An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