Plant Functional Genomics Methods and Protocols, Volume 2

This detailed book gathers hands-on techniques to characterize, identify, localize, profile, and determine genome functions in plants. Volume 2 opens with metabolomic methods that uncover chemical intricacies, exploring glycome mixtures, cell wall components, and computational metabolomics, and it continues with sections on plant genome validation, computational approaches and bioinformatic tools, and case studies exploring the biological effects of magnetic fields and the study of cyanobacteria. 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. 

Carotenoid Extraction from Plant Tissues.- Sample Preparation from Plant Tissue for Gas Chromatography–Mass Spectrometry (GC–MS).- Identification of Volatiles in Tomato Fruit Using Headspace Solid-Phase-Micro-Extraction (HS-SPME) Coupled with Gas Chromatography-Mass Spectrometry (GC-MS).- Determination of Molecular Dimensions of Carbohydrate Polymers (Polysaccharides) by Size Exclusion Chromatography (SEC).- Monosaccharide Analysis after One-Pot Derivatization Followed by Reverse-Phase Liquid Chromatography Separation and UV/Vis Detection.- Atomic Force Microscopy in the Characterization of the Structure of Cell Wall Components.- Studying Plant Specialized Metabolites Using Computational Metabolomics Strategies.- pyPGCF: A Python Software for Phylogenomic Analysis, Species Demarcation, Identification of Core and Fingerprint Proteins of Bacterial Genomes that Are Important for Plants.- Application of Integrated Computational Approaches in Prediction of Plant Virus Encoded miRNAs and Their Targeted Plant Genes.- Gene Co-Expression Network Analysis to Mine Genes Involved in Plant Secondary Metabolite Biosynthesis and Regulation.- Organic Supplementation of Vaccinium corymbosum Micropropagation Media.- Coffee Cell Suspensions as a Platform for Transient Gene Expression Analysis.- Agroinfiltration for Enhanced Transgene Expression in Coffee Leaves (Coffea arabica L.).- In Vitro Gamma Mutagenesis Techniques in Rice (Oryza sativa L. var. Lazarroz FL).- CRISPR/Cas9-Mediated Genome Editing in Indica Rice (Oryza sativa L. subsp. indica var. CR-5272).- Dual-Luciferase Reporter Assay for Pre-Screening CRISPR (d)Cas9-Mediated Epigenetic Editing on a Plant Promoter Using Human Cells.- In Silico Design of gRNA for CRISPR/Cas9-Mediated Gene Knock-Out.- CRISPR/Cas9 Vector Construction for Gene Knock-Out.- A Comprehensive Protocol for Assembly of Multiple gRNAs into a Direct Vector for Genome Editing in Tomato.- Genome Editing in Brassica juncea Using CRISPR/Cas9 Technology.- Precision Genome Editing with CRISPR-Cas9.- Using Magnetic Fields to Enhance the Seed Germination, Growth, and Yield of Plants.- Phenotypic and Genotypic Methods for the Identification and Quantification of Cyanobacteria in Lake Water.