion and future trends 3018 Where to look for further information 3029 Acknowledgements 302

10 References 303

13 Recent progress in understanding three major bacterial diseases of sugarcane: gumming, leaf scald and ratoon stunting 311Monique Royer, Isabelle Pieretti and Stéphane Cociancich, CIRAD, France; and Philippe Rott, University of Florida, USA

1 Introduction 3112 Bacterial pathogens of sugarcane 3133 Genomic features of bacterial pathogens of sugarcane 3164 Transposon mutagenesis studies to identify genes for pathogenicity 3195 Genomic features indicating spreading strategies 3206 Bacterial invasion of xylem vessels and non-vascular tissues

of sugarcane 3237 Genomics-based hypotheses on the origin and adaptation

of bacterial pathogens of sugarcane 3268 Conclusion and future trends 3299 Where to look for further information 330

10 References 330

14 Managing the soil biological community to improve soil health and reduce losses from nematode pests 337Graham R. Stirling, Biological Crop Protection Pty Ltd, Australia

1 Introduction 3372 Nematode pests of sugarcane 338


Contents ix

3 Economic importance of plant-parasitic nematodes 3414 Nematode control measures 3415 Nematode management from a systems perspective 3446 Nematode pests: only one component of the soil

biological community 3457 Integrated soil biology management 3478 Improving soil health and reducing losses from nematode pests 3489 Sugarcane farming systems to improve soil health and

enhance sustainability 34810 The impact of improved farming systems on nematode pests and

their natural enemies 34911 Future challenges 35212 Conclusions 35513 Where to look for further information 35614 References 356

15 Progress in understanding and managing insect pests affecting sugarcane 363François-Régis Goebel, CIRAD, France; Julien M. Beuzelin, University of Florida, USA; and Mike J. Way, South African Sugarcane Research Institute (SASRI), South Africa

1 Introduction 3632 Categories of sugarcane pests 3643 Estimating sugarcane crop losses from pests 3664 Biological control and habitat management of sugarcane pests 3695 Cultural control of sugarcane pests 3726 Insecticides 3767 Remote sensing, GIS and population modelling of sugarcane pests 3798 Biosecurity 3839 Conclusion and future trends 384

10 Where to look for further information 38611 References 386

16 Integrated disease management strategies in sugarcane cultivation 395Jack C. Comstock and Sushma G. Sood, USDA-ARS, USA

1 Introduction 3952 Integrated disease management (IDM) 4003 Managing diseases by controlling the pathogens 4004 Managing diseases through the host 4075 Managing diseases by controlling environment 4126 Factors considered in integrated disease management strategies 4127 Future trends 4138 Where to look for further information 4159 References 417

17 Integrated weed management in sugarcane cultivation 421Calvin Odero, University of Florida, USA

1 Introduction 4212 Integrated weed management: overview and cultural control 424

x Contents


3 Integrated weed management: mechanical weed control 4274 Chemical weed control as part of integrated weed management:

overview and preplant and pre-emergence herbicides 4285 Chemical weed control as part of integrated weed management:

post-emergence herbicides 4326 Conclusion 4337 Where to look for further information 4348 References 434

Index 441


IntroductionSugarcane is the source of about three quarters of the world’s sugar, and is grown widely in the tropics and sub-tropics. Despite rising demand, average yields have not increased significantly, partly because of continued vulnerability to pests and diseases. In addition, cultivation has been seen as damaging biodiversity and soil health with a negative effect on both yields and the environment.

These volumes on achieving sustainable cultivation of sugarcane summarise the wealth of research addressing these challenges. Volume 1 reviews cultivation techniques and sustainability issues. This volume, Volume 2 reviews how the challenges facing sugarcane production can be addressed through developments in breeding as well as better management of pests and diseases. The volume covers key advances in breeding, including conventional and molecular breeding techniques. It also summarises key advances in understanding bacterial, fungal and viral diseases of sugarcane and assesses best practices in integrated disease, pest and weed management.

