plant genes

Summary

Summary: The functional hereditary units of PLANTS.

Top Publications

  1. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
  2. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
  3. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
  4. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
  5. ncbi Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant J 31:279-92. 2002
  6. ncbi Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
    T Thiel
    Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
    Theor Appl Genet 106:411-22. 2003
  7. ncbi Plant pathogens and integrated defence responses to infection
    J L Dangl
    Department of Biology and Curriculum in Genetics, University of North Carolina at Chapel Hill, 27599 3280, USA
    Nature 411:826-33. 2001
  8. pmc PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
  9. ncbi microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    Edwards Allen
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Cell 121:207-21. 2005
  10. ncbi Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006

Detail Information

Publications298 found, 100 shown here

  1. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
    ..About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance...
  2. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
    ..This report summarizes the present status of this database and available tools...
  3. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
    ..The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future...
  4. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
    ..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants...
  5. ncbi Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant J 31:279-92. 2002
    Full-length cDNAs are essential for functional analysis of plant genes in the post-sequencing era of the Arabidopsis genome...
  6. ncbi Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
    T Thiel
    Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
    Theor Appl Genet 106:411-22. 2003
    ....
  7. ncbi Plant pathogens and integrated defence responses to infection
    J L Dangl
    Department of Biology and Curriculum in Genetics, University of North Carolina at Chapel Hill, 27599 3280, USA
    Nature 411:826-33. 2001
    ..We include a few crucial concepts to compare and contrast plant innate immunity with that more commonly associated with animals. There are appreciable differences, but also surprising parallels...
  8. pmc PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
    ..New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/...
  9. ncbi microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    Edwards Allen
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Cell 121:207-21. 2005
    ....
  10. ncbi Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006
    ....
  11. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  12. ncbi The B73 maize genome: complexity, diversity, and dynamics
    Patrick S Schnable
    Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA
    Science 326:1112-5. 2009
    ..These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize...
  13. ncbi Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress
    Nathalie Nicot
    Centre de Recherche Public Gabriel Lippmann, Environment and Biotechnologies Research Unit, 41 rue du Brill, L 4422 Belvaux, Luxembourg
    J Exp Bot 56:2907-14. 2005
    ..The relative quantification of the hsp20.2 gene varied according to the internal control and the number of internal controls used, thus highlighting the importance of the choice of internal controls in such experiments...
  14. pmc The Arabidopsis Information Resource (TAIR): gene structure and function annotation
    David Swarbreck
    Carnegie Institution, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA
    Nucleic Acids Res 36:D1009-14. 2008
    ..A total of 681 new genes and 1002 new splice variants were added. Overall, 10,098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release...
  15. pmc A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress
    K Yamaguchi-Shinozaki
    Laboratory of Plant Molecular Biology, Institute of Physical and Chemical Research RIKEN, Tsukuba Life Science Center, Ibaraki, Japan
    Plant Cell 6:251-64. 1994
    ..Different cis-acting elements seem to function in the two-step induction of rd29A and in the slow induction of rd29B under conditions of dehydration, high salt, or low temperature...
  16. pmc Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process
    Marino Expósito-Rodríguez
    Instituto de Productos Naturales y Agrobiología CSIC, Avda, Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain
    BMC Plant Biol 8:131. 2008
    ..In the present report we describe the first systematic evaluation of potential internal controls during tomato development process to identify which are the most reliable for transcript quantification by real-time RT-PCR...
  17. ncbi Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    Daniel Zilberman
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Nat Genet 39:61-9. 2007
    ..Our results indicate that genic transcription and DNA methylation are closely interwoven processes...
  18. ncbi The R2R3-MYB gene family in Arabidopsis thaliana
    R Stracke
    Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D 50829, Koln, Germany
    Curr Opin Plant Biol 4:447-56. 2001
    ..R2R3-type MYB genes control many aspects of plant secondary metabolism, as well as the identity and fate of plant cells...
  19. ncbi Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters
    Kazuko Yamaguchi-Shinozaki
    Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    Trends Plant Sci 10:88-94. 2005
    ....
  20. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
    ..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
  21. pmc Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR
    Shin Young Hong
    Department of Chemistry, Seoul National University, Seoul, 151 742, Korea
    BMC Plant Biol 8:112. 2008
    ..Therefore, stable reference genes are necessary to normalize the gene expression data...
