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 ArabidopsisGrowth of Plants and Preservation of SeedsLuz Rivero-Lepinckas, Deborah Crist, and Randy SchollPrevention and Control of Pests and DiseasesJenifer Bush, Georg Jander, and Frederick M. AusubelGrowth of Other Species Related to Arabidopsis thalianaKrithika Yogeeswaran and Mikhail Elia Nasrallah. Grafting, Katherine Bainbridge, Tom Bennett, Colin Turnbull, and Ottoline LeyserSynchronization, Transformation, and Cryopreservation of Suspension-Cultured CellsMargit Menges and James A. H. MurrayPart II. Genetic AnalysesGenetic AnalysisMaarten Koornneef, Carlos Alonso-Blanco, and Piet StamQTL AnalysisCarlos Alonso-Blanco, Maarten Koornneef, and Johan W. van OoijenEMS Mutagenesis of ArabidopsisYongSig Kim, Karen S. Schumaker, and Jian-Kang ZhuLow-Resolution Mapping of Untagged MutationsM. Rosa Ponce, Pedro Robles, Francisca M. Lozano, M. Asunción Brotóns, and José L. MicolGene Identification and Cloning by Molecular Marker MappingGeorg JanderHigh-Throughput TILLING for ArabidopsisBradley 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 HenikoffGenotyping and Mapping With High-Density Oligonucleotide ArraysJustin BorevitzForward Genetic Screening of Insertional MutantsAnja Schneider and Dario LeisterPCR-Based Screening for Insertional MutantsAnna N. Stepanova and Jose M. AlonsoCytogenetic Analysis of ArabidopsisMartin Lysak, Paul Fransz, and Ingo SchubertUsing Information From Public Arabidopsis Databases to Aid ResearchMargarita Garcia-Hernandez and Leonore ReiserPart III. Transient and Stable TransformationIn PlantaAgrobacterium-Mediated Transformation by Vacuum InfiltrationBrian W. Tague and Joanna MantisTransient Expression Assay by Agroinfiltration of LeavesMin Woo Lee and Yinong YangFunctional Analysis of Transcription Factors by Microparticle BombardmentIda Ruberti, Giovanna Sessa, and Giorgio MorelliTransfection Assays With Protoplasts Containing Integrated Reporter GenesShiv Tiwari, Shucai Wang, Gretchen Hagen, and Tom J. GuilfoyleChloroplast Genetic Engineering Via Organogenesis or Somatic EmbryogenesisAmit Dhingra and Henry Daniellb-Glucuronidase as Reporter Gene: Advantages and LimitationsKye-Won Kim, Vincent R. Franceschi, Laurence B. Davin, and Norman G. LewisUse of Fluorescent Proteins as ReportersGuido JachLuciferases as Reporter GenesMegan M. Southern, Paul E. Brown, and Anthony HallAequorin as a Reporter GeneChristoph PliethApplications of Chemical-Inducible Expression Systems in Functional Genomics and BiotechnologyJianru Zuo, Peter D. Hare, and Nam-Hai ChuaPart IV. TranscriptomicsRNA ExtractionHuazhong Shi and Ray BressanTarget Preparation for DNA Microarray HybridizationTong Zhu, Sherman H. Chang, and Pedro GilStatistical Issues in Microarray Data AnalysisWillem A. Rensink and Samuel P. HazenPreparation and Quality Assesment of RNA From Cell-Specific Samples Obtained by Laser MicrodissectionRegine Kleber and Julia KehrPart V. ProteomicsProtein Isolation and Second-Dimension Electrophoretic SeparationBernhard Schlesier and Hans-Peter MockIsolation of Nuclear ProteinsTomasz T. Calikowski and Iris MeierPurification and Fractionation of Membranes for Proteomic AnalysisAnne Marmagne, Daniel Salvi, Norbert Rolland, Geneviève Ephritikhine, Jacques