The Biology of Plants

Symposium Participants v Foreword xv

Germline

Reprogramming the Epigenome in Arabidopsis Pollen F. Borges, J.P. Calarco, and R.A. Martienssen 1 Surprises from the Chromosome Front: Lessons from Arabidopsis on Telomeres and Telomerase A.D.L. Nelson and D.E. Shippen 7 Reproductive Versatility and the Epigenetic Control of Female Gametogenesis J.-P. Vielle-Calzada, E. Herna´ndez-Lagana, D. Rodrı´guez-Leal, I. Rodrı´guez-Are´valo, G. Leo´n-Martı´nez, U. Abad-Vivero, E. Demesa-Are´valo, A. Armenta-Medina, and C. Alvarez-Mejı´a 17 Hypothesis: Selection of Imprinted Genes Is Driven by Silencing Deleterious Gene Activity in Somatic Tissues F. Berger, T.M. Vu, J. Li, and B. Chen 23

Stem Cells and Polarity

Of Blades and Branches: Understanding and Expanding the Arabidopsis Ad/Abaxial Regulatory Network through Target Gene Identification T. Liu, B.J. Reinhart, E. Magnani, T. Huang, R. Kerstetter, and M.K. Barton 31 How to Pattern a Leaf N. Bolduc, D. O’Connor, J. Moon, M. Lewis, and S. Hake 47 On Fate and Flexibility in Stomatal Development D.L. Wengier and D.C. Bergmann 53

Signaling and Development

Developmental Plasticity in Plants M. de Jong and O. Leyser 63 Stem Cell Signaling in Immunity and Development H. Lee, O.-K. Chah, J. Plotnikov, and J. Sheen 75 A Tale of Two Systems: Peptide Ligand–Receptor Pairs in Plant Development J.S. Lee and K.U. Torii 83 Toward a Systems Analysis of the Root P.N. Benfey 91

Domestication and Evolution

Epigenetic Variation, Inheritance, and Selection in Plant Populations S. Hirsch, R. Baumberger, and U. Grossniklaus 97 The Molecular Basis of Vernalization in Different Plant Groups T.S. Ream, D.P. Woods, and R.M. Amasino 105 Color and Scent: How Single Genes Influence Pollinator Attraction H. Sheehan, K. Hermann, and C. Kuhlemeier 117

Epigenetics

Epiallelic Variation in Arabidopsis thaliana R.C. O’Malley and J.R. Ecker 135 DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression D. Coleman-Derr and D. Zilberman 147 What Triggers Differential DNA Methylation of Genes and TEs: Contribution of Body Methylation? S. Inagaki and T. Kakutani 155 Active DNA Demethylation in Plants and Animals H. Zhang and J.-K. Zhu 161 Illustrations of Mathematical Modeling in Biology: Epigenetics, Meiosis, and an Outlook D. Richards, S. Berry, and M. Howard 175

Small RNAs

microRNA Biogenesis and Turnover in Plants K. Rogers and X. Chen 183 Use of Forward Genetic Screens to Identify Genes Required for RNA-Directed DNA Methylation in Arabidopsis thaliana C. Eun, Z.J. Lorkovic, T. Sasaki, U. Naumann, A.J.M. Matzke, and M. Matzke 195 ATranscription Fork Model for Pol IVand Pol V–Dependent RNA-Directed DNA Methylation C.S. Pikaard, J.R. Haag, O.M.F. Pontes, T. Blevins, and R. Cocklin 205 Deep Sequencing from hen1 Mutants to Identify Small RNA 30 Modifications J. Zhai and B.C. Meyers 213 Small RNA-Regulated Networks and the Evolution of Novel Structures in Plants Y. Plavskin and M.C.P. Timmermans 221

Plant Pathogen Responses

Effector Biology of Plant-Associated Organisms: Concepts and Perspectives J. Win, A. Chaparro-Garcia, K. Belhaj, D.G.O. Saunders, K. Yoshida, S. Dong, S. Schornack, C. Zipfel, S. Robatzek, S.A. Hogenhout, and S. Kamoun 235 Effector Recognition and Activation of the Arabidopsis thaliana NLR Innate Immune Receptors A.D. Steinbrenner, S. Goritschnig, K.V. Krasileva, K.J. Schreiber, and B.J. Staskawicz 249 A Rolling Stone Gathers No Moss, but Resistant Plants Must Gather Their MOSes K.C.M. Johnson, O.X. Dong, Y. Huang, and X. Li 259 Natural Variation in Maize Defense against Insect Herbivores L.N. Meihls, H. Kaur, and G. Jander 269 Mechanisms of Nuclear Suppression of Host Immunity by Effectors from the Arabidopsis Downy Mildew Pathogen Hyaloperonospora arabidopsidis (Hpa) M.-C. Caillaud, L. Wirthmueller, G. Fabro, S.J.M. Piquerez, S. Asai, N. Ishaque, and J.D.G. Jones 285

Photosynthesis and Metabolism

Photosystem II: The Water-Splitting Enzyme of Photosynthesis J. Barber 295 The Remarkable Pliability and Promiscuity of Specialized Metabolism J.-K.Weng and J.P. Noel 309 Author Index 321 Subject Index 322