  22. ncbi The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants
    Laurent Gutierrez
    Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden
    Plant Biotechnol J 6:609-18. 2008
    ..For the first time, the extent to which the lack of a systematic validation of reference genes is a stumbling block to the reliability of results obtained by RT-PCR in plants is clearly shown...
  23. pmc The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development
    Herve Vaucheret
    Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, INRA, 78026 Versailles Cedex, France
    Genes Dev 18:1187-97. 2004
    ....
  24. pmc Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 18:1944-54. 2008
    ..Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes...
  25. pmc Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses
    Bjorn Usadel
    Max Planck Institute of Molecular Plant Physiology, 14476 Golm, Germany
    Plant Physiol 138:1195-204. 2005
    ....
  26. pmc The Arabidopsis basic/helix-loop-helix transcription factor family
    Gabriela Toledo-Ortiz
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Plant Cell 15:1749-70. 2003
    ..These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis...
  27. pmc The Rice Annotation Project Database (RAP-DB): 2008 update
    Tsuyoshi Tanaka
    National Institute of Agrobiological Sciences, Ibaraki 305 8602, Japan
    Nucleic Acids Res 36:D1028-33. 2008
    ..We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/...
  28. pmc A gateway cloning vector set for high-throughput functional analysis of genes in planta
    Mark D Curtis
    Institute of Plant Biology and Zurich Basel Plant Science Centre, University of Zurich, Zollikerstrasse 107, Ch 8008 Zurich, Switzerland
    Plant Physiol 133:462-9. 2003
    ..All vectors were derived from pCambia T-DNA cloning vectors, with the exception of a chemically inducible vector, for Agrobacterium sp.-mediated transformation of a wide range of plant species...
  29. pmc An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development
    Karen E Reid
    Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
    BMC Plant Biol 6:27. 2006
    ..Few statistically validated reference genes have been reported in grapevine. Moreover, success in isolating high quality RNA from grapevine tissues is typically limiting due to low pH, and high polyphenolic and polysaccharide contents...
  30. pmc Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element
    M Ohme-Takagi
    Plant Molecular Biology Laboratory, National Institute of Bioscience and Human Technology, Ibaraki, Japan
    Plant Cell 7:173-82. 1995
    ..RNA gel blot analysis revealed that accumulation of mRNAs for EREBPs was induced by ethylene, but individual EREBPs exhibited different patterns of expression...
  31. pmc The wheat and barley vernalization gene VRN3 is an orthologue of FT
    L Yan
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 103:19581-6. 2006
    ..002). These results confirmed that the wheat and barley FT genes are responsible for natural allelic variation in vernalization requirement, providing additional sources of adaptive diversity to these economically important crops...
  32. pmc High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
    PLoS ONE 2:e219. 2007
    ..We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks...
  33. ncbi 'Green revolution' genes encode mutant gibberellin response modulators
    J Peng
    John Innes Centre, Norwich Research Park, UK
    Nature 400:256-61. 1999
    ..Transgenic rice plants containing a mutant GAI allele give reduced responses to gibberellin and are dwarfed, indicating that mutant GAI orthologues could be used to increase yield in a wide range of crop species...
  34. ncbi DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression
    Yoh Sakuma
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki, 305 8686, Japan
    Biochem Biophys Res Commun 290:998-1009. 2002
    ..The DREB subfamily included three novel DREB1A- and six DREB2A-related proteins. We analyzed expression of novel genes for these proteins and discuss their roles in stress-responsive gene expression...
  35. pmc Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics
    David M Brown
    Faculty of Life Science, University of Manchester, Manchester M13 9PT United Kingdom
    Plant Cell 17:2281-95. 2005
    ..These genes are likely to define entirely novel processes in secondary cell wall formation and illustrate the success of combining expression data with reverse genetics to address gene function...
  36. pmc Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit
    E J Stockinger
    Department of Crop and Soil Sciences, Michigan State University, East Lansing 48824, USA
    Proc Natl Acad Sci U S A 94:1035-40. 1997
    ..We conclude that CBF1 can function as a transcriptional activator that binds to the C-repeat/DRE DNA regulatory element and, thus, is likely to have a role in cold- and dehydration-regulated gene expression in Arabidopsis...
