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Computational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as "-omics," have been used to study plant biology for well over a decade now. As these technologies mature, plant and crop scientists have started using these methods to improve crop varieties. Omics in Plant Breeding provides a timely introduction to key omicsbased methods and their application in plant breeding. Omics in Plant Breeding is a practical and accessible overview of specific omics-based methods ranging from metabolomics to phenomics. Covering a single methodology…mehr
Computational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as "-omics," have been used to study plant biology for well over a decade now. As these technologies mature, plant and crop scientists have started using these methods to improve crop varieties. Omics in Plant Breeding provides a timely introduction to key omicsbased methods and their application in plant breeding. Omics in Plant Breeding is a practical and accessible overview of specific omics-based methods ranging from metabolomics to phenomics. Covering a single methodology within each chapter, this book provides thorough coverage that ensures a strong understanding of each methodology both in its application to, and improvement of, plant breeding. Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field. * A valuable overview of high-throughput, genomics-based technologies and their applications to plant breeding * Each chapter explores a single methodology, allowing for detailed and thorough coverage * Coverage ranges from well-established methodologies, such as genomics and proteomics, to emerging technologies, including phenomics and physionomics Aluízio Borém is a Professor of Plant Breeding at the University of Viçosa in Brazil. Roberto Fritsche-Neto is a Professor of Genetics and Plant Breeding at the University of São Paulo in Brazil.
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Autorenporträt
Aluzio Borem de Olieviera is a Professor of Crop Science at the University of Viçosa in Brazil. Prof. Borem received his Ph.D from the University of Minnesota. He has written, or contributed to, more than 50 books in his career. Roberto Fritsche-Neto is an Adjunct Professor of Crop Science at the University of Viçosa in Brazil. Dr. Fritsche-Neto has co-edited two volumes, Plant Breeding for Biotic Stress Resistance and Plant Breeding for Abiotic Stress Resistance. Both published by Springer in 2012.
Inhaltsangabe
List of Contributors ix Foreword xiii 1 Omics: Opening up the "Black Box" of the Phenotype 1 Roberto Fritsche-Neto and Aluizio Borem The Post-Genomics Era 3 The Omics in Plant Breeding 4 Genomics, Precision Genomics, and RNA Interference 5 Transcriptomics and Proteomics 8 Metabolomics and Physiognomics 8 Phenomics 9 Bioinformatics 10 Prospects 10 References 10 2 Genomics 13 Antonio Costa de Oliveira, Luciano Carlos da Maia, Daniel da Rosa Farias, and Naciele Marini The Rise of Genomics 13 DNA Sequencing 13 Development of Sequence-based Markers 18 Genome Wide Selection (GWS) 25 Structural and Comparative Genomics 27 References 28 3 Transcriptomics 33 Carolina Munari Rodrigues, Valeria S. Mafra, and Marcos Antonio Machado Methods of Studying the Transcriptome 34 Applications of Transcriptomics Approaches for Crop Breeding 46 Conclusions and Future Prospects 51 Acknowledgements 51 References 51 4 Proteomics 59 Ilara Gabriela F. Budzinski, Thais Regiani, Monica T. Veneziano Labate, Simone Guidetti-Gonzalez, Danielle Izilda R. da Silva, Maria Juliana Calderan Rodrigues, Janaina de Santana Borges, Ivan Miletovic Mozol, and Carlos Alberto Labate History 59 Different Methods for the Extraction of Total Proteins 60 Subcellular Proteomics 64 Post-Translational Modifications 66 Quantitative Proteomics 69 Perspectives 72 