Plant Genomics: Methods and Protocols

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

J?rg 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 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 G?schl, 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 B?gman, 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 R?diger 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