  37. ncbi Auxin-responsive gene expression: genes, promoters and regulatory factors
    Gretchen Hagen
    Department of Biochemistry, University of Missouri, Columbia 65211, USA
    Plant Mol Biol 49:373-85. 2002
    ..Auxin may regulate transcription on early response genes by influencing the types of interactions between ARFs and Aux/IAAs...
  38. ncbi FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex
    Mitsutomo Abe
    Department of Botany, Graduate School of Science, Kyoto University, Sakyo ku, Kyoto 606 8502, Japan
    Science 309:1052-6. 2005
    ..FT may represent a long-distance signal in flowering...
  39. ncbi Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem
    K F Mayer
    Lehrstuhl für Entwicklungsgenetik, Universitat Tubingen, Federal Republic of Germany
    Cell 95:805-15. 1998
    ....
  40. pmc Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
    Simon Moxon
    School of Computing, University of East Anglia, Norwich NR4 7TJ, United Kingdom
    Genome Res 18:1602-9. 2008
    ..This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation...
  41. pmc Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome
    Akio Miyao
    Molecular Genetics Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305 8602, Japan
    Plant Cell 15:1771-80. 2003
    ..The nucleotide sequence data were uploaded to the DDBJ, EMBL, and GenBank nucleotide sequence databases under accession numbers AG020727 to AG025611 and AG205093 to AG215049...
  42. pmc Identification and validation of reference genes for quantitative RT-PCR normalization in wheat
    Anna R Paolacci
    Dipartimento di Agrobiologia ed Agrochimica, Universita della Tuscia, Via S Camillo de Lellis, 01100 Viterbo, Italy
    BMC Mol Biol 10:11. 2009
    ..For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR...
  43. ncbi Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots
    J R McConnell
    Department of Genetics, University of Wisconsin Madison, 53706, USA
    Nature 411:709-13. 2001
    ..This change probably renders the protein constitutively active, implicating this domain as a central regulator of protein function and the PHB and PHV proteins as receptors for an adaxializing signal...
  44. pmc Genetic and functional diversification of small RNA pathways in plants
    Zhixin Xie
    Center for Gene Research and Biotechnology and Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
    PLoS Biol 2:E104. 2004
    ..We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense...
  45. pmc Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
    Staffan Persson
    Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:8633-8. 2005
    ..Thus, the general approach developed here is useful for identification of elements of multicomponent processes...
  46. ncbi Activation tagging of the floral inducer FT
    I Kardailsky
    Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 286:1962-5. 1999
    ..Instead, it is similar to the sequence of TERMINAL FLOWER 1 (TFL1), an inhibitor of flowering that also shares sequence similarity with membrane-associated mammalian proteins...
  47. pmc Sucrose-specific induction of anthocyanin biosynthesis in Arabidopsis requires the MYB75/PAP1 gene
    Sheng Teng
    Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
    Plant Physiol 139:1840-52. 2005
    ..Sequence analysis showed that the Cvi and C24 accessions harbor mutations both inside and downstream of the DNA-binding domain of the MYB75/PAP1 protein, which most likely result in loss of activity...
  48. ncbi The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family
    Chen Yanhui
    Peking Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, National Key Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, 100871, Beijing, People s Republic of China
    Plant Mol Biol 60:107-24. 2006
    ..Our comprehensive analysis of this largest transcription factor superfamily of Arabidopsis and rice may help elucidate the possible biological roles of the MYB genes in various aspects of flowering plants...
  49. ncbi A pair of related genes with antagonistic roles in mediating flowering signals
    Y Kobayashi
    Department of Botany, Graduate School of Science, Kyoto University, Sakyo ku, Kyoto 606 8502, Japan
    Science 286:1960-2. 1999
    ..FT acts in part downstream of CO and mediates signals for flowering in an antagonistic manner with its homologous gene, TERMINAL FLOWER1 (TFL1)...
  50. pmc miRU: an automated plant miRNA target prediction server
    Yuanji Zhang
    Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
    Nucleic Acids Res 33:W701-4. 2005
    ..The miRU web server is available at http://bioinfo3.noble.org/miRU.htm...
  51. pmc Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis
    H Jin
    John Innes Centre, Colney, Norwich NR4 7UH, Institute of Food Research, Colney, Norwich NR4 7UH, UK
    EMBO J 19:6150-61. 2000
    ..It belongs to a novel group of plant R2R3 MYB proteins involved in transcriptional silencing. The balance between MYB activators and repressors on common target promoters may provide extra flexibility in transcriptional control...