Part 1 Plant physiology and breedingThe first part of the volume assesses the latest research on sugarcane genetics, physiology and genetic diversity, and how this is informing advances in conventional and molecular breeding techniques. The focus of Chapter 1 is on sugarcane genome sequencing and genetic mapping. The chapter explains the difficulties of sequencing and mapping the genome of sugarcane and strategies to overcome these difficulties. The chapter outlines progress on sugarcane sequencing, genetic mapping of simply inherited and complex traits. The chapter then focuses on the mapping of a gene controlling sugarcane brown rust resistance, Bru1, which exemplifies the potential of marker-assisted selection. Finally, the chapter discusses prospects for future research in sugarcane genome sequencing and genetic mapping.

Following on from the previous chapter’s focus on sugarcane genomics, Chapter 2 examines advances in understanding sugarcane plant growth and physiology. Crop yield in sugarcane depends on how well the source leaves can supply the assimilates needed for the growth and filling of the harvestable plant. This is the source-sink relationship which remains poorly understood in sugarcane. The chapter discusses significant advances made in this area in the past few decades, as well as suggesting future trends in research such as high throughput genomic, metabolomic and phenotypic analyses that could allow refinement in crop and metabolic modelling, as well as improved breeding and production strategies.

Returning to the theme of the genetics of sugarcane, Chapter 3 examines the challenges of ensuring and exploiting the genetic diversity of sugarcane. The majority of cultivars in current commercial sugarcane breeding programs can be traced back to a few key interspecific hybrids that were developed during the early 1900s. Sugarcane breeders have expressed concerns about the narrow sampling of ancestral clones in modern sugarcane breeding programs, and this concern has prompted periodic attempts at so-called ‘base-broadening’ programs. The chapter provides an overview of sugarcane germplasm collections and then describes introgression-related research and breeding efforts focused on use of plant species belonging to the genera of Saccharum, Erianthus and others. It emphasizes the difficulties and challenges that need to be overcome in

xviii Introduction


order to achieve successful outcomes from introgression breeding, and considers a few possible future directions for research.

Chapter 4 shifts the focus to advances in conventional sugarcane breeding programs. All sugarcane cultivars currently grown throughout the world arise from breeding programs which have used a reasonably similar approach sustained over many decades. This approach comprises a continuous pipeline of regular (usually annual) crossing among selected parent clones to produce large populations of seedling clones, followed by selection of these clones in successive stages of field trials for 9–12 years for important traits. The chapter outlines the history and structure of sugarcane breeding programs as a context for considering efforts to advance rates of progress. The chapter reviews studies conducted in the last 30 years to improve many specific aspects of operations in sugarcane breeding programs. The chapter describes emerging concerns about whether current rates of genetic gain in sugarcane are optimal, and suggests some avenues for faster gains.

Continuing the theme of sugarcane breeding and complementing the preceding chapter, Chapter 5 considers advances in marker-assisted breeding of sugarcane. Sugarcane breeding has, until very recently, been based solely on phenotype, and marker-assisted breeding of sugarcane remains in its infancy compared with row crops such as maize and soybean. A major reason for this is the complex genetics of sugarcane. This chapter reviews the uses of DNA marker technology in sugarcane for fingerprinting and diversity analysis. This is followed by a review of the development of linkage maps and initial trait/QTL mapping, including the Bru1 locus for resistance to brown rust (Puccinia melanocephala). Finally, the chapter reviews the use of newer next generation sequencing (NGS)-based technologies in sugarcane, including genome-wide association analysis (GWAS) and genomic selection (GS).

Concluding the first part of the volume, Chapter 6 focusses on genetic improvement of sugarcane by transgenic, intragenic and genome editing technologies. The chapter explores the role of tissue culture, gene transfer and selectable marker systems in genetically improving sugarcane. It includes a detailed case study on transgenic, intragenic and genome editing approaches to improve bioethanol production from sugarcane. The chapter also addresses the role of metabolic engineering in elevating sucrose yields and producing alternative sugars or value-added biomaterials.

