Bioenergy Feedstocks Breeding and Genetics

Bioenergy and biofuels are generated from a wide variety of feedstock. Fuels have been converted from a wide range of sources from vegetable oils to grains and sugarcane. Second generation biofuels are being developed around dedicated, non-food energy crops, such as switchgrass and Miscanthus, with an eye toward bioenergy sustainability.  Bioenergy Feedstocks: Breeding and Genetics looks at advances in our understanding of the genetics and breeding practices across this diverse range of crops and provides readers with a valuable tool to improve cultivars and increase energy crop yields.

Bioenergy Feedstocks: Breeding and Genetics opens with chapters focusing primarily on advances in the genetics and molecular biology of dedicated energy crops. These chapters provide in-depth coverage of new, high-potential feedstocks. The remaining chapters provide valuable overview of breeding efforts of current feedstocks with specific attention paid to the development of bioenergy traits. Coverage in these chapters includes crops such as sorghum, energy canes, corn, and other grasses and forages.

The final chapters explore the role of transgenics in bioenergy feedstock production and the development of low-input strategies for producing bioenergy crops. A timely collection of work from a global team of bioenergy researchers and crop scientists, Bioenergy Feedstocks: Breeding and Genetics is an essential reference on cultivar improvement of biomass feedstock crops.

The Editors xi

List of Contributors xiii

Preface xix

1 Introduction 1

1.1 Historical Development 2

1.2 Cultivar Development 2

1.3 Breeding Approach 3

1.4 Molecular Tools 3

1.5 Future Outlook 4

References 4

2 Switchgrass Genetics and Breeding Challenges 7

2.1 Introduction 7

2.2 Origin and Distribution 9

2.3 Growth and Development, Genome Structure and Cytogenetics 9

2.3.1 Growth and Development 10

2.3.2 Genome Structure and Cytogenetics 12

2.4 Genetic Diversity 12

2.5 Phenotypic Variability and Inheritance 13

2.6 Conventional Breeding Approaches 14

2.6.1 Early Work 15

2.6.2 Systematic Recurrent Selection 15

2.6.3 Heterosis 17

2.7 Molecular Breeding 18

2.7.1 Molecular Markers Used for Switchgrass and Other Polyploids 18

2.7.2 Molecular Mapping 20

2.7.3 Association Mapping 22

2.7.4 Transgenic Approaches 23

2.8 Conclusions and Future Directions 23

References 24

3 Switchgrass Genomics 33

3.1 Introduction 33

3.2 Genome Sequencing 34

3.2.1 Other Available Sequence Resources 35

3.3 Analysis of Expressed Sequences in Switchgrass 36

3.4 Linkage Mapping 40

3.5 Cytoplasmic Genome 42

3.6 Genome-enabled Improvement of Switchgrass 42

3.7 Conclusions 45

References 45

4 Germplasm Resources of Miscanthus and Their Application in Breeding 49

4.1 Introduction 49

4.2 Species Belonging to Miscanthus Genus, Their Characteristics, and Phylogenetic Relationships 50

4.2.1 Section: Eumiscanthus 50

4.2.2 Section: Triarrhena 53

4.2.3 Section: Kariyasu 54

4.3 Natural Hybrids between Miscanthus Species 55

4.4 Karyotype Analysis 55

4.5 Phylogenetic Relationships between Miscanthus Species 56

4.6 Genetic Improvement of Miscanthus 57

4.6.1 Germplasm Collection and Management 57

4.6.2 Artificial Hybridization 57

4.6.3 Polyploidization 58

4.7 Variations in Several Agronomical Traits Related to Yield and Plant Performance 58

4.7.1 Variation in Flowering Time 58

4.7.2 Variation in Cold Tolerance 58

4.7.3 Variation in Lignin, Cellulose, and Mineral Content 59

4.8 Molecular Resources 60

4.8.1 Development of Linkage Map for Miscanthus 60

4.8.2 QTL Analysis of Traits Related to Yield and Mineral Content 60

4.8.3 Molecular Markers for Hybrids Identification 61

4.9 Transgenic Miscanthus 61

4.10 Future Studies 62

References 62

5 Breeding Miscanthus for Bioenergy 67

5.1 Introduction 67

5.2 Miscanthus as a Biomass Crop 67

5.3 Breeding Strategy 68

5.3.1 Collection and Characterization 68

5.3.2 Hybridization 68

5.3.3 Ex Situ Phenotypic Characterization 69

5.3.4 Large-scale Demonstration Trials 69

5.4 Genetic Diversity 69

5.5 Breeding Targets 70

5.5.1 Biomass Yield 70

5.5.2 Morphological Traits Contributing to High Yield Potential 75

5.5.3 Seed Propagation: Crop Diversification and Reducing the Cost of Establishment 77

5.6 Incorporating Bioinformatics, Molecular Marker-Assisted Selection (MAS), and Genome-Wide Association Selection (GWAS) 77

