Reverse Genetic Approaches for Functional Genomics of Rice

T-DNA and transposable elements e.g., Ds and Tos17, are used to generate a large number of insertional mutant lines in rice. Some carry the GUS or GFP reporter for gene trap or enhancer trap. These reporter systems are valuable for identifying tissue- or organ-preferential genes. Activation tagging lines have also been generated for screening mutants and isolating mutagenized genes. To utilize these resources more efficiently, tagged lines have been produced for reverse genetic approaches. DNA pools of the T-DNA tagged lines and Tos17 lines have been prepared for PCR screening of insertional mutants in a given gene. Tag end sequences (TES) of the inserts have also been produced. TES databases are beneficial for analyzing the function of a large number of rice genes.

[1]  G. Glazko,et al.  Origin of a substantial fraction of human regulatory sequences from transposable elements. , 2003, Trends in genetics : TIG.

[2]  C. R. McClung,et al.  Enhancer Trapping Reveals Widespread Circadian Clock Transcriptional Control in Arabidopsis1[w] , 2003, Plant Physiology.

[3]  S. Wessler,et al.  Isolation of the transposable maize controlling elements Ac and Ds , 1983, Cell.

[4]  Gl Wang,et al.  Evidence of multiple complex patterns of T-DNA integration into the rice genome , 2000, Theoretical and Applied Genetics.

[5]  S. Yamamoto,et al.  The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets , 2001, Molecular Genetics and Genomics.

[6]  Hong-Gyu Kang,et al.  Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice1 , 2003, Plant Physiology.

[7]  V. Sundaresan,et al.  Analysis of Flanking Sequences from Dissociation Insertion Lines: A Database for Reverse Genetics in Arabidopsis , 1999, Plant Cell.

[8]  Ping Wu,et al.  Distribution and characterization of over 1000 T-DNA tags in rice genome. , 2003, The Plant journal : for cell and molecular biology.

[9]  H. Hayashi,et al.  Activation tagging: a means of isolating genes implicated as playing a role in plant growth and development , 1994, Plant Molecular Biology.

[10]  S. Kaeppler,et al.  Genetic instability of plant tissue cultures: breakdown of normal controls. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. Nekrutenko,et al.  Transposable elements are found in a large number of human protein-coding genes. , 2001, Trends in genetics : TIG.

[12]  L. Luo,et al.  Generation and flanking sequence analysis of a rice T-DNA tagged population , 2004, Theoretical and Applied Genetics.

[13]  H. Hirochika,et al.  Applications of retrotransposons as genetic tools in plant biology. , 2001, Trends in plant science.

[14]  G. Bernardi,et al.  Two classes of genes in plants. , 2000, Genetics.

[15]  H. Hirochika,et al.  Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate , 1998, Plant Molecular Biology.

[16]  S. Lukyanov,et al.  An improved PCR method for walking in uncloned genomic DNA. , 1995, Nucleic acids research.

[17]  S. Iida,et al.  Trans-activation and stable integration of the maize transposable element Ds cotransfected with the Ac transposase gene in transgenic rice plants , 1993, Molecular and General Genetics MGG.

[18]  K. Jung,et al.  T-DNA insertional mutagenesis for functional genomics in rice. , 2000, The Plant journal : for cell and molecular biology.

[19]  M. Fladung,et al.  Transgene repeats in aspen: molecular characterisation suggests simultaneous integration of independent T-DNAs into receptive hotspots in the host genome , 2000, Molecular and General Genetics MGG.

[20]  J. Paszkowski,et al.  Plant genome modification by homologous recombination. , 2003, Current opinion in plant biology.

[21]  Jonathan D. G. Jones,et al.  Multiple Independent Defective Suppressor-mutator Transposon Insertions in Arabidopsis: A Tool for Functional Genomics , 1999, Plant Cell.

[22]  L. Mur,et al.  Targeted gene inactivation in petunia by PCR-based selection of transposon insertion mutants. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[23]  S. McKnight,et al.  Functional dissection of VP16, the trans-activator of herpes simplex virus immediate early gene expression. , 1988, Genes & development.

[24]  J. Chory,et al.  Activation tagging of the floral inducer FT. , 1999, Science.

