Cover -- Title Page -- Copyright -- Contents -- List of Contributors -- Foreword -- Chapter 1 Omics: Opening up the "Black Box" of the Phenotype -- The Post-Genomics Era -- The Omics in Plant Breeding -- Genomics, Precision Genomics, and RNA Interference -- Transcriptomics and Proteomics -- Metabolomics and Physiognomics -- Phenomics -- Bioinformatics -- Prospects -- References -- Chapter 2 Genomics -- The Rise of Genomics -- DNA Sequencing -- Development of Sequence-based Markers -- Genetic Mapping -- Association Mapping -- Genome Wide Selection (GWS) -- Comparative Genomics -- Structural and Comparative Genomics -- Applications of Genomics in Plant Breeding -- References -- Chapter 3 Transcriptomics -- Methods of Studying the Transcriptome -- Construction of cDNA Libraries for EST Sequencing -- Suppression Subtractive Hybridization (SSH) -- Serial Analysis of Gene Expression (SAGE) -- Microarrays -- RNA-seq -- Applications of Transcriptomics Approaches for Crop Breeding -- Conclusions and Future Prospects -- Acknowledgements -- References -- Chapter 4 Proteomics -- History -- Different Methods for the Extraction of Total Proteins -- Importance of High-quality Protein Extracts -- Extraction with TCA/Acetone -- Phenolic Extraction -- Extraction with Phenol and Precipitation with TCA/Acetone -- Protein Extraction: Removal of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO) -- Subcellular Proteomics -- Post-Translational Modifications -- Phosphorylation -- Quantitative Proteomics -- Quantification with Isotope Labeling of Proteins and Peptides -- Label-free Quantification -- Perspectives -- References -- Chapter 5 Metabolomics -- Introduction -- Metabolomic and Biochemical Molecules -- Technologies for Metabolomics -- Metabolomic Database Analysis -- Metabolomics Applications.

Metabolomics-assisted Plant Breeding -- Plant Breeding for Quality Metabolic Compounds -- Metabolites QTLs (mQTLs) Expression -- Simple Studies on the Yield Components -- Studies of Multiple Character Production -- Associative Genome Mapping and mQTL Profiles -- Large-scale Phenotyping Using Metabolomics -- Conclusion and Outlook -- References -- Chapter 6 Physionomics -- Introduction -- Early Studies on Plant Physiology and the Discovery of Photosynthesis -- Biochemical Approaches to Plant Physiology and the Discovery of Plant Hormones -- Genetic Approaches to Plant Physiology and the Discovery of Hormone Signal Transduction Pathways -- Alternative Genetic Models for Omics Approaches in Plant Physiology -- "Physionomics" as an Integrator of Various Omics for Functional Studies and Plant Breeding -- Acknowledgements -- References -- Chapter 7 Phenomics -- Introduction -- Examples of Large-scale Phenotyping -- Important Aspects for Phenomics Implementation -- Sampling versus Controlling Environmental Variation -- Storage and Data Management -- Statistical Analysis of Data -- Main Breeding Applications -- Germplasm Characterization -- Genomic Selection (GS) -- QTL Identification -- Final Considerations -- References -- Chapter 8 Electrophoresis, Chromatography, and Mass Spectrometry -- Introduction -- Two-dimensional Electrophoresis (2DE) -- Chromatography -- Liquid Chromatography -- Gas Chromatography -- Mass Spectrometry -- Ionization Sources -- Analyzers and Detectors -- Hybrid Analyzers: Quadrupole endash Time-of-Flight -- Ion Detectors -- Data Analysis -- References -- Chapter 9 Bioinformatics -- Introduction -- The "Omics" Megadata and Bioinformatics -- Hardware for Modern Bioinformatics -- Software for Genomic Sequencing -- Software for Contig Assembling -- Assembly Using the Graph Theory.

New Approaches in Bioinformatics for DNA and RNA Sequencing -- Databases, Identification of Homologous Sequences and Functional Annotation -- Annotation of a Complete Genome -- Computational System with Chained Tasks Manager (Workflow) -- Applications for Studies in Plants -- Final Considerations -- References -- Chapter 10 Precision Genetic Engineering -- Introduction -- Zinc Finger Nucleases (ZFNs) -- Transcription Activator-like Effector Nucleases (TALENs) -- Meganucleases (LHEs: LAGLIDADG Homing Endonucleases) -- Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) -- Implications and Perspectives of the use of PGE in Plant Breeding -- References -- Chapter 11 RNA Interference -- Introduction -- Discovery of RNAi -- Mechanism of RNA Interference -- Applications in Plant Breeding: Naturally Occurring Gene Silencing and Modification by Genetic Engineering -- Resistance to Viruses -- Host-induced Gene Silencing -- Insect and Disease Control -- Improving Nutritional Values -- Secondary Metabolites -- Perspectives -- References -- Index -- Supplemental Images.