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ICAR 2011 University of Wisconsin–Madison is generally enriched in the meristematic zone compared to the elongation and differentiation zones and vice versa for auxin-repressed genes. This approach exposes a remarkably sizeable scope of influence on gene expression along the longitudinal axis of the root. Tissue-specific analysis further highlights the effects of auxin on transcriptional cell identity and maturation, particularly in the stele, where genes characteristic for developing xylem are induced by auxin and markers for mature xylem are repressed. Additionally, we study the effect of auxin signal deprivation on meristem maintenance and cell differentiation by using inducible expression of gainof-function Aux/IAA repressors. Note: Also a poster presentation. 88 LEAFY Target Genes Reveal Floral Regulatory Logic, cis Motifs, and a Link to Biotic Stimulus Response Cara Winter 1 , Ryan Austin 2 , Servane Blanvillain-Baufume 3 , Maxwell Reback 4 , Marie Monniaux 5 , Miin-Feng Wu 4 , Yi Sang 4 , Ayako Yamaguchi 4 , Nobutoshi Yamaguchi 4 , Jane Parker 3 , Francois Parcy 5 , Shane Jensen 4 , Hongzhe Li 4 , Doris Wagner 4 1 Duke University, Durham, NC, USA, 2 University of Toronto, Toronto, Canada, 3 Max-Planck Institute for Plant Breeding Research, 4 University of Pennsylvania, Philadelphia, PA, USA, 5 Laboratorie Physiologie Cellulaire et Vegetale CNRS, iRTSV/CEA, INRA, UJF Grenoble, Grenoble, France The transition from vegetative growth to flower formation is critical for the survival of flowering plants. The plant-specific transcription factor LEAFY (LFY) has central, evolutionarily conserved roles in this process, both in the formation of the first flower and later in floral patterning. We performed genome-wide binding and expression studies to elucidate the molecular mechanisms by which LFY executes these roles. Our study reveals that LFY directs an elaborate regulatory network in control of floral homeotic gene expression. LFY also controls the expression of genes that regulate the response to external stimuli in Arabidopsis. Thus, our findings support a key role for LFY in the coordination of reproductive stage development and disease response programs in plants that may ensure optimal allocation of plant resources for reproductive fitness. Finally, motif analyses reveal a possible mechanism for stage-specific LFY recruitment and suggest a role for LFY in overcoming polycomb repression. 89 Contributions of the Maternal, Paternal and Zygotic Genomes during Early Plant Embryogenesis Michael Nodine, David Bartel Whitehead Institute, Cambridge, MA, USA In animals, maternally-derived gene products control early embryonic development prior to the activation of the zygotic genome. However, it has been unclear whether a prolonged period of maternal control also occurs in plant embryos. To investigate this issue directly, we crossed different Arabidopsis thaliana accessions and performed transcriptome profiling on hybrid embryos at the 1-cell/2- cell, 8-cell and ~32-cell stages using mRNA-Seq. Single-nucleotide polymorphisms within the mRNA-Seq tags revealed maternal and paternal genome contributions to more than 7000 transcripts. For the vast majority of genes, the maternally and paternally derived loci contributed approximately equal amounts of transcripts – even in the 1-cell/2-cell stages. Thus in contrast to previously proposed models, our results indicate that both parental genomes are active very early during Arabidopsis embryogenesis. Although most transcripts were biallelic, we identified >100 transcripts that were derived predominantly or exclusively from the maternal locus and >100 transcripts preferentially or exclusively derived from the paternal locus. These parent-of-origin–dependent transcripts encode proteins with annotated functions including transcriptional regulation, RNA binding, chromatin remodeling, signal transduction and hormone metabolism. We are currently testing whether these transcripts are inherited from the gametes or derived from imprinted loci. Since only a few examples of inherited transcripts or gene imprinting in plant embryos have been reported, our identification of hundreds of parent-of-origin–dependent transcripts suggests that one or both of these mechanisms play an important role in shaping the early embryonic transcriptome. Note: Also a poster presentation. 