Plant Genomics: Methods and Protocols

ISBN-13: 9781493983643 / Angielski / Miękka / 2018 / 317 str.

Wolfgang Busch

Spis treści

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

Jörg 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 Göschl, and Wolfgang Busch<

 

11. Large-scale Phenotyping of Root Traits in the Model Legume Lotus japonicus

Marco Giovannetti, Anna Małolepszy, 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 Göschl, 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 Bågman, 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 Rüdiger 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

Blurb

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.