Omics in Plant Breeding

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.

• List of Contributors ix Foreword xiii1 Omics: Opening up the "Black Box" of the Phenotype 1Roberto Fritsche-Neto and Aluizio BoremThe Post-Genomics Era 3The Omics in Plant Breeding 4Genomics, Precision Genomics, and RNA Interference 5Transcriptomics and Proteomics 8Metabolomics and Physiognomics 8Phenomics 9Bioinformatics 10Prospects 10References 102 Genomics 13Antonio Costa de Oliveira, Luciano Carlos da Maia, Daniel da Rosa Farias, and Naciele MariniThe Rise of Genomics 13DNA Sequencing 13Development of Sequence-based Markers 18Genome Wide Selection (GWS) 25Structural and Comparative Genomics 27References 283 Transcriptomics 33Carolina Munari Rodrigues, Valeria S. Mafra, and Marcos Antonio MachadoMethods of Studying the Transcriptome 34Applications of Transcriptomics Approaches for Crop Breeding 46Conclusions and Future Prospects 51Acknowledgements 51References 514 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 LabateHistory 59Different Methods for the Extraction of Total Proteins 60Subcellular Proteomics 64Post-Translational Modifications 66Quantitative Proteomics 69Perspectives 72References 735 Metabolomics 81Valdir Diola (in memoriam), Danilo de Menezes Daloso, and Werner Camargos AntunesIntroduction 81Metabolomic and Biochemical Molecules 83Technologies for Metabolomics 83Metabolomic Database Analysis 86Metabolomics Applications 89Metabolomics-assisted Plant Breeding 91Associative Genome Mapping and mQTL Profiles 95Large-scale Phenotyping Using Metabolomics 97Conclusion and Outlook 98References 996 Physionomics 103Frederico Almeida de Jesus, Agustin Zsogon, and Lazaro Eustaquio Pereira PeresIntroduction 103Early Studies on Plant Physiology and the Discovery of Photosynthesis 104Biochemical Approaches to Plant Physiology and the Discovery of Plant Hormones 104Genetic Approaches to Plant Physiology and the Discovery of Hormone Signal Transduction Pathways 106Alternative Genetic Models for Omics Approaches in Plant Physiology 112"Physionomics" as an Integrator of Various Omics for Functional Studies and Plant Breeding 117Acknowledgements 121References 1217 Phenomics 127Roberto Fritsche-Neto, Aluizio Borem, and Joshua N. CobbIntroduction 127Examples of Large-scale Phenotyping 128Important Aspects for Phenomics Implementation 134Main Breeding Applications 141Final Considerations 144References 1448 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 LabateIntroduction 147Two-dimensional Electrophoresis (2DE) 148Chromatography 150Mass Spectrometry 155Data Analysis 161References 1649 Bioinformatics 167J. Miguel Ortega and Fabricio R. SantosIntroduction 167The "Omics" Megadata and Bioinformatics 167Hardware for Modern Bioinformatics 169Software for Genomic Sequencing 170Software for Contig Assembling 172Assembly Using the Graph Theory 173New Approaches in Bioinformatics for DNA and RNA Sequencing 174Databases, Identification of Homologous Sequences and Functional Annotation 175Annotation of a Complete Genome 179Computational System with Chained Tasks Manager (Workflow) 181Applications for Studies in Plants 182Final Considerations 183References 18410 Precision Genetic Engineering 187Thiago J. Nakayama, Aluizio Borem, Lucimara Chiari, Hugo Bruno Correa Molinari, and Alexandre Lima NepomucenoIntroduction 187Zinc Finger Nucleases (ZFNs) 190Transcription Activator-like Effector Nucleases (TALENs) 193Meganucleases (LHEs: LAGLIDADG Homing Endonucleases) 194Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) 195Implications and Perspectives of the use of PGE in Plant Breeding 197References 20211 RNA Interference 207Francisco J.L. Aragao, Abdulrazak B. Ibrahim, and Maria Laine P. TinocoIntroduction 207Discovery of RNAi 208Mechanism of RNA Interference 209Applications in Plant Breeding: Naturally Occurring Gene Silencing and Modification by Genetic Engineering 211Resistance to Viruses 215Host-induced Gene Silencing 218Insect and Disease Control 218Improving Nutritional Values 219Secondary Metabolites 220Perspectives 220References 222Index 229

“Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field.”  (Biotechnology, Agronomy, Society and Environment, 1 October 2014)