RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice

[1]  V. Sundaresan,et al.  Somatic embryo initiation by rice BABY BOOM1 involves activation of zygote-expressed auxin biosynthesis genes. , 2023, The New phytologist.

[2]  Jiong Hui Liu,et al.  Regulation of WOX11 Expression Represents the Difference Between Direct and Indirect Shoot Regeneration , 2022, Frontiers in Plant Science.

[3]  Jia-Wei Wang,et al.  A robust mechanism for resetting juvenility during each generation in Arabidopsis , 2022, Nature Plants.

[4]  Junhui Wang,et al.  Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis , 2020, BMC plant biology.

[5]  Javier F. Palatnik,et al.  A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants , 2020, Nature Biotechnology.

[6]  F. Frugier,et al.  The NIN transcription factor coordinates CEP and CLE signaling peptides that regulate nodulation antagonistically , 2020, Nature Communications.

[7]  Y. A. Purwestri,et al.  Establishment of a plant tissue culture system and genetic transformation for agronomic improvement of Indonesian black rice (Oryza sativa L.) , 2020, Plant Cell, Tissue and Organ Culture (PCTOC).

[8]  Li Yang,et al.  Jasmonate-mediated wound signalling promotes plant regeneration , 2019, Nature Plants.

[9]  Jiamu Du,et al.  Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis , 2019, Nature Plants.

[10]  Nigel P. Dyer,et al.  LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics , 2019, PeerJ.

[11]  V. Sundaresan,et al.  A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds , 2018, Nature.

[12]  K. Singh,et al.  Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.) , 2018, PloS one.

[13]  Paul T. Tarr,et al.  Characterization of somatic embryogenesis initiated from the Arabidopsis shoot apex. , 2018, Developmental biology.

[14]  I. Efroni A Conceptual Framework for Cell Identity Transitions in Plants. , 2018, Plant & cell physiology.

[15]  Siobhan M Brady,et al.  A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration , 2018, Plant & cell physiology.

[16]  K. Shirasu,et al.  Regulation of floral meristem activity through the interaction of AGAMOUS, SUPERMAN, and CLAVATA3 in Arabidopsis , 2017, Plant Reproduction.

[17]  Lisha Shen,et al.  Embryonic epigenetic reprogramming by a pioneer transcription factor in plants , 2017, Nature.

[18]  Gerco C. Angenent,et al.  The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis1[OPEN] , 2017, Plant Physiology.

[19]  Zhou Du,et al.  agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update , 2017, Nucleic Acids Res..

[20]  R. Pratiwi,et al.  Black rice as a functional food in Indonesia , 2017 .

[21]  L. Altschmied,et al.  RWP-RK domain-containing transcription factors control cell differentiation during female gametophyte development in Arabidopsis. , 2017, The New phytologist.

[22]  Jenny Banh,et al.  Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation[OPEN] , 2016, Plant Cell.

[23]  J. Bowman,et al.  Marchantia MpRKD Regulates the Gametophyte-Sporophyte Transition by Keeping Egg Cells Quiescent in the Absence of Fertilization , 2016, Current Biology.

[24]  K. Yamato,et al.  An Evolutionarily Conserved Plant RKD Factor Controls Germ Cell Differentiation , 2016, Current Biology.

[25]  R. Satija,et al.  Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions , 2016, Cell.

[26]  Mathew G. Lewsey,et al.  Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape , 2016, Cell.

[27]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[28]  V. Loyola-Vargas,et al.  The Relationship Between Stress and Somatic Embryogenesis , 2016 .

[29]  A. Fehér Somatic embryogenesis - Stress-induced remodeling of plant cell fate. , 2015, Biochimica et biophysica acta.

[30]  H. Ezura,et al.  WIND1-based acquisition of regeneration competency in Arabidopsis and rapeseed , 2015, Journal of Plant Research.

[31]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[32]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[33]  T. Girin,et al.  The plant RWP-RK transcription factors: key regulators of nitrogen responses and of gametophyte development. , 2014, Journal of experimental botany.

[34]  C. Dean,et al.  Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state , 2014, Nature.

[35]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[36]  Masaharu Suzuki,et al.  Regulation of the seed to seedling developmental phase transition by the LAFL and VAL transcription factor networks , 2014, Wiley interdisciplinary reviews. Developmental biology.

[37]  So-Young Park,et al.  Bioreactor Culture of Shoots and Somatic Embryos of Medicinal Plants for Production of Bioactive Compounds , 2014 .

[38]  Fuguang Li,et al.  Induced Expression of AtLEC1 and AtLEC2 Differentially Promotes Somatic Embryogenesis in Transgenic Tobacco Plants , 2013, PloS one.

[39]  L. Pâques,et al.  Somatic embryogenesis in forestry with a focus on Europe: state-of-the-art, benefits, challenges and future direction , 2013, Tree Genetics & Genomes.

[40]  J. A. Teixeira da Silva,et al.  Synseed technology-a complete synthesis. , 2013, Biotechnology advances.

[41]  S. E. Perry,et al.  Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development1[C][W][OA] , 2013, Plant Physiology.

[42]  Jun-ichi Itoh,et al.  RiceFREND: a platform for retrieving coexpressed gene networks in rice , 2012, Nucleic Acids Res..

[43]  M. Kubo,et al.  AP2-type transcription factors determine stem cell identity in the moss Physcomitrella patens , 2012, Development.