  52. pmc Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 104:19369-74. 2007
    ..Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements...
  53. ncbi Rice domestication by reducing shattering
    Changbao Li
    Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
    Science 311:1936-9. 2006
    ..The substitution undermined the gene function necessary for the normal development of an abscission layer that controls the separation of a grain from the pedicel...
  54. pmc Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism
    Rongchen Wang
    Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla 92093 0116, USA
    Plant Physiol 132:556-67. 2003
    ..These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism...
  55. ncbi The effects of artificial selection on the maize genome
    Stephen I Wright
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Science 308:1310-4. 2005
    ..If we assume that our sample of genes is representative, approximately 1200 genes throughout the maize genome have been affected by artificial selection...
  56. pmc ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
    ..With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis...
  57. ncbi Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis
    A Samach
    John Innes Centre, Norwich NR4 7UH, UK
    Science 288:1613-6. 2000
    ..The SOC1 and FT genes are also regulated by a second flowering-time pathway that acts independently of CO. Thus, early target genes of CO define common components of distinct flowering-time pathways...
  58. ncbi Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance
    K R Jaglo-Ottosen
    Department of Crop and Soil Sciences, Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824 1325, USA
    Science 280:104-6. 1998
    ..We conclude that CBF1 is a likely regulator of the cold acclimation response, controlling the level of COR gene expression, which in turn promotes tolerance to freezing...
  59. ncbi The wheat VRN2 gene is a flowering repressor down-regulated by vernalization
    Liuling Yan
    Department of Agronomy and Range Science, University of California, Davis, CA 95616, USA
    Science 303:1640-4. 2004
    ..Reduction of the RNA level of VRN2 by RNA interference accelerated the flowering time of transgenic winter-wheat plants by more than a month...
  60. ncbi The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley
    Adrian Turner
    Crop Genetics Department, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
    Science 310:1031-4. 2005
    ....
  61. ncbi Gene silencing in plants using artificial microRNAs and other small RNAs
    Stephan Ossowski
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Plant J 53:674-90. 2008
    ..A recently introduced approach is the use of artificial microRNAs (amiRNAs). Here, we review various strategies for small RNA-based gene silencing, and describe in detail the design and application of amiRNAs in many plant species...
  62. ncbi Stress-responsive microRNAs in Populus
    Shanfa Lu
    Forest Biotechnology Group, Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA
    Plant J 55:131-51. 2008
    ..These results reveal possible roles for miRNAs in the regulatory networks associated with the long-term growth of tree species and provide useful information for developing trees with a greater level of stress resistance...
  63. pmc Identification of genes required for embryo development in Arabidopsis
    Iris Tzafrir
    Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078, USA
    Plant Physiol 135:1206-20. 2004
    ..These candidates should facilitate the recovery of additional genes required for seed development...
  64. ncbi The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering
    R Schaffer
    John Innes Centre, Norwich, United Kingdom
    Cell 93:1219-29. 1998
    ..Thus, constant expression of LHY disrupts several distinct circadian rhythms in Arabidopsis, and LHY may be closely associated with the central oscillator of the circadian clock...
  65. ncbi The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    Stefan A Rensing
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
    Science 319:64-9. 2008
    ..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics...
  66. ncbi A central integrator of transcription networks in plant stress and energy signalling
    Elena Baena-Gonzalez
    Department of Genetics, Harvard Medical School, Massachusetts General Hospital, Boston Massachusetts 02114, USA
    Nature 448:938-42. 2007
    ....
  67. pmc Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling
    Ralf Stracke
    Department of Biology, Genome Research, Bielefeld University, D 33594 Bielefeld, Germany
    Plant J 50:660-77. 2007
    ..Therefore, we refer to these genes as PFG1-3 for 'PRODUCTION OF FLAVONOL GLYCOSIDES'...
  68. ncbi Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana
    Hisako Ooka
    Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2 1 2 Kannon dai, Tsukuba, Ibaraki 305 8602, Japan
    DNA Res 10:239-47. 2003
    ..We discuss the relationship between the structure and function of the NAC family proteins in light of our results and the published data. Our results will aid further functional analysis of NAC family genes...
  69. ncbi Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice
    Kenong Xu
    Department of Plant Pathology, University of California, Davis, California 95616, USA
    Nature 442:705-8. 2006
    ..Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers...