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

The second part of the volume discusses progress in understanding bacterial, fungal and viral diseases and their management, followed by the management of insect and nematode pests as well as weeds. Chapter 7 focusses on the challenge of ensuring biosecurity in sugarcane cultivation. Biosecurity is an important factor in maintaining and improving yields. It can refer to the day-to-day management of established pests, diseases, and weeds, as well as preparing for unusual threats to the industry, and safeguarding agriculture and natural resources. The chapter focuses on the sugarcane industry’s preparedness for exotic pathogens, describing techniques such as pest risk analysis, quarantine control and surveys. The chapter discusses emerging technologies and examines and compares current guidelines. Finally, the chapter presents a case study of the 2006 sugarcane smut incursion in Australia.


Introduction xix

Continuing the theme of understanding diseases of sugarcane, Chapter 8 addresses viral metagenomics and sugarcane pathogens. Plant viral metagenomics has recently proved effective for studying the collection of plant viruses. The advent of metagenomics-based approaches has led to the discovery and characterization of new plant viruses and helped solving etiological enigmas. The chapter describes the plant virus metagenomics methods developed during the last decade before focusing on the use and application of these approaches in the field of sugarcane pathology. The chapter presents three recent studies that have used viral metagenomics-based approaches aimed at solving long-standing etiological enigmas, identifying known and potentially new sugarcane viruses in a sugarcane quarantine context, and assessing the diversity of a known sugarcane virus (Sugarcane yellow leaf virus). Finally, the chapter discusses the challenges and opportunities of using such approaches to address issues of plant pathology.

Moving from viral to fungal diseases of sugarcane, Chapter 9 discusses progress in understanding fungal diseases affecting sugarcane, with a specific focus on red rot, a disease of sugarcane stalks caused by the fungal pathogen Colletotrichum falcatum. Red rot has been recorded in 77 countries worldwide, but occurs most severely in south Asian countries, especially India, Nepal, Pakistan, Myanmar and Bangladesh, as well as Thailand and Vietnam. Developing red rot-resistant varieties has been the major management strategy to deal with the disease in most countries. The chapter reviews the economic impact of red rot, diagnosis, pathogen variability, application of molecular tools to understand pathogen biology, varietal resistance, screening methods and new management approaches including fungicide delivery.

Complementing the previous chapter’s focus on fungal diseases of sugarcane, Chapter 10 focuses on sugarcane smut. Fungal diseases of sugarcane constitute a worldwide threat to cultivation. Smut is caused by the biotrophic fungus Sporisorium scitamineum. After offering a historical perspective on the disease, the chapter presents an overview of data gathered over the past few years using ‘omics’ techniques (genomics, transcriptomics, proteomics and metabolomics) in combination with functional studies performed to identify candidate genes involved in the interaction between the pathogen and the host plant. The chapter discusses studies aimed at deciphering the molecular cross-talking between sugarcane and Sporisorium scitamineum along with new trends and recurring issues in the study of smut disease.

Continuing the theme of fungal diseases, Chapter 11 considers progress in understanding sugarcane rusts. Rust fungi (Uredinales or Pucciniales) are a globally distributed order of obligate parasitic fungi occurring on vascular plants. The typical symptom is a ‘rust-coloured’ (often orange or yellow) pustule on a plant leaf. Economically, rust fungi cause enormous crop losses, including in sugarcane. The chapter summarizes current knowledge of sugarcane rusts in terms of the relevant background biology, pathogen dispersal, disease identification, environmental conditions favouring disease emergence, crop loss, host-plant resistance and control measures. The chapter focuses on the history, identification and control of three rust diseases of sugarcane: brown, orange and tawny rust.

