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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 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.
Auteur
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.
Résumé
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.
Contenu
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 Asse...