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This detailed book gathers hands-on techniques to characterize, identify, localize, profile, and determine genome functions in plants. Volume 1 opens with a section exploring protocols to advance our understanding of plant genetics and ecology via phenomics, and it continues with chapters on plant genetics, transcriptomics, and proteomics to unravel plant protein structures and functions, bridging proteomics and phosphoproteomics. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and comprehensive, Plant Functional Genomics: Methods and Protocols serves as an ideal guide to the immense promise of functional genomics, spanning from fundamental evolutionary studies to practical advancements in crop improvement.
List of contents
An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management.- A High-Throughput Approach for Photosynthesis Studies in a Brassicaceae Panel.- Methods for Functional Physiological Phenotyping and High-Order Data Quantification.- Physiotyping of Plants and Modeling the Soil Plant Atmospheric Continuum (SPAC).- Root Hair Imaging Using Confocal Microscopy.- Cytogenetic Bioindication in Root Meristems for Vitality Assessment of Trees.- Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.- Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data.- Identification of Induced Copy Number Variation from Low Coverage Sequence Data.- Genetic Map Construction Using F2 and RIL/DH Mapping Population.- QTL Mapping Using RIL Population.- Sample and Library Preparation for PacBio Long Read Sequencing in Grapevine.- RNA Isolation Method in Marginal Crops with High Agronomic Potential.- A General Protocol for Gene Expression Analysis in Chemically Mutant Coffee Plants in Response to Rust (Hemileia vastatrix Berk & Broome) Infection.- Transcriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example.- Quantitative Estimation of Promoter Activity in Cannabis sativa Using Agroinfiltration-Based Transient Gene Expression.- Indophenol Blue Colorimetric Method to Determine Grain Protein Content of Cereal Plants.- One-Dimensional Acrylamide Gel Electrophoresis for Analysis of Plant Samples.- Two-Dimensional Gel Electrophoresis for Separation of Plant Samples.- Sample Preparation and Phosphopeptide Enrichment for Plant Phosphoproteomics via Label-Free Mass Spectrometry.- Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf.- Determining Macromolecular Structures Using Cryo-Electron Microscopy.- Determining Protein Structures Using X-Ray Crystallography.