  70. pmc Common functions for diverse small RNAs of land plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:1750-69. 2007
    ..Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants...
  71. pmc Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases
    S H Shiu
    Department of Botany, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 98:10763-8. 2001
    ....
  72. ncbi A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat
    Cristobal Uauy
    Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
    Science 314:1298-301. 2006
    ..Reduction in RNA levels of the multiple NAM homologs by RNA interference delayed senescence by more than 3 weeks and reduced wheat grain protein, zinc, and iron content by more than 30%...
  73. pmc Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice
    Honghong Hu
    National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Wuhan 430070, China
    Proc Natl Acad Sci U S A 103:12987-92. 2006
    ..DNA chip analysis revealed that a large number of stress-related genes were up-regulated in the SNAC1-overexpressing rice plants. Our data suggest that SNAC1 holds promising utility in improving drought and salinity tolerance in rice...
  74. pmc Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula
    Carine Ameline-Torregrosa
    Laboratoire des Interactions Plantes Microorganismes, UMR CNRS INRA 442 2594, 31326, Castanet Tolosan, France
    Plant Physiol 146:5-21. 2008
    ..This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome...
  75. ncbi CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis
    P Suárez-López
    John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
    Nature 410:1116-20. 2001
    ..In addition, the late flowering phenotype of such mutants is corrected by overexpressing CO. Thus, CO acts between the circadian clock and the control of flowering, suggesting mechanisms by which day length regulates flowering time...
  76. pmc Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant
    K H Wolfe
    Department of Biology, Indiana University, Bloomington 47405
    Proc Natl Acad Sci U S A 89:10648-52. 1992
    ..Remarkably, this massive pruning occurred with a virtual absence of gene order change...
  77. ncbi Establishment of polarity in lateral organs of plants
    Y Eshed
    Section of Plant Biology, Division of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
    Curr Biol 11:1251-60. 2001
    ..This suggests that the establishment of polarity in plant lateral organs occurs via mutual repression interactions between ab/ad factors after primordium emergence, consistent with the results of classical dissection experiments...
  78. ncbi The AP2/EREBP family of plant transcription factors
    J L Riechmann
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Biol Chem 379:633-46. 1998
    ....
  79. ncbi The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis
    T Laux
    Lehrstuhl fur Genetik, Ludwig Maximilian Universitat Munchen, Germany
    Development 122:87-96. 1996
    ..Our results suggest that the WUS gene is specifically required for central meristem identity of shoot and floral meristems to maintain their structural and functional integrity...
  80. ncbi TAL effectors: finding plant genes for disease and defense
    Adam J Bogdanove
    Department of Plant Pathology, Iowa State University, USA
    Curr Opin Plant Biol 13:394-401. 2010
    ..This article reviews the most significant findings in TALE research, with a focus on recent advances, and discusses future prospects including pressing questions yet to be answered...
  81. ncbi A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.)
    James Beales
    Crop Genetics Department, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
    Theor Appl Genet 115:721-33. 2007
    ....
  82. ncbi Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)
    Susan R McCouch
    Plant Breeding Dept, Cornell University, Ithaca, NY 14853 1901, USA
    DNA Res 9:199-207. 2002
    ..In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb...
  83. ncbi Understanding mechanisms of novel gene expression in polyploids
    Thomas C Osborn
    Dept of Agronomy, University of Wisconsin, Madison, WI 53706, USA
    Trends Genet 19:141-7. 2003
    ..New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy...
  84. ncbi A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance
    Manu Agarwal
    Institute for Integrative Genome Biology and Department of Botany and Plant Science, University of California, Riverside, California 92521, USA
    J Biol Chem 281:37636-45. 2006
    ..Our results suggest that MYB15 is part of a complex network of transcription factors controlling the expression of CBFs and other genes in response to cold stress...
  85. pmc microRNA172 down-regulates glossy15 to promote vegetative phase change in maize
    Nick Lauter
    Department of Crop Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 102:9412-7. 2005
    ..Our results also suggest that the balance of activities between APETALA2-like genes and miR172 may be a general mechanism for regulating vegetative phase change in higher plants...
  86. ncbi Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation
    A M Lindroth
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Science 292:2077-80. 2001
    ..They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing...