Chapter 12 moves from fungi to consider progress in understanding viruses affecting sugarcane. There are currently around ten diseases of sugarcane known to be caused by viruses. In recent years, our understanding of these diseases has greatly benefitted from access to low cost sequencing technologies which have revolutionised virus discovery, improved our understanding of genetic variation in viral populations, improved diagnostic options and helped us to understand gene functions and identify gene targets for control. The chapter addresses the broad themes of virus discovery, genetic variation, diagnostic

xx Introduction


technologies and control. The chapter presents case studies describing the impact of two major viral diseases in Papua New Guinea and Indonesia.

Switching to bacterial diseases of sugarcane, Chapter 13 considers recent progress in understanding three major bacterial diseases: gumming, leaf scald and ratoon stunting. The chapter describes new insights provided by genomic and microscopy analyses of the bacterial pathogens Xanthomonas vasicola pv. vasculorum, X. albilineans, and Leifsonia xyli subsp. xyli, the causal agents of gumming, leaf scald, and ratoon stunting, respectively. The chapter addresses genomic-based hypotheses regarding adaptation of the three pathogens to sugarcane and the origin of their respective ancestors. It examines the strategies used by X. albilineans and L. xyli subsp. xyli to spread in sugarcane, including bacterial invasion of xylem vessels and non-vascular tissues. The chapter looks ahead to the development of further functional studies to improve the understanding of the interactions between sugarcane and bacterial pathogens, which are likely to contribute to better control of bacterial diseases of sugarcane.

Chapter 14 moves to consider the challenge of nematode pests of sugarcane by focussing on managing the soil biological community to improve soil health and reduce losses from nematode pests. Most sugarcane fields are infested with at least five species of plant-parasitic nematodes, with Pratylenchus and Meloidogyne considered the most damaging genera. The chapter describes the main nematode pests and the community of organisms with which they co-exist before analysing existing nematode control measures and their economic importance. The chapter then describes how a broader approach focusing on improving soil health can mitigate the impact of nematodes and ensure sustainable sugarcane production.

The theme of Chapter 15 is progress in understanding and managing insect pests affecting sugarcane. The chapter describes major achievements in pest management in sugarcane agroecosystems based on applied research conducted in different countries. The focus of the chapter is on two major groups of pests, stalk borers (Lepidoptera) and white grubs (Coleoptera). Chapter sections address determination of crop losses, biological control using parasitoids and entomopathogens, push-pull strategies with the use of companion (or service) plants, agricultural practices and their influence on pest population dynamics, insecticide use and biosecurity. The chapter also discusses new tools for pest detection and management such as modeling, remote sensing, and use of geographical information systems (GIS). The chapter looks ahead to future developments in integrated pest management of sugarcane.

Bringing together the insights of preceding chapters on particular diseases, Chapter 16 focuses on Integrated Disease Management (IDM) strategies in sugarcane cultivation. As has been noted, sugarcane diseases cause severe losses to sugar production around the world. More than a hundred bacterial, fungal, phytoplasma and viral diseases are present in sugarcane growing areas worldwide. Some diseases are present in most sugarcane growing regions while others are confined to specific countries. The chapter outlines and explores the various disease management strategies used in sugarcane cropping systems around the world and the potential for integrated disease management to minimize losses and maximize profitability. The chapter covers management of diseases by controlling the pathogens, management of diseases through the host, and management of diseases by controlling the environment, before looking ahead to future research trends in this field.

Complementing the preceding chapter’s focus on integrated disease management, the volume’s concluding chapter, Chapter 17, concentrates on the related challenges of Integrated Weed Management (IWM) in sugarcane cultivation. Weeds reduce sugarcane


Introduction xxi

yield by competing for water, nutrients and light. They may also act as alternate hosts for disease and insect pests, increase production costs and lower land value. Implementation of integrated weed management in sugarcane is essential for reducing the negative impact of weeds to economically acceptable levels. Understanding of the critical period of weed control is important so that IWM strategies can be developed to maximize control measures. The chapter deals with an integrated approach involving different methods for effective weed management in sugarcane that can be adopted for sustainable production, involving cultural, mechanical and chemical weed control.