[25]  W Henke,et al.  Betaine improves the PCR amplification of GC-rich DNA sequences. , 1997, Nucleic acids research.

[26]  Sean R. Eddy,et al.  An active DNA transposon family in rice , 2003, Nature.

[27]  D. Hartl,et al.  Genetic applications of an inverse polymerase chain reaction. , 1988, Genetics.

[28]  Jonathan D. G. Jones,et al.  Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. , 1995, Genes & development.

[29]  Accumulation on the cytoplasmic membrane of the precursor to dimethyl sulfoxide reductase in molybdenum cofactor-deficient mutants of Rhodobacter sphaeroides f. sp. denitrificans , 1992 .

[30]  L. Herrera-Estrella,et al.  Activation Tagging Using the En-I Maize Transposon System in Arabidopsis , 2002, Plant Physiology.

[31]  P. Abad,et al.  Flanking sequence tags in Arabidopsis thaliana T-DNA insertion lines: a pilot study. , 2002, Comptes rendus biologies.

[32]  F. Nagy,et al.  Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter , 1985, Nature.

[33]  D. Luth,et al.  Activity of a maize ubiquitin promoter in transgenic rice , 1993, Plant Molecular Biology.

[34]  H. Hirochika.  Contribution of the Tos17 retrotransposon to rice functional genomics. , 2001, Current opinion in plant biology.

[35]  Y. Machida,et al.  Frequency and pattern of transposition of the maize transposable element Ds in transgenic rice plants. , 2000, Plant & cell physiology.

[36]  D. Prasher,et al.  Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Jonathan D. G. Jones,et al.  Function Search in a Large Transcription Factor Gene Family in Arabidopsis: Assessing the Potential of Reverse Genetics to Identify Insertional Mutations in R2R3 MYB Genes , 1999, Plant Cell.

[38]  K. Shimamoto,et al.  Two-Step Regulation and Continuous Retrotransposition of the Rice LINE-Type Retrotransposon Karma Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011809. , 2003, The Plant Cell Online.

[39]  A. Meijer,et al.  Transpositional behaviour of an Ac/Ds system for reverse genetics in rice , 2003, Theoretical and Applied Genetics.

[40]  S. Kay,et al.  A novel circadian phenotype based on firefly luciferase expression in transgenic plants. , 1992, The Plant cell.

[41]  M. Cho,et al.  Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. , 1999, The Plant journal : for cell and molecular biology.

[42]  M. Lorieux,et al.  Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy , 2003, Theoretical and Applied Genetics.

[43]  Rossana Henriques,et al.  Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes. , 2002, The Plant journal : for cell and molecular biology.

[44]  H. Hirochika,et al.  Transposition of the maize Ds element from a viral vector to the rice genome. , 1994, The Plant journal : for cell and molecular biology.

[45]  T. Komari,et al.  Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. , 1994, The Plant journal : for cell and molecular biology.

[46]  E. Meyerowitz,et al.  Overexpression of a Gene Encoding a Cytochrome P450, CYP78A9, Induces Large and Seedless Fruit in Arabidopsis , 2000, Plant Cell.

[47]  R. Dixon,et al.  Activation tagging in Arabidopsis. , 2000, Plant physiology.

[48]  Srinivasan Ramachandran,et al.  Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. , 2004, The Plant journal : for cell and molecular biology.

[49]  K. Shimamoto,et al.  FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets , 2003, Development.

[50]  P. Hengen.  Optimizing multiplex and LA-PCR with betaine. , 1997, Trends in biochemical sciences.

[51]  G. Agrawal,et al.  Screening of the rice viviparous mutants generated by endogenous retrotransposon Tos17 insertion. Tagging of a zeaxanthin epoxidase gene and a novel ostatc gene. , 2001, Plant physiology.

[52]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[53]  K. Lindsey,et al.  Promoter trap markers differentiate structural and positional components of polar development in Arabidopsis. , 1997, The Plant cell.

[54]  J. D. Jones,et al.  Novel GUS expression patterns following transposition of an enhancer trap Ds element in Arabidopsis , 1995, Molecular and General Genetics MGG.

[55]  K. Feldmann.  T‐DNA insertion mutagenesis in Arabidopsis: mutational spectrum , 1991 .