  87. ncbi Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells
    T Lotan
    Division of Biological Sciences, University of California, Davis 95616, USA
    Cell 93:1195-205. 1998
    ..Our results suggest that LEC1 is an important regulator of embryo development that activates the transcription of genes required for both embryo morphogenesis and cellular differentiation...
  88. pmc NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis
    June M Kwak
    Cell and Developmental Biology Section, Division of Biological Sciences and Center for Molecular Genetics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0116, USA
    EMBO J 22:2623-33. 2003
    ..These data provide direct molecular genetic and cell biological evidence that ROS are rate-limiting second messengers in ABA signaling, and that the AtrbohD and AtrbohF NADPH oxidases function in guard cell ABA signal transduction...
  89. ncbi Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis
    Gabriela C Pagnussat
    Section of Plant Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
    Development 132:603-14. 2005
    ..These results provide a first comprehensive overview of the genes and gene products involved in female gametophyte development and function within a flowering plant...
  90. pmc Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27
    Franziska Turck
    Abteilung Entwicklungsbiologie der Pflanzen, Max Planck Institut fur Zuchtungsforschung, Cologne, Germany
    PLoS Genet 3:e86. 2007
    ..Rather, our data suggest that TFL2/LHP1 recognizes specifically H3K27me3 in vivo as part of a mechanism that represses the expression of many genes targeted by PRC2...
  91. pmc Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant
    M Aida
    Department of Botany, Graduate School of Science, Kyoto University, Japan
    Plant Cell 9:841-57. 1997
    ..We cloned the CUC2 gene and found that the encoded protein was homologous to the petunia NO APICAL MERISTEM (NAM) protein, which is thought to act in the development of embryos and flowers...
  92. pmc A genome-wide characterization of microRNA genes in maize
    Lifang Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS Genet 5:e1000716. 2009
    ..As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes...
  93. ncbi CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees
    Henrik Böhlenius
    Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S 90183 Umeå, Sweden
    Science 312:1040-3. 2006
    ..This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe...
  94. pmc A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis
    Ik Young Choi
    Soybean Genomics and Improvement Laboratory, USDA, ARS, Beltsville, Maryland 20705, USA
    Genetics 176:685-96. 2007
    ....
  95. pmc IRT1, an Arabidopsis transporter essential for iron uptake from the soil and for plant growth
    Grégory Vert
    Biochimie et Physiologie Moleculaire des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5004, Universite Montpellier II, 2 place Viala, F 34060 Montpellier Cedex 1, France
    Plant Cell 14:1223-33. 2002
    ..These results clearly demonstrate that IRT1 is the major transporter responsible for high-affinity metal uptake under iron deficiency...
  96. ncbi Functional markers in plants
    Jeppe R Andersen
    Department of Plant Biology, Danish Institute of Agricultural Sciences, Research Center Flakkebjerg, 4200, Slagelse, Denmark
    Trends Plant Sci 8:554-60. 2003
    ..Functional markers are superior to random DNA markers such as RFLPs, SSRs and AFLPs owing to complete linkage with trait locus alleles. We outline the definition, development, application and prospects of functional markers...
  97. pmc Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing
    Zhonghua Wang
    Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
    Plant Cell 18:676-87. 2006
    ..In the presence of both restorers, RF1A was epistatic over RF1B in the mRNA processing. We have also shown that RF1A plays an additional role in promoting the editing of atp6 mRNAs, independent of its cleavage function...
  98. pmc The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes
    S B Milligan
    Center for Engineering Plants for Resistance Against Pathogens, University of California, Davis, California 95616, USA
    Plant Cell 10:1307-19. 1998
    ....
  99. pmc The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor
    R R Finkelstein
    Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA
    Plant Cell 12:599-609. 2000
    ..Comparison of seed and ABA-inducible vegetative gene expression in wild-type and abi5-1 plants indicates that ABI5 regulates a subset of late embryogenesis-abundant genes during both developmental stages...
  100. ncbi Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 422:433-8. 2003
    ....
  101. ncbi Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression
    Z Y Wang
    Department of Molecular, Cell, and Developmental Biology, UCLA, Los Angeles, California 90095 1606, USA
    Cell 93:1207-17. 1998
    ..Furthermore, the expression of both endogenous CCA1 and the related LHY gene was suppressed. Our results suggest that CCA1 is a part of a feedback loop that is closely associated with the circadian clock in Arabidopsis...