Avoidance, of IDM 412

Bacterial pathogensdescription 313–316genomic features of 316–318, 320–323genomics-based hypotheses 326–328overview 311–313transposon mutagenesis 319–320xylem vessels and non-vascular tissues

323–326Biological control, red rot 211Biomass yield 115–118Biosecurity 383–384

National Plant Protection Organisation (NPPO) 158

overview 157–158quarantine arrangements

clonal materials 167–169closed facility requirements 165–166disease and pathogen testing laboratory

requirements 166‘endpoint’ facilities 164–165open facility requirements 166pathogen diagnostics 169–170setts 167tissue cultures 167true seed 169Visacane 164

risk analysis offinal PRA 161–162initiation 159pest risk management 160–161PRA 159–160

sugarcane smut incursion 170–173surveying

future of surveillance 163sugarcane streak mosaic virus

(SCSMV) 163–164survey design 162

Brown rustconditions favouring 258–262control 264history 256–258identification 258resistance 262–263yield losses 262

Bru1 23–24, 114–115

C. falcatumgenome and transcriptome 212pathogenic variation of 212

Carbon partitioning 44–46Chemical control, red rot 209–211Chemical weed control

overview 428–429

post-emergence herbicides 432–433preplant and pre-emergence

herbicides 429–431Clonal materials 167–169Clonal selection systems 86–88Closed facility requirements 165–166Conventional sugarcane breeding

clonal selection systems 86–88current programmes 78–81disease and pest resistance 91–94history of 77–78long-term genetic gain 94–96objectives and traits of 81–84overview 75–76parental selection and crossing 85–86phenotyping 88–90taxonomy and origin 76–77use of DNA markers 96–97

Crop and metabolic modelling 51Crop rotation 341–342Cultural control, of sugarcane pests 372–376Cultural weed control 425–426

Disease and pathogen testing laboratory requirements 166

Disease-free seedcane nurseries 406Disease resistance 119–120Diversity analysis 111–113DNA markers 96–97

‘Endpoint’ facilities 164–165Entomopathogens 371Erianthus 64–66

Feedback inhibition 42Fingerprinting and variety identification

110–111Free-living nematodes 345–346Fungal and oomycete pathogens 346Fungal diseases

brown rustconditions favouring 258–262control 264history 256–258identification 258resistance 262–263yield losses 262

host plant resistancebreeding for 253–254non-host resistance 249–252race-nonspecific (quantitative) 252–253race-specific (qualitative) 252

orange rustconditions favouring 265control 267

Index


Index442


history 264identification 264–265resistance 266–267yield loss 266

overview 245–246rusts

biological control of 256chemical control of 254–255dispersal 248–249genetic variability 249life cycle 246–248plant nutrition 256

tawny rustconditions favouring 270–271history 268–269identification 269–270resistance 271

Genetic diversityErianthus 64–66germplasm collections 61–62other genera and species 66–67overview 59–61Saccharum spontaneum 62–64

Genetic improvementgene transfer and selectable marker

systems 135–136genome editing approaches 141–142intragenic approaches 140–141overview 133–134polyhydroxybutyrate (PHB) 144stem-specific expression 143–144sucrose and sucrose isomers 142–143tissue culture 134–135transgene expression 136–139transgenic approaches 139–140triacylglycerol (TAG) 144–145

Genetic linkage mappingdescription 10–11hybrids and commercial cultivars 17–18population and marker systems 11–13of Saccharum officinarum 17of Saccharum spontaneum 13–17

Gene transfer 135–136Genome editing approaches 141–142Genome sequencing and genetic mapping

Bru1 marker 23–24difficulties and strategies 5–6genetic linkage mapping

description 10–11hybrids and commercial cultivars 17–18population and marker systems 11–13of Saccharum officinarum 17of Saccharum spontaneum 13–17

mapping simply inherited traits 18–19overview 3–5progress of 6–8

QTL mapping of complex traits 20–23transcriptome sequencing 8–10

Genomic features, of bacterial pathogens 316–318

Genomics-based hypotheses 326–328Genomic selection 123–127Germplasm collections 61–62GWAS/SNP-based mapping 121–122

