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Omics in Plant Breeding

  • ID: 2899022
  • Book
  • 248 Pages
  • John Wiley and Sons Ltd
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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.

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List of Contributors ix

Foreword xiii

1 Omics: Opening up the "Black Box" of the Phenotype 1Roberto 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 13Antonio 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 33Carolina 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 59Ilara 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 81Valdir 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 103Frederico 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 127Roberto 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 147Thais 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 167J. 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 187Thiago 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 207Francisco 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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Aluízio Borém
Roberto Fritsche–Neto
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