[56]  G. An,et al.  T-DNA Insertional Mutagenesis for Activation Tagging in Rice1 , 2002, Plant Physiology.

[57]  B Keller,et al.  Activation tagging of the LEAFY PETIOLE gene affects leaf petiole development in Arabidopsis thaliana. , 2000, Development.

[58]  Yaoguang Liu,et al.  Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. , 1995, Genomics.

[59]  A. Miyao,et al.  Target Site Specificity of the Tos17 Retrotransposon Shows a Preference for Insertion within Genes and against Insertion in Retrotransposon-Rich Regions of the Genome Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012559. , 2003, The Plant Cell Online.

[60]  W. M. Robertson,et al.  Regulatory sequences of Arabidopsis drive reporter gene expression in nematode feeding structures. , 1997, The Plant cell.

[61]  K. Jung,et al.  Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system. , 2003, Plant & cell physiology.

[62]  A. Rosenthal,et al.  Genomic walking and sequencing by oligo-cassette mediated polymerase chain reaction. , 1990, Nucleic acids research.

[63]  Y. Elkind,et al.  Technical advance: a high throughput system for transposon tagging and promoter trapping in tomato. , 2000, The Plant journal : for cell and molecular biology.

[64]  P. Ouwerkerk,et al.  Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics , 2003, Theoretical and Applied Genetics.

[65]  V. Sundaresan,et al.  Functional genomics in Arabidopsis: large-scale insertional mutagenesis complements the genome sequencing project. , 2000, Current opinion in biotechnology.

[66]  L. Campisi,et al.  Generation of enhancer trap lines in Arabidopsis and characterization of expression patterns in the inflorescence. , 1999, The Plant journal : for cell and molecular biology.

[67]  Y. Machida,et al.  Characterization of the transposition pattern of the Ac element in Arabidopsis thaliana using endonuclease I-SceI. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[68]  B. Mueller‐Roeber,et al.  Cloning of regulatory sequences mediating guard-cell-specific gene expression. , 2000, Gene.

[69]  Xianghe Yan,et al.  Use of the Transposon Ac as a Gene-Searching Engine in the Maize Genome , 2002, The Plant Cell Online.

[70]  S. Briggs,et al.  Diversification of C-Function Activity in Maize Flower Development , 1996, Science.

[71]  T. Gojobori,et al.  The genome sequence and structure of rice chromosome 1 , 2002, Nature.

[72]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica) , 2002, Science.

[73]  C. Koncz,et al.  Gene Trapping with Firefly Luciferase in Arabidopsis. Tagging of Stress-Responsive Genes1[w] , 2004, Plant Physiology.

[74]  J. McDonald,et al.  Long terminal repeat retrotransposons of Oryza sativa , 2002, Genome Biology.

[75]  G. An,et al.  Gene tagging in rice: a high throughput system for functional genomics. , 2001, Plant science : an international journal of experimental plant biology.

[76]  K. Shimamoto,et al.  Ac as a tool for the functional genomics of rice. , 1999, The Plant journal : for cell and molecular biology.

[77]  M. Schmid,et al.  Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana , 2003, Science.

[78]  K. Feldmann,et al.  T-DNA insertion mutagenesis in Arabidopsis: going back and forth. , 1997, Trends in genetics : TIG.

[79]  P. Springer.  Gene Traps: Tools for Plant Development and Genomics , 2000, Plant Cell.

[80]  V. Sundaresan.  Horizontal spread of transposon mutagenesis: new uses for old elements , 1996 .

[81]  H. Leung,et al.  Rice Mutant Resources for Gene Discovery , 2004, Plant Molecular Biology.

[82]  E. Meyerowitz,et al.  Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[83]  A. Miyao,et al.  Three Distinct Rice Cellulose Synthase Catalytic Subunit Genes Required for Cellulose Synthesis in the Secondary Wall1 , 2003, Plant Physiology.

[84]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[85]  K. K. Narayanan,et al.  An iAc/Ds gene and enhancer trapping system for insertional mutagenesis in rice. , 2002, Functional plant biology : FPB.

[86]  S. Iida,et al.  Introduction and transposition of the maize transposable element Ac in rice (Oryza sativa L.) , 1991, Molecular and General Genetics MGG.