References 73 5 Metabolomics 81 Valdir Diola (in memoriam), Danilo de Menezes Daloso, and Werner Camargos Antunes Introduction 81 Metabolomic and Biochemical Molecules 83 Technologies for Metabolomics 83 Metabolomic Database Analysis 86 Metabolomics Applications 89 Metabolomics-assisted Plant Breeding 91 Associative Genome Mapping and mQTL Profiles 95 Large-scale Phenotyping Using Metabolomics 97 Conclusion and Outlook 98 References 99 6 Physionomics 103 Frederico Almeida de Jesus, Agustin Zsogon, and Lazaro Eustaquio Pereira Peres Introduction 103 Early Studies on Plant Physiology and the Discovery of Photosynthesis 104 Biochemical Approaches to Plant Physiology and the Discovery of Plant Hormones 104 Genetic Approaches to Plant Physiology and the Discovery of Hormone Signal Transduction Pathways 106 Alternative Genetic Models for Omics Approaches in Plant Physiology 112 "Physionomics" as an Integrator of Various Omics for Functional Studies and Plant Breeding 117 Acknowledgements 121 References 121 7 Phenomics 127 Roberto Fritsche-Neto, Aluizio Borem, and Joshua N. Cobb Introduction 127 Examples of Large-scale Phenotyping 128 Important Aspects for Phenomics Implementation 134 Main Breeding Applications 141 Final Considerations 144 References 144 8 Electrophoresis, Chromatography, and Mass Spectrometry 147 Thais Regiani, Ilara Gabriela F. Budzinski, Simone Guidetti-Gonzalez, Monica T. Veneziano Labate, Fernando Cotinguiba, Felipe G. Marques, Fabricio E. Moraes, and Carlos Alberto Labate Introduction 147 Two-dimensional Electrophoresis (2DE) 148 Chromatography 150 Mass Spectrometry 155 Data Analysis 161 References 164 9 Bioinformatics 167 J. Miguel Ortega and Fabricio R. Santos Introduction 167 The "Omics" Megadata and Bioinformatics 167 Hardware for Modern Bioinformatics 169 Software for Genomic Sequencing 170 Software for Contig Assembling 172 Assembly Using the Graph Theory 173 New Approaches in Bioinformatics for DNA and RNA Sequencing 174 Databases, Identification of Homologous Sequences and Functional Annotation 175 Annotation of a Complete Genome 179 Computational System with Chained Tasks Manager (Workflow) 181 Applications for Studies in Plants 182 Final Considerations 183 References 184 10 Precision Genetic Engineering 187 Thiago J. Nakayama, Aluizio Borem, Lucimara Chiari, Hugo Bruno Correa Molinari, and Alexandre Lima Nepomuceno Introduction 187 Zinc Finger Nucleases (ZFNs) 190 Transcription Activator-like Effector Nucleases (TALENs) 193 Meganucleases (LHEs: LAGLIDADG Homing Endonucleases) 194 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) 195 Implications and Perspectives of the use of PGE in Plant Breeding 197 References 202 11 RNA Interference 207 Francisco J.L. Aragao, Abdulrazak B. Ibrahim, and Maria Laine P. Tinoco Introduction 207 Discovery of RNAi 208 Mechanism of RNA Interference 209 Applications in Plant Breeding: Naturally Occurring Gene Silencing and Modification by Genetic Engineering 211 Resistance to Viruses 215 Host-induced Gene Silencing 218 Insect and Disease Control 218 Improving Nutritional Values 219 Secondary Metabolites 220 Perspectives 220 References 222 Index 229
List of Contributors ix Foreword xiii 1 Omics: Opening up the "Black Box" of the Phenotype 1 Roberto Fritsche-Neto and Aluizio Borem The Post-Genomics Era 3 The Omics in Plant Breeding 4 Genomics, Precision Genomics, and RNA Interference 5 Transcriptomics and Proteomics 8 Metabolomics and Physiognomics 8 Phenomics 9 Bioinformatics 10 Prospects 10 References 10 2 Genomics 13 Antonio Costa de Oliveira, Luciano Carlos da Maia, Daniel da Rosa Farias, and Naciele Marini The Rise of Genomics 13 DNA Sequencing 13 Development of Sequence-based Markers 18 Genome Wide Selection (GWS) 25 Structural and Comparative Genomics 27 References 28 3 Transcriptomics 33 Carolina Munari Rodrigues, Valeria