For several decades, Arabidopsis thaliana has been the organism of choice in the laboratories of many plant geneticists, physiologists, developmental biologists, and biochemists around the world. During this time, a huge amount of knowledge has been acquired on the biology of this plant species, which has resulted in the development of molecular tools that account for much more efficient research. The significance that Arabidopsis would attain in biological research may have been difficult to foresee in the 1980s, when its use in the laboratory started. In the meantime, it has become the model plant organism, much the same way as Drosophila, Caenorhabditis, or mouse have for animal systems. Today, it is difficult to envision research at the cutting edge of plant biology without the use of Arabidopsis. Since the first edition of Arabidopsis Protocols appeared, new developments have fostered an impressive advance in plant biology that prompted us to prepare Arabidopsis Protocols, Second Edition. Completion of the Arabidopsis genome sequence offered for the first time the opportunity to have in hand all of the genetic information required for studying plant function. In addition, the development of whole systems approaches that allow global analysis of gene expression and protein and metabolite dynamics has encouraged scientists to explore new scenarios that are extending the limits of our knowledge.

Part I. Growing Arabidopsis

Growth of Plants and Preservation of Seeds
Luz Rivero-Lepinckas, Deborah Crist, and Randy Scholl

Prevention and Control of Pests and Diseases
Jenifer Bush, Georg Jander, and Frederick M. Ausubel

Growth of Other Species Related to Arabidopsis thaliana
Krithika Yogeeswaran and Mikhail Elia Nasrallah. Grafting, Katherine Bainbridge, Tom Bennett, Colin Turnbull, and Ottoline Leyser

Synchronization, Transformation, and Cryopreservation of Suspension-Cultured Cells
Margit Menges and James A. H. Murray

Part II. Genetic Analyses

Genetic Analysis
Maarten Koornneef, Carlos Alonso-Blanco, and Piet Stam

QTL Analysis
Carlos Alonso-Blanco, Maarten Koornneef, and Johan W. van Ooijen

EMS Mutagenesis of Arabidopsis
YongSig Kim, Karen S. Schumaker, and Jian-Kang Zhu

Low-Resolution Mapping of Untagged Mutations
M. Rosa Ponce, Pedro Robles, Francisca M. Lozano, M. Asunción Brotóns, and José L. Micol

Gene Identification and Cloning by Molecular Marker Mapping
Georg Jander

High-Throughput TILLING for Arabidopsis
Bradley J. Till, Trenton Colbert, Christine Codomo, Linda Enns, Jessica Johnson, Steven H. Reynolds, Jorja G. Henikoff, Elizabeth A. Greene, Michael N. Steine, Luca Comai, and Steven Henikoff

Genotyping and Mapping With High-Density Oligonucleotide Arrays
Justin Borevitz

Forward Genetic Screening of Insertional Mutants
Anja Schneider and Dario Leister

PCR-Based Screening for Insertional Mutants
Anna N. Stepanova and Jose M. Alonso

Cytogenetic Analysis of Arabidopsis
Martin Lysak, Paul Fransz, and Ingo Schubert

Using Information From Public Arabidopsis Databases to Aid Research
Margarita Garcia-Hernandez and Leonore Reiser

Part III. Transient and Stable Transformation

In PlantaAgrobacterium-Mediated Transformation by Vacuum Infiltration
Brian W. Tague and Joanna Mantis

Transient Expression Assay by Agroinfiltration of Leaves
Min Woo Lee and Yinong Yang

Functional Analysis of Transcription Factors by Microparticle Bombardment
Ida Ruberti, Giovanna Sessa, and Giorgio Morelli

Transfection Assays With Protoplasts Containing Integrated Reporter Genes
Shiv Tiwari, Shucai Wang, Gretchen Hagen, and Tom J. Guilfoyle

Chloroplast Genetic Engineering Via Organogenesis or Somatic Embryogenesis
Amit Dhingra and Henry Daniell

b-Glucuronidase as Reporter Gene: Advantages and Limitations
Kye-Won Kim, Vincent R. Franceschi, Laurence B. Davin, and Norman G. Lewis

Use of Fluorescent Proteins as Reporters
Guido Jach

Luciferases as Reporter Genes
Megan M. Southern, Paul E. Brown, and Anthony Hall

Aequorin as a Reporter Gene
Christoph Plieth

Applications of Chemical-Inducible Expression Systems in Functional Genomics and Biotechnology
Jianru Zuo, Peter D. Hare, and Nam-Hai Chua

Part IV. Transcriptomics

RNA Extraction
Huazhong Shi and Ray Bressan

Target Preparation for DNA Microarray Hybridization
Tong Zhu, Sherman H. Chang, and Pedro Gil

Statistical Issues in Microarray Data Analysis
Willem A. Rensink and Samuel P. Hazen

Preparation and Quality Assesment of RNA From Cell-Specific Samples Obtained by Laser Microdissection
Regine Kleber and Julia Kehr

Part V. Proteomics

Protein Isolation and Second-Dimension Electrophoretic Separation
Bernhard Schlesier and Hans-Peter Mock

Isolation of Nuclear Proteins
Tomasz T. Calikowski and Iris Meier

Purification and Fractionation of Membranes for Proteomic Analysis
Anne Marmagne, Daniel Salvi, Norbert Rolland, Geneviève Ephritikhine, Jacques