Description
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.
Chapter
Development of Sequence-based Markers
Genome Wide Selection (GWS)
Structural and Comparative Genomics
Applications of Genomics in Plant Breeding
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)
Applications of Transcriptomics Approaches for Crop Breeding
Conclusions and Future Prospects
Different Methods for the Extraction of Total Proteins
Importance of High-quality Protein Extracts
Extraction with TCA/Acetone
Extraction with Phenol and Precipitation with TCA/Acetone
Protein Extraction: Removal of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO)
Post-Translational Modifications
Quantification with Isotope Labeling of Proteins and Peptides
Label-free Quantification
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
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
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
Chapter 8 Electrophoresis, Chromatography, and Mass Spectrometry
Two-dimensional Electrophoresis (2DE)
Hybrid Analyzers: Quadrupole endash Time-of-Flight
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
Chapter 10 Precision Genetic Engineering
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
Chapter 11 RNA Interference
Mechanism of RNA Interference
Applications in Plant Breeding: Naturally Occurring Gene Silencing and Modification by Genetic Engineering
Host-induced Gene Silencing
Insect and Disease Control
Improving Nutritional Values
Omics in Plant Breeding
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