Root Development

Description

This detailed volume provides diverse elegant methods, complemented with existing protocols, which are optimized for the current needs in plant root biology as well as for use in plant species other than Arabidopsis thaliana. The collection covers methods ranging from genetic screens, phenotypic analysis, and cell biology methods to systems biology tools and genome-wide approaches. The collection contains a range of complexity from fundamental methods for quantification of different root developmental processes to complex methods that require sophisticated equipment. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Root Development: Methods and Protocols serves as a valuable tool for plant biologists specialized in root development, from beginners to experienced researchers in the field. Front Matter ....Pages i-xii Front Matter ....Pages 1-1 Measuring Plant Root Traits Under Controlled and Field Conditions: Step-by-Step Procedures (Benjamin M. Delory, Emanuela W. A. Weidlich, Richard van Duijnen, Loïc Pagès, Vicky M. Temperton)....Pages 3-22 Phenotyping Crop Root Crowns: General Guidance and Specific Protocols for Maize, Wheat, and Soybean (Larry M. York)....Pages 23-32 Developmental Analysis of Arabidopsis Root Meristem (Riccardo Di Mambro, Sabrina Sabatini)....Pages 33-45 Genetic and Phenotypic Analysis of Lateral Root Development in Arabidopsis thaliana (Selene Napsucialy-Mendivil, Joseph G. Dubrovsky)....Pages 47-75 Adapting the Lateral Root-Inducible System to Medicago truncatula (Violaine Herrbach, Fabienne Maillet, Sandra Bensmihen)....Pages 77-83 Characterization of Root Epidermal Cell Patterning and Differentiation in Arabidopsis (Jorge E. Salazar-Henao, Girish Mokkapati, Eunice Han Xian Khor, Yi-Chia Chou, Wann-Neng Jane, Wolfgang Schmidt)....Pages 85-93 In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls (Hoang Khai Trinh, Inge Verstraeten, Danny Geelen)....Pages 95-102 Root Gravitropism: Quantification, Challenges, and Solutions (Lukas Muller, Malcolm J. Bennett, Andy French, Darren M. Wells, Ranjan Swarup)....Pages 103-112 Front Matter ....Pages 113-113 Calcium Ion Dynamics in Roots: Imaging and Analysis (Ellie Himschoot, Melanie Krebs, Alex Costa, Tom Beeckman, Steffen Vanneste)....Pages 115-130 Optimized Whole-Mount In Situ Immunolocalization for Arabidopsis thaliana Root Meristems and Lateral Root Primordia (Michael Karampelias, Ricardo Tejos, Jiří Friml, Steffen Vanneste)....Pages 131-143 Light Sheet Fluorescence Microscopy Optimized for Long-Term Imaging of Arabidopsis Root Development (Paolo Baesso, Ricardo S. Randall, Giovanni Sena)....Pages 145-163 Histological Profiling Over Time to Optimize Root Cell Type-Specific Reporter Lines for Cell Sorting (Beatriz Lagunas, Liam Walker, Rana Muhammad Fraz Hussain, Ian Hands-Portman, Kate Woolley-Allen, Miriam L. Gifford)....Pages 165-175 Long-Term In Vivo Imaging of Luciferase-Based Reporter Gene Expression in Arabidopsis Roots (Wei Xuan, Davy Opdenacker, Steffen Vanneste, Tom Beeckman)....Pages 177-190 Cortical Cell Length Analysis During Gravitropic Root Growth (Maria Schöller, Jürgen Kleine-Vehn, Elena Feraru)....Pages 191-197 Growth Rate Normalization Method to Assess Gravitropic Root Growth (Maria Schöller, Elizabeth Sarkel, Jürgen Kleine-Vehn, Elena Feraru)....Pages 199-208 Immunoprecipitation of Membrane Proteins from Arabidopsis thaliana Root Tissue (Sascha Waidmann, Lucinda De-Araujo, Jürgen Kleine-Vehn, Barbara Korbei)....Pages 209-220 Front Matter ....Pages 221-221 Monitoring Transcriptomic Changes in Soil-Grown Roots and Shoots of Arabidopsis thaliana Subjected to a Progressive Drought Stress (Khurram Bashir, Sultana Rasheed, Akihiro Matsui, Kei Iida, Maho Tanaka, Motoaki Seki)....Pages 223-230 Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis (Sandra Cortijo, Varodom Charoensawan, François Roudier, Philip A. Wigge)....Pages 231-248 μChIP-Seq for Genome-Wide Mapping of In Vivo TF-DNA Interactions in Arabidopsis Root Protoplasts (Alessia Para, Ying Li, Gloria M. Coruzzi)....Pages 249-261 Proteome Analysis of Arabidopsis Roots (Natalia Nikonorova, Lam Dai Vu, Elisabeth Stes, Kris Gevaert, Ive De Smet)....Pages 263-274 Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data (Orlando Contreras-López, Tomás C. Moyano, Daniela C. Soto, Rodrigo A. Gutiérrez)....Pages 275-301 GWA-Portal: Genome-Wide Association Studies Made Easy (Ümit Seren)....Pages 303-319 Erratum to: Long-Term In Vivo Imaging of Luciferase-Based Reporter Gene Expression in Arabidopsis Roots (Wei Xuan, Davy Opdenacker, Steffen Vanneste, Tom Beeckman)....Pages E1-E1 Back Matter ....Pages 321-324