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 2.4 Genetic Diversity 12 2.5 Phenotypic Variability and Inheritance 13 2.6 Conventional Breeding Approaches 14 2.7 Molecular Breeding 18 2.8 Conclusions and Future Directions 23 References 24 3 Switchgrass Genomics 33 3.1 Introduction 33 3.2 Genome Sequencing 34 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 4.3 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 4.7 Variations in Several Agronomical Traits Related to Yield and Plant Performance 58 4.8 Molecular Resources 60 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 5.4 Genetic Diversity 69 5.5 Breeding Targets 70 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 6.3 Traditional Breeding and Development 86 6.4 Approaches to Breeding Sorghum as a Bioenergy Crop 90 6.5 Composition in Energy Sorghum Breeding 93 6.6 Genetic Variation and Inheritance 95 6.7 Wide Hybridization 106 6.8 Conclusions 107 References 107 7 Energy Cane 117 7.1 Introduction 117 7.2 Sugar and Energy Production Systems 118 7.3 Sugarcane Improvement 124 7.4 Selection of Sugarcane Genotypes for Energy Production 134 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 8.5 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 9.3 Bluestems 181 9.4 Eastern Gamagrass 191 References 197 10 Alfalfa as a Bioenergy Crop 207 10.1 Introduction 207 10.2 Biomass for Biofuels 208 10.3 Why Alfalfa? 211 10.4 Breeding Strategies 213 10.5 Breeding Targets 217 10.6 Management and Production Inputs 221 10.7 Processing for Biofuels 222 10.8 Additional Value from Alfalfa Production 223 10.9 Summary 223 Acknowledgments 224 References 224 11 Transgenics for Biomass 233 11.1 Introduction 233 11.2 Transgenic Approaches 235 11.3 Transgenic Approaches for Biomass Improvement 237 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 Color plate is located between pages 172 and 173.

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.

“While some of the more in depth sections about the analysis of DNA sequences and plant proteins may be beyond the requirements of casual readers and feedstock producers, there is much here which is relevant to increasing yields and comparing production techniques, making it a useful reference for anyone seriously involved in the production of bioenergy crops, particularly agronomists and advisors.”  ( Bioenergy Weekly , 15 July 2013)