Plant genomics : methods and protocols
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Bibliographic Information
Plant genomics : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 1610）（Springer protocols）
Humana Press : Springer Nature, c2017
- : hard
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"This Humana Press imprint is published by Springer Nature. The registered company is Springer Science+Business Media LLC"--T.p. verso
Includes bibliographical references and index
Description and Table of Contents
Description
This volume provides protocols that revolve around three pillars of progress in the plant genomics field: genotypes, phenotypes, and the molecular processes in between. Chapters in Plant Genomics: Methods and Protocols are not restricted to the predominant model species Arabidopsis thaliana, hoping to encourage and facilitate other researchers to expand their research to other species. Written in the highly successful Methods in Molecular Biology series format, 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, Plant Genomics: Methods and Protocols aims to serve as an inspiration for further studies in plant genomics.
Table of Contents
Part I: Genotypes 1. CRISPR/Cas-mediated in planta Gene Targeting
Simon Schiml, Friedrich Fauser, and Holger Puchta
2. User Guide for the LORE1 Insertion Mutant Resource
Terry Mun, Anna Malolepszy, Niels Sandal, Jens Stougaard, and Stig U. Andersen
3. Enabling Reverse Genetics in Medicago truncatula Using High Throughput Sequencing for Tnt1 Flanking Sequence Recovery
Xiaofei Cheng, Nick Krom, Shulan Zhang, Kirankumar S. Mysore, Michael Udvardi, and Jiangqi Wen
4. Generation of Doubled Haploid Lines for QTL Mapping Daniele L. Filiault, Danelle K. Seymour, Ravi Maruthachalam, and Julin N. Maloof
Part II: Phenotypes
5. Assessing Distribution and Variation of Genome-wide DNA Methylation using Short Read Sequencing
Joerg Hagmann and Claude Becker
6. Circular Chromosome Conformation Capture in Plants
Stefan Grob
7. Genome Wide Profiling of Histone Modifications and Histone Variants in Arabidopsis thaliana and Marchantia polymorpha
Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, and Tomokazu Kawashima
8. Tissue-Specific Transcriptome Profiling in Arabidopsis Roots
Erin E. Sparks and Philip N. Benfey
9. Sample Preparation Protocols for Protein Abundance, Acetylome and Phosphoproteome Profiling of Plant Tissues
Gaoyuan Song, Maxwell R McReynolds, and Justin W Walley
10. Automated High-throughput Root Phenotyping of Arabidopsis thaliana under Nutrient Deficiency Conditions
Santosh B. Satbhai, Christian Go schl, and Wolfgang Busch<
11. Large-scale Phenotyping of Root Traits in the Model Legume Lotus japonicus
Marco Giovannetti, Anna Malolepszy, Christian Goeschl, and Wolfgang Busch
12. Long-term Confocal Imaging of Arabidopsis thaliana Roots for Simultaneous Quantification of Root Growth and Fluorescent Signals
Delyana Stoeva, Christian Goeschl, and Wolfgang Busch
Part III: Molecular Bases of Phenotypes
13. Identification of Protein-DNA Interactions Using Enhanced Yeast One-Hybrid Assays and a Semi-Automated Approach
Allison Gaudinier, Michelle Tang, Anne-Maarit Bagman, and Siobhan M. Brady
14. Mapping Protein- protein Interaction using High-throughput Yeast-2-Hybrid
Jessica Lopez and M. Shahid Mukhtar
15. Mapping Protein-protein Interactions using Affinity Purification and Mass Spectrometry
Chin-Mei Lee, Christopher Adamchek, Ann Feke, Dmitri A. Nusinow, and Joshua M. Gendron
16. Measuring Protein Movement, Oligomerization State, and Protein-Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (scanning FCS)
Natalie M. Clark and Rosangela Sozzani
17. Studying Protein-Protein Interactions in planta using Advanced Fluorescence Microscopy
Marc Somssich and Rudiger Simon
18. Chemiluminescence Based Detection of Peptide Activity and Peptide-Receptor Binding in Plants
Mari Wildhagen, Markus Albert, and Melinka A. Butenko
19. Application of Chemical Genomics to Plant-Bacteria Communication: A High-Throughput System to Identify Novel Molecules Modulating the Induction of Bacterial Virulence Genes by Plant Signals
Elodie Vandelle, Maria Rita Puttilli, Andrea Chini, Giulia Devescovi, Vittorio Venturi, and Annalisa Polverari
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