[44]  Chongsheng He,et al.  Reprogramming of H3K27me3 Is Critical for Acquisition of Pluripotency from Cultured Arabidopsis Tissues , 2012, PLoS genetics.

[45]  P. Ronald,et al.  Establishment of Glucocorticoid-Mediated Transcriptional Induction of the Rice XA21 Pattern Recognition Receptor , 2012, Journal of Plant Biology.

[46]  M. Catterou,et al.  De novo shoot organogenesis: from art to science. , 2011, Trends in plant science.

[47]  K. Nakajima,et al.  The Arabidopsis RWP-RK Protein RKD4 Triggers Gene Expression and Pattern Formation in Early Embryogenesis , 2011, Current Biology.

[48]  W. Lukowitz,et al.  The RWP-RK Factor GROUNDED Promotes Embryonic Polarity by Facilitating YODA MAP Kinase Signaling , 2011, Current Biology.

[49]  X. Zhang,et al.  DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling , 2011, PLoS genetics.

[50]  U. Grossniklaus,et al.  Members of the RKD transcription factor family induce an egg cell-like gene expression program. , 2011, The Plant journal : for cell and molecular biology.

[51]  M. Seki,et al.  The AP2/ERF Transcription Factor WIND1 Controls Cell Dedifferentiation in Arabidopsis , 2011, Current Biology.

[52]  G. Angenent,et al.  Efficient sweet pepper transformation mediated by the BABY BOOM transcription factor , 2011, Plant Cell Reports.

[53]  Mingwei Zhang,et al.  Phenolic profiles and antioxidant activity of black rice bran of different commercially available varieties. , 2010, Journal of agricultural and food chemistry.

[54]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[55]  J. Long,et al.  Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors , 2010, Nature.

[56]  W. Deng,et al.  A novel method for induction of plant regeneration via somatic embryogenesis , 2009 .

[57]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[58]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[59]  K. Jung,et al.  Binary vectors for efficient transformation of rice , 1999, Journal of Plant Biology.

[60]  A. Oskooi Molecular Evolution and Phylogenetics , 2008 .

[61]  M. Barton,et al.  A Feedback Regulatory Module Formed by LITTLE ZIPPER and HD-ZIPIII Genes[W][OA] , 2007, The Plant Cell Online.

[62]  Renze Heidstra,et al.  PLETHORA proteins as dose-dependent master regulators of Arabidopsis root development , 2007, Nature.

[63]  S. Oka,et al.  Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. , 2006, The Plant journal : for cell and molecular biology.

[64]  G. Angenent,et al.  Heterologous expression of the BABY BOOM AP2/ERF transcription factor enhances the regeneration capacity of tobacco (Nicotiana tabacum L.) , 2006, Planta.

[65]  M. Kang,et al.  Antioxidative activities of bran extracts from twenty one pigmented rice cultivars , 2006 .

[66]  L. Schauser,et al.  Evolution of NIN-Like Proteins in Arabidopsis, Rice, and Lotus japonicus , 2005, Journal of Molecular Evolution.

[67]  R. Amasino,et al.  The PLETHORA Genes Mediate Patterning of the Arabidopsis Root Stem Cell Niche , 2004, Cell.

[68]  Michelle T. Juarez,et al.  microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity , 2004, Nature.

[69]  Andrey Rzhetsky,et al.  Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference , 1992, Journal of Molecular Evolution.

[70]  E. Guiderdoni,et al.  Plant regeneration from leaf and seed-derived calli and suspension cultures of the African perennial wild rice, Oryza longistaminata , 1990, Plant Cell Reports.

[71]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[72]  V. Sharma,et al.  Ectopic Expression of BABY BOOM Triggers a Conversion from Vegetative to Embryonic Growth Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001941. , 2002, The Plant Cell Online.

[73]  N. Chua,et al.  The WUSCHEL gene promotes vegetative-to-embryonic transition in Arabidopsis. , 2002, The Plant journal : for cell and molecular biology.

[74]  L. Lepiniec,et al.  LEAFY COTYLEDON2 encodes a B3 domain transcription factor that induces embryo development , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[75]  U. Grossniklaus,et al.  The Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE 1 gene is expressed in developing ovules and embryos and enhances embryogenic competence in culture. , 2001, Plant physiology.

[76]  Leif Schauser,et al.  A plant regulator controlling development of symbiotic root nodules , 1999, Nature.

[77]  Robert B Goldberg,et al.  Arabidopsis LEAFY COTYLEDON1 Is Sufficient to Induce Embryo Development in Vegetative Cells , 1998, Cell.

[78]  U. Goodenough,et al.  Mating type in Chlamydomonas is specified by mid, the minus-dominance gene. , 1997, Genetics.

[79]  P. McCourt,et al.  A regulatory role for the ABI3 gene in the establishment of embryo maturation in Arabidopsis thaliana , 1995 .

[80]  C. Peterson,et al.  Efficient lipid staining in plant material with sudan red 7B or fluorol [correction of fluoral] yellow 088 in polyethylene glycol-glycerol. , 1991, Biotechnic & histochemistry : official publication of the Biological Stain Commission.

[81]  N. Saito The neighbor-joining method : A new method for reconstructing phylogenetic trees , 1987 .

[82]  L. Pauling,et al.  Evolutionary Divergence and Convergence in Proteins , 1965 .

[83]  F. Steward,et al.  GROWTH AND DEVELOPMENT OF CULTURED PLANT CELLS. , 1964, Science.