Research Grants19

  1. Toxoplasma Epigenomics and Gene Expression
    Kami Kim; Fiscal Year: 2013
    ..These genes, the AP2 family, may be new drug targets because they resemble plant genes rather than genes seen in mammals...
  2. MOLECULAR STUDY OF GIBBERELLIN REGULATED GENE EXPRESSION
    Neil Olszewski; Fiscal Year: 1992
    ..The specific aims of this project are to identify plant genes whose expression in flowers is regulated by gibberellin, and to begin to elucidate the mechanism of this ..
  3. DEVELOPMENT OF LARGE DNA METHODS FOR ARABIDOPSIS
    Joseph Ecker; Fiscal Year: 1991
    ..At present, the cloning of plant genes about which nothing more is known than genetic map position is technically difficult...
  4. MOLECULAR GENETICS OF DISEASE RESISTANCE IN ARABIDOPSIS
    BARBARA KUNKEL; Fiscal Year: 1999
    ..A combination of genetic, molecular and biochemical approaches will be used to identify and characterize plant genes that control disease resistance in Arabidopsis thaliana to the bacterial pathogen Pseudomonas syringae. The A...
  5. CIS & TRANS-ACTING COMPONENTS OF T-DNA PROMOTER FUNCTION
    WILLIAM GURLEY; Fiscal Year: 1992
    ..Although T-DNA genes may be bacterial in evolutionary origin, and certainly by lineage, they have achieved a close mimicry of plant genes from a functional standpoint and in their interactions with the trans-acting factors.
  6. REGULATION OF SYMBIOTIC PLANT GENES
    Mary Dunn; Fiscal Year: 1990
    The primary objective of this project is to examine the regulation of symbiotic plant genes induced during the nodulation of alfalfa...
  7. Understanding the role of N, a TIR-NB-LRR protein, in plant innate immunity
    Savithramma P Dinesh Kumar; Fiscal Year: 2010
    ..We therefore need increased knowledge of plant genes in order to manipulate them to engineer improved crops...
  8. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 2001
    ..We are elucidating a molecular genetic basis for heterochrony, the prevailing theory that links evolution with developmental biology. ..
  9. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin O Borevitz; Fiscal Year: 2010
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. ..
  10. Expression of Human Therapeutic Proteins in Transgenic Tobacco Chloroplasts
    Henry Daniell; Fiscal Year: 2010
    ..Successful completion of these studies would make transgenic chloroplasts ideal bioreactors for the production of safe and less expensive therapeutic proteins and open the door for in depth studies of membrane proteins. ..
  11. GENETIC ANALYSIS OF RNA VIRUS-HOST INTERACTION
    JAMES CARRINGTON; Fiscal Year: 2007
    ..Interactions between several viral silencing suppressors and cellular complexes and regulatory RNAs, and the interactions between suppressors and microRNA-controlled developmental pathways, will be examined. ..
  12. Self recognition and signaling in plant reproduction
    JUNE NASRALLAH; Fiscal Year: 2005
    ..abstract_text> ..
  13. ACTIVITY AND TRANSPORT OF TOBACCO ETCH VIRUS PROTEINASE
    JAMES CARRINGTON; Fiscal Year: 2003
    ..Identification of these host mutants will provide the starting point for isolation of genes involved in NIa-interacting reactions and pathways. ..
  14. ANALYSIS OF A LIGHT-REGULATED DEVELOPMENT SWITCH
    Xing Wang Deng; Fiscal Year: 2003
    ..abstract_text> ..
  15. Zeiss LSM 510 META Confocal Microscope
    JAMES CARRINGTON; Fiscal Year: 2003
    ....
  16. EVOLUTIONARY GENETICS OF R LOCI IN ARABIDOPSIS
    Joy Bergelson; Fiscal Year: 2007
    ..abstract_text> ..
  17. TRANSGRESSIVE SEGREGATION, ADAPTATION, AND SPECIATION
    Loren Rieseberg; Fiscal Year: 2008
    ..The proposed work represents an important step toward understanding the contribution of hybridization to adaptive evolution and speciation. ..
  18. EVOLUTIONARY DYNAMICS OF GENE-FOR-GENE SYSTEMS
    Joy Bergelson; Fiscal Year: 2004
    ..They can then use their estimate of allele frequency fluctuations to make testable predictions about observable patterns, such as the distribution of nucleotide polymorphisms. ..