5.7 Summary 78

Acknowledgments 79

References 79

6 Breeding Sorghum as a Bioenergy Crop 83

6.1 Introduction 83

6.2 Botanical Description and Evolution 84

6.2.1 Basic Characteristics 84

6.2.2 Evolution and Distribution 85

6.3 Traditional Breeding and Development 86

6.3.1 Initial Sorghum Improvement 86

6.3.2 Development of Hybrid Sorghum and Heterosis 86

6.3.3 Current Sorghum Breeding Approaches 88

6.3.4 Germplasm Resources 88

6.4 Approaches to Breeding Sorghum as a Bioenergy Crop 90

6.4.1 Grain Sorghum 90

6.4.2 Sweet Sorghum 90

6.4.3 Biomass Sorghum 93

6.5 Composition in Energy Sorghum Breeding 93

6.6 Genetic Variation and Inheritance 95

6.6.1 Grain Sorghum 95

6.6.2 Grain Quality/Starch Composition 96

6.6.3 Dual Purpose—Grain and Stalk 97

6.6.4 Soluble Carbohydrates 97

6.6.5 Breeding for Stress Tolerance 99

6.7 Wide Hybridization 106

6.7.1 Interspecific Hybridization 106

6.7.2 Intergeneric Hybridization 107

6.8 Conclusions 107

References 107

7 Energy Cane 117

7.1 Introduction 117

7.2 Sugar and Energy Production Systems 118

7.2.1 Current Global Sugarcane Production 118

7.2.2 Bioenergy Production from Sugarcane in Brazil 120

7.2.3 Overview of Main Components in Existing Sugarcane Production Systems 120

7.2.4 Overview and Potential Trends 123

7.3 Sugarcane Improvement 124

7.3.1 Taxonomy and Crop Physiology 124

7.3.2 History of Sugarcane Breeding 127

7.3.3 Basic Features of Sugarcane Breeding Programs 128

7.3.4 Composition of Cane for Sugar or Energy Production 130

7.3.5 Application of Molecular Genetics in Developing Energy Cane 131

7.4 Selection of Sugarcane Genotypes for Energy Production 134

7.4.1 Overall Directions 134

7.4.2 Example of Economic Weightings for Selecting Sugarcane for Energy Products 136

7.4.3 Progress in Breeding for Energy Production 138

7.5 Conclusion 141

Acknowledgments 141

References 141

8 Breeding Maize for Lignocellulosic Biofuel Production 151

8.1 Introduction 151

8.2 General Attributes of Maize as a Biofuel Crop 151

8.3 Potential Uses of Maize Stover for Bioenergy 153

8.4 Breeding Maize for Biofuels 154

8.4.1 Selection Criteria 154

8.4.2 Stover Yield 157

8.4.3 Maximum Biomass Yield and the Effects of Time and Latitude 159

8.4.4 Stover Quality 161

8.4.5 Sustainability Parameters 163

8.4.6 Breeding Methods 164

8.5 Single Genes and Transgenes 165

8.6 Future Outlook 167

References 167

9 Underutilized Grasses 173

9.1 Introduction 173

9.2 Prairie Cordgrass 174

9.2.1 Importance 174

9.2.2 Genetic Variation and Breeding Methods 176

9.2.3 Future Goals 180

9.3 Bluestems 181

9.3.1 Importance 181

9.3.2 Genetic Variation and Breeding Methods 184

9.3.3 Future Goals 190

9.4 Eastern Gamagrass 191

9.4.1 Importance 191

9.4.2 Genetic Variation and Breeding Methods 192

9.4.3 Future Goals 196

References 197

10 Alfalfa as a Bioenergy Crop 207

10.1 Introduction 207

10.2 Biomass for Biofuels 208

10.2.1 Lignocellulose-based Biofuels 208

10.2.2 Plant Cell Wall Components 209

10.3 Why Alfalfa? 211

10.3.1 Background 211

10.3.2 Prospect as a Biofuel Feedstock 212

10.4 Breeding Strategies 213

10.4.1 Germplasm Resources 213

10.4.2 Cultivar Development 214

10.4.3 Synthetic Cultivars and Heterosis 214

10.4.4 Molecular Breeding 215

10.4.5 Trait Integration Through Biotechnology 216

10.5 Breeding Targets 217

10.5.1 Biomass Yield 217

10.5.2 Forage Quality and Composition 218

10.5.3 Stress Tolerance 219

10.5.4 Winter Hardiness 220

10.6 Management and Production Inputs 221

10.7 Processing for Biofuels 222

10.8 Additional Value from Alfalfa Production 223

10.8.1 Environmental Benefits 223

10.8.2 Alfalfa Co-products 223

10.9 Summary 223

Acknowledgments 224

References 224

11 Transgenics for Biomass 233

11.1 Introduction 233

11.1.1 Biomass for Biofuels 233

11.1.2 Biofuels 234

11.1.3 Lignocellulosic Biomass 234

11.2 Transgenic Approaches 235

11.2.1 Biolistics Transformation 235

11.2.2 Agrobacterium-mediated Transformation 236

11.3 Transgenic Approaches for Biomass Improvement 237

11.3.1 Improving Biomass Yield 237

11.3.2 Modifying Biomass Composition 240

11.3.3 Regulatory Issues of Transgenic Bioenergy Crops 242

11.4 Summary 242

Acknowledgments 242

References 243

12 Endophytes in Low-input Agriculture and Plant Biomass Production 249

12.1 Introduction 249

12.2 What are Endophytes? 249

12.3 Endophytes of Cool Season Grasses 251

12.4 Endophytes of Warm Season Grasses 251

12.5 Endophytes of Woody Angiosperms 253

12.6 Other Fungal Endophytes 253

12.7 Endophytes in Biomass Crop Production 254

12.8 The Use of Fungal Endophytes in Bioenergy Crop Production Systems 256

12.9 Endophyte Consortia 256

12.10 Source of Novel Compounds 257

12.11 Endophyte in Genetic Engineering of Host Plants 258

12.12 Conclusions 258

Acknowledgments 259

References 259

Index 267

Malay C. Saha is an Associate Professor and Principal Investigator of the Molecular Markers Lab, Forage Improvement Division at The Samuel Roberts Noble Foundation in Ardmore, OK.

Hem S. Bhandari is an Assistant Professor of Bioenergy/Biomass Feedstock Breeding and Genetics at the University of Tennessee, Knoxville, TN.

Joseph H. Bouton is the former Director and Senior Vice President, Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OKand Emeritus Professor of Crop and Soil Sciences at the University of Georgia, Athens, GA.