S. Mafra, and Marcos Antonio Machado Methods of Studying the Transcriptome 34 Applications of Transcriptomics Approaches for Crop Breeding 46 Conclusions and Future Prospects 51 Acknowledgements 51 References 51 4 Proteomics 59 Ilara Gabriela F. Budzinski, Thais Regiani, Monica T. Veneziano Labate, Simone Guidetti-Gonzalez, Danielle Izilda R. da Silva, Maria Juliana Calderan Rodrigues, Janaina de Santana Borges, Ivan Miletovic Mozol, and Carlos Alberto Labate History 59 Different Methods for the Extraction of Total Proteins 60 Subcellular Proteomics 64 Post-Translational Modifications 66 Quantitative Proteomics 69 Perspectives 72 References 73 5 Metabolomics 81 Valdir Diola (in memoriam), Danilo de Menezes Daloso, and Werner Camargos Antunes Introduction 81 Metabolomic and Biochemical Molecules 83 Technologies for Metabolomics 83 Metabolomic Database Analysis 86 Metabolomics Applications 89 Metabolomics-assisted Plant Breeding 91 Associative Genome Mapping and mQTL Profiles 95 Large-scale Phenotyping Using Metabolomics 97 Conclusion and Outlook 98 References 99 6 Physionomics 103 Frederico Almeida de Jesus, Agustin Zsogon, and Lazaro Eustaquio Pereira Peres Introduction 103 Early Studies on Plant Physiology and the Discovery of Photosynthesis 104 Biochemical Approaches to Plant Physiology and the Discovery of Plant Hormones 104 Genetic Approaches to Plant Physiology and the Discovery of Hormone Signal Transduction Pathways 106 Alternative Genetic Models for Omics Approaches in Plant Physiology 112 "Physionomics" as an Integrator of Various Omics for Functional Studies and Plant Breeding 117 Acknowledgements 121 References 121 7 Phenomics 127 Roberto Fritsche-Neto, Aluizio Borem, and Joshua N. Cobb Introduction 127 Examples of Large-scale Phenotyping 128 Important Aspects for Phenomics Implementation 134 Main Breeding Applications 141 Final Considerations 144 References 144 8 Electrophoresis, Chromatography, and Mass Spectrometry 147 Thais Regiani, Ilara Gabriela F. Budzinski, Simone Guidetti-Gonzalez, Monica T. Veneziano Labate, Fernando Cotinguiba, Felipe G. Marques, Fabricio E. Moraes, and Carlos Alberto Labate Introduction 147 Two-dimensional Electrophoresis (2DE) 148 Chromatography 150 Mass Spectrometry 155 Data Analysis 161 References 164 9 Bioinformatics 167 J. Miguel Ortega and Fabricio R. Santos Introduction 167 The "Omics" Megadata and Bioinformatics 167 Hardware for Modern Bioinformatics 169 Software for Genomic Sequencing 170 Software for Contig Assembling 172 Assembly Using the Graph Theory 173 New Approaches in Bioinformatics for DNA and RNA Sequencing 174 Databases, Identification of Homologous Sequences and Functional Annotation 175 Annotation of a Complete Genome 179 Computational System with Chained Tasks Manager (Workflow) 181 Applications for Studies in Plants 182 Final Considerations 183 References 184 10 Precision Genetic Engineering 187 Thiago J. Nakayama, Aluizio Borem, Lucimara Chiari, Hugo Bruno Correa Molinari, and Alexandre Lima Nepomuceno Introduction 187 Zinc Finger Nucleases (ZFNs) 190 Transcription Activator-like Effector Nucleases (TALENs) 193 Meganucleases (LHEs: LAGLIDADG Homing Endonucleases) 194 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) 195 Implications and Perspectives of the use of PGE in Plant Breeding 197 References 202 11 RNA Interference 207 Francisco J.L. Aragao, Abdulrazak B. Ibrahim, and Maria Laine P. Tinoco Introduction 207 Discovery of RNAi 208 Mechanism of RNA Interference 209 Applications in Plant Breeding: Naturally Occurring Gene Silencing and Modification by Genetic Engineering 211 Resistance to Viruses 215 Host-induced Gene Silencing 218 Insect and Disease Control 218 Improving Nutritional Values 219 Secondary Metabolites 220 Perspectives 220 References 222 Index 229
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