90 RUG8, a Novel Player in Auxin-Dependent Stem Cell Specification and Meristem Patterning in Arabidopsis Roots Ulrich Wenig, Stefan Meyer, Ruth Stadler, Norbert Sauer University of Erlangen, Germany A screen for putative plasmodesmata mutants, based on pAtSUC2::GFP plants, revealed a mutation in a previously unknown gene that was named REDUCED UNLOADING OF GFP8 (RUG8), based on the observed phenotype. RUG8 encodes a putative, plant specific transcription factor, which is involved in stem cell specification and meristem patterning processes in the Arabidopsis root. Loss of this gene leads to an altered appearance of the quiescent center (QC), premature differentiated stem cells and premature elongated meristematic cells. All affected cells show RUG8 expression in wild type plants, which was analyzed in plants expressing a pRUG8::RUG8-GFP construct. In line with the phenotypic differences, the mutant plants failed to form an auxin maximum in the QC and showed a shift of PINFORMED1 (PIN1) expression to the columellar region. Our working hypothesis is that the ectopic PIN1 expression causes the observed loss of the auxin maximum in the QC, which in turn leads to altered expression of other auxin regulated genes. This includes WUSCHEL-RELATED HOMEOBOX5 (WOX5) and the members of the PLETHORA (PLT) gene family. In addition, rug8 mutants show patchy expression of SCARECROW (SCR), which leads to random, mostly periclinal cell divisions or supernumerary cell files in the ground tissue. These results indicate, that RUG8 is a novel, so far uncharacterized key-regulator of the meristem and an important factor for the auxin distribution in the root. Concurrent Session 10: Development II: Cell Specification
ICAR 2011 University of Wisconsin–Madison 91 Gramene: It’s Not Just For Grasses Anymore Joshua Stein 1 , Ken Youens-Clark 1 , Aaron Chuah 1 , Genevieve DeClerck 2 , Sharon Wei 1 , William Spooner 1 , Terry Casstevens 2 , Jim Thomason 1 , Jon Zhang 2 , Charles Chen 2 , AS Karthikeyan 2 , Palitha Dharmawardhana 3 , Marcela Monaco 1 , Pankaj Jaiswal 3 , Edward Buckler 4,5 , Susan McCouch 2 , Doreen Ware 1,5 1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA, 2 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, 3 Department of Botany and Plant Breeding, Oregon State University, Corvallis, OR, USA, 4 Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA, 5 USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, USA Gramene (http://www.gramene.org) is a curated resource for comparative functional genomics in crops and model plant species. Its strength derives from the integration of genome annotation and functional data with the use of ontologies and by applying a phylogenetic framework for genome comparison. In addition to Arabidopsis thaliana and A. lyrata, we host genome browsers for eight other species spanning a broad taxonomic range. Navigation and visualization tools promote interspecies browsing and the simultaneous display of multiple species based on whole genome alignments. Gramene additionally provides comparative information in the form of browsable phylogenetic trees and the assignment of orthology and paralogy relationships. Gramene's genetic diversity database holds genotype, phenotype, and germplasm data for the major population studies in Arabidopsis. Tools for searching and viewing SNP data include the display of diversity data in the context of functional impacts on gene structure. Platforms for conducting genome wide association studies (GWAS) currently employ external analysis tools Tassel and Flapjack. Gramene is supported by grants NSF DEB- 0723510, NSF IOS-0703908, and USDA CRIS 1907-21000-030. 92 Integrating Diverse Data And Knowledge In A Large Collaborative Project Sean Walsh 1 , Katja Baerenfaller 1 , Matthias Hirsch-Hoffman 1 , Agron-omics Consortium Data Contributers 3,2 , Pierre Hilson 4 , Wilhelm Gruissem 1 1 ETH, Zurich, 2 MPI-MPP, Golm, 3 LEPSE, Montpellier, 4 VIB, Ghent A substantial part of the Agron-omics consortium resource is devoted to profiling the Arabidopsis leaf in a number of environmental conditions at four developmental- and two diurnal- time-points during growth. A diverse range of quantitative molecular and phenotypic data is generated in this and other sub-projects. Integrating and interrogating this information is especially challenging when contributing partners are geographically dispersed. Vital to our analytical pipeline is a database integration that exploits standard and advanced features of the MySQL database engine (e.g. stored routines) and tools. This implementation is utilized for the processes of data capture, validation, documentation, the tracking of provenance, for certain mathematical-, statistical- and structural data transformations, for integration with R/Matlab and for storing visualization routines. In addition, the system provides access controlled user workspaces and the ability to run high performance queries across multiple/high volume datasets. Novel datasets also require the integration of pre-existing knowledge and consequently a range of molecular annotations and classifications are included. Since the database engine and tools are freely available, the data and code can be simply and rapidly replicated for community dissemination and/or extension. This development provides a useful template for a computational platform that has analytical value during a project and beyond. 