Host plant resistancebreeding for 253–254non-host resistance 249–252race-nonspecific (quantitative) 252–253race-specific (qualitative) 252

Hot water treatment, and inoculum 403–405Hymenoptera parasitoids 370–371

IDM. see integrated disease management (IDM)Inoculum eradiation

disease-free seedcane nurseries 406hot water treatment and tissue culture

403–405sanitation 406

Integrated disease management (IDM)avoidance 412clean seedcane 415detection 414exclusion 400–403factors considered in 412–413forecasting 414host resistance 407–411inoculum eradiation

disease-free seedcane nurseries 406hot water treatment and tissue

culture 403–405sanitation 406

overview 395–399protection 411resistance 414–415therapy 406–407

Integrated weed managementchemical weed control

overview 428–429post-emergence herbicides 432–433preplant and pre-emergence

herbicides 429–431cultural weed control 425–426mechanical weed control 427–428overview 421–424

Intragenic approaches 140–141

Leaf feeders 365Leaf senescence and sucrose 42Linkage mapping and QTL analysis

Bru1 114–115disease resistance 119–120new marker technologies 120–121


Index 443

nutrient use efficiency 120sucrose content and biomass yield 115–118

Lodging 49Long-term genetic gain 94–96

Marker-assisted breedingdiversity analysis 111–113fingerprinting and variety identification

110–111genomic selection 123–127GWAS/SNP-based mapping and QTL

analysis 121–122linkage mapping and QTL analysis

Bru1 114–115disease resistance 119–120new marker technologies 120–121nutrient use efficiency 120sucrose content and biomass yield

115–118overview 109–110

Mastrevirus 187Mechanical weed control 427–428Multi-segmented Ramu stunt virus 186

National Plant Protection Organisation (NPPO) 158

Nematicides 343Nematode pests

crop rotation 341–342impact of improved farming systems

on 349–352key pests 340nematicides 343other plant-feeding nematodes 340–341reducing losses from 348resistance and tolerance 342–343second-tier pests 340systems perspective 344–345

Nitrogen use efficiency 41NPPO. see National Plant Protection

Organisation (NPPO)Nutrient use efficiency 120

Open facility requirements 166Orange rust

conditions favouring 265control 267history 264identification 264–265resistance 266–267yield loss 266

Pathogen diagnostics 169–170Pest risk management 160–161Phenotyping 88–90Plant growth and physiology

crop and metabolic modelling 51importance of 36

lodging 49overview 35–36radiation use efficiency (RUE) 48–49ripening 47–48sink metabolism

carbon partitioning 44–46respiration 46sink strength 43–44sucrose accumulation 46–47

source metabolismdescription 38–40environmental factors 40–41feedback inhibition 42leaf senescence and sucrose 42nitrogen use efficiency 41

sugarcane floweringimportance in plant breeding 50–51negative impact on yield 50

supply and demand 37–38Polyhydroxybutyrate (PHB) 144Post-emergence herbicides 432–433Preplant and pre-emergence herbicides

429–431Push-pull strategy and companion plants

371–372

QTL analysisand GWAS/SNP-based mapping 121–122linkage mapping and

Bru1 114–115disease resistance 119–120new marker technologies 120–121nutrient use efficiency 120sucrose content and biomass yield

115–118Quarantine arrangements

clonal materials 167–169closed facility requirements 165–166disease and pathogen testing laboratory

requirements 166‘endpoint’ facilities 164–165open facility requirements 166pathogen diagnostics 169–170setts 167tissue cultures 167true seed 169Visacane 164

Radiation use efficiency (RUE) 48–49Red rot

biological control 211breeding for resistance 208–209C. falcatum

genome and transcriptome 212pathogenic variation of 212

characterization of pathogenicity 214–215chemical control 209–211detection of 207–208

Index444


disease transmission 206–207identification of 212–214induced resistance 214overview 201–202symptoms and economic impact 202–206systemic resistance 211–212