[87]  S. Goff,et al.  A High-Throughput Arabidopsis Reverse Genetics System Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.004630. , 2002, The Plant Cell Online.

[88]  D. Bouchez,et al.  Arabidopsis gene knockout: phenotypes wanted. , 2001, Current opinion in plant biology.

[89]  A. Levy,et al.  Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat , 2003, Nature Genetics.

[90]  R. Wu,et al.  Isolation of an efficient actin promoter for use in rice transformation. , 1990, The Plant cell.

[91]  M. Bevan,et al.  GUS fusions: beta‐glucuronidase as a sensitive and versatile gene fusion marker in higher plants. , 1987, The EMBO journal.

[92]  G. Coupland,et al.  A Dissociation insertion causes a semidominant mutation that increases expression of TINY, an Arabidopsis gene related to APETALA2. , 1996, The Plant cell.

[93]  J. Chory,et al.  BAS1: A gene regulating brassinosteroid levels and light responsiveness in Arabidopsis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[94]  Hong-Gyu Kang,et al.  Generation of T-DNA Tagging Lines with a Bidirectional Gene Trap Vector and the Establishment of an Insertion-Site Database , 2004, Plant Molecular Biology.

[95]  Yutaka Okumoto,et al.  Mobilization of a transposon in the rice genome , 2003, Nature.

[96]  G. An,et al.  Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case. , 2003, Plant & cell physiology.

[97]  M. Fromm,et al.  An Improved Green Fluorescent Protein Gene as a Vital Marker in Plants , 1996, Plant physiology.

[98]  M. Matsuoka,et al.  Loss‐of‐function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants , 1999, The EMBO journal.

[99]  S. Gan,et al.  Networking senescence-regulating pathways by using Arabidopsis enhancer trap lines. , 2001, Plant physiology.

[100]  Daoxiu Zhou,et al.  Development of enhancer trap lines for functional analysis of the rice genome. , 2003, The Plant journal : for cell and molecular biology.

[101]  J. S. Lee,et al.  The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis. , 2000, Genes & development.

[102]  G. Bernardi,et al.  The distribution of T‐DNA in the genomes of transgenic Arabidopsis and rice , 2000, FEBS letters.

[103]  Jonathan D. G. Jones,et al.  ATIDB: Arabidopsis thaliana insertion database. , 2003, Nucleic acids research.

[104]  M. Sussman,et al.  T-DNA as an Insertional Mutagen in Arabidopsis , 1999, Plant Cell.

[105]  V. Walbot,et al.  Saturation mutagenesis using maize transposons. , 2000, Current opinion in plant biology.

[106]  N. Murai,et al.  Transposition of the maize activator element in transgenic rice plants. , 1991, Nucleic acids research.

[107]  Johnf . Thompson,et al.  Modulation of firefly luciferase stability and impact on studies of gene regulation. , 1991, Gene.

[108]  D. Kemp,et al.  A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. , 1988, Nucleic acids research.

[109]  V. Walbot.  Reactivation of Mutator transposable elements of maize by ultraviolet light , 1992, Molecular and General Genetics MGG.

[110]  H. Hirochika,et al.  Retrotransposons of rice involved in mutations induced by tissue culture. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[111]  Masaki Furuya,et al.  Isolation and Characterization of Rice Phytochrome A Mutants , 2001, Plant Cell.

[112]  B. Je,et al.  Reprogramming of the activity of the activator/dissociation transposon family during plant regeneration in rice. , 2002, Molecules and cells.

[113]  B. Bartel,et al.  A library of Arabidopsis 35S-cDNA lines for identifying novel mutants , 2001, Plant Molecular Biology.

[114]  S. Kaeppler,et al.  Epigenetic aspects of somaclonal variation in plants , 2000, Plant Molecular Biology.

[115]  Kazuhiro Kikuchi,et al.  The plant MITE mPing is mobilized in anther culture , 2003, Nature.

[116]  D. Galbraith,et al.  Systematic reverse genetics of transfer-DNA-tagged lines of Arabidopsis. Isolation of mutations in the cytochrome p450 gene superfamily. , 1998, Plant physiology.