Omics in Plant Breeding

Content: 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