Remote sensing, and GIS 379–383Respiration 46Ripening 47–48Risk analysis, of biosecurity

final PRA 161–162initiation 159pest risk management 160–161PRA 159–160

Root feeders 365RUE. see radiation use efficiency (RUE)Rusts

biological control of 256chemical control of 254–255dispersal 248–249genetic variability 249life cycle 246–248plant nutrition 256

Saccharum officinarum 17Saccharum spontaneum 62–64

genetic linkage mapping of 13–17Sanitation, and inoculum eradiation 406Sap feeders 366SCSMV. see sugarcane streak mosaic virus

(SCSMV)SCYLV. see Sugarcane yellow leaf virus (SCYLV)Second-tier pests 340Selectable marker systems 135–136Setts 167Sink metabolism

carbon partitioning 44–46respiration 46sink strength 43–44sucrose accumulation 46–47

Sink strength 43–44Smut fungi

characteristics 223–225disease control and pathogen

detection 225–226invasiveness and development 231–234overview 221–223Sporisorium scitamineum

biology based on genomic and transcriptomic data 229–231

pathogenic and molecular variability of 226–228

Soil biological communitybeneficial species 346–347free-living nematodes 345–346fungal and oomycete pathogens 346holistic management of 354–355increasing organic carbon levels in 352–354

integrated management 347nematode pests

crop rotation 341–342impact of improved farming systems

on 349–352key pests 340nematicides 343other plant-feeding nematodes 340–341reducing losses from 348resistance and tolerance 342–343second-tier pests 340systems perspective 344–345

overview 337–338plant-parasitic nematodes 341 345sugarcane farming systems 348–349

Source metabolismdescription 38–40environmental factors 40–41feedback inhibition 42leaf senescence and sucrose 42nitrogen use efficiency 41

Sporisorium scitamineumbiology based on genomic and

transcriptomic data 229–231pathogenic and molecular variability

of 226–228Stalk feeders 364–365Stem-specific expression 143–144Sucrose accumulation 46–47Sucrose content and biomass yield 115–118Sucrose isomers 142–143Sugarcane flowering

importance in plant breeding 50–51negative impact on yield 50

Sugarcane pestsbiosecurity 383–384crop losses from 366–369cultural control of 372–376entomopathogens 371hymenoptera parasitoids 370–371insecticides 376–379leaf feeders 365overview 363–364push-pull strategy and companion plants

in 371–372remote sensing and GIS 379–383root feeders 365sap feeders 366stalk feeders 364–365

Sugarcane smut incursion 170–173Sugarcane streak mosaic virus (SCSMV)

163–164Sugarcane yellow leaf virus (SCYLV) 187–191Surveying, and biosecurity

future of surveillance 163sugarcane streak mosaic virus (SCSMV)

163–164survey design 162


Index 445

TAG. see triacylglycerol (TAG)Tawny rust

conditions favouring 270–271history 268–269identification 269–270resistance 271

Tissue cultures 134–135, 167and inoculum 403–405

Transgene expression 136–139Transgenic approaches 139–140Transposon mutagenesis 319–320Triacylglycerol (TAG) 144–145True seed 169

Viral metagenomicsapproaches 184–186challenge of determining causation 193challenge of sanitation and legal

aspects 193–194challenge of sharing datasets 194–195

computational identification 191ecological role of cryptic viruses 192–193mastrevirus 187multi-segmented Ramu stunt virus 186overview 183–184Sugarcane yellow leaf virus (SCYLV) 187–191‘unknown’ reads and contigs 191–192

Viruses, affecting sugarcaneoverview 285–286progress in controlling 291–293progress in detecting strain variation

288–289progress in viral diagnostics 289–291progress in viral discovery 286–287Ramu stunt disease in Papua New

Guinea 293–297streak mosaic in Indonesia 297–301

Visacane 164

Xylem vessels, and non-vascular tissues 323–326

Documents

Per McCord, USDA-ARS, USA