93 Integrating Proteomics Data: pep2pro, MASCP Gator and Combined Analyses with Transcript Data Katja Baerenfaller 1 , Matthias Hirsch-Hoffmann 1 , Sean Walsh 1 , Lars Hennig 2 , Daniel Stekhoven 1 , Sacha Baginsky 3 , Wilhelm Gruissem 1 1 ETH Zurich, 2 Swedish University of Agricultural Sciences, 3 Martin-Luther-Universität Halle Mass spectrometry-based proteomics has now become an important tool for obtaining qualitative and quantitative protein information. Data analysis of the proteomics data usually requires integration of search results from different experiments and search algorithms. The results are then often combined with other proteome data or compared with additional datasets like transcript data. To accomplish the integration of proteomics data at these different levels specialised tools have been built that are presented here. pep2pro is a comprehensive proteome analysis database that offers solutions to the various challenges of developing a proteome data analysis database. Its capacity for the integration and analysis of large proteome databases was demonstrated by creating the organspecific Arabidopsis thaliana dataset containing 14'522 identified proteins based on more than 2.6 million spectra that can be accessed at www.pep2pro.ethz.ch. The datasets in this database have been aggregated with other large-scale Arabidopsis proteome datasets in the MASCP Gator aggregation portal (http://gator.masc-proteomics.org/), which has been built as a proteomics community effort lead by Joshua Heazlewood. For combined analyses of the Agron-omics quantitative proteomics data on leaf 6 with additional datasets, the final proteomics result data that had been processed in pep2pro have been integrated into the AgroRDB. Querying this database followed by statistical analyses allows effective data analysis and reveals new insights into the regulation of protein and transcript levels. 94 Discriminative Expression Signatures In Microarray Data For Functional Network Inference Tomas Puelma, Alvaro Soto, Rodrigo Gutierrez Pontificia Universidad Católica de Chile, Santiago, Chile DNA microarray technology is currently the most widely used approach for profiling gene expression changes in model organisms. There are thousands of publicly available microarray data, which provides information on the expression of thousands of genes under many experimental conditions. This tremendous resource can be used to understand gene expression and to predict new properties of Arabidopsis genes. Workshops
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SPONSORS General Meeting Sponsors G
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Research Positions Available Every
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EXHIBITORS Gold Exhibitors Booth 14
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ab Berthold’s newest instrument i
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PROGRAM Poster schedule All posters
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12:00 - 1:30 pm Lunch Inn Wisconsin
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4:50 pm Magali Moreau, Boyce Thomps
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1:55 pm Volker Bischoff, INRA The R
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6:00 - 7:30 pm Dinner Inn Wisconsin
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5:32 pm Terri Long, University of I
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Thursday, June 23: 12:30 - 1:30 pm
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every two weeks from the latest pub
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1 Suppression of plant immunity by
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ICAR 2011 PRESENTER EMAIL ADDRESS U
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Kenobi, Kim Kim.Kenobi nottingham.a
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Syed, Naeem nsyed scri.ac.uk Synek,
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ICAR 2011 AUTHOR INDEX University o
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22nd International Conference on Ar
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Plant Resource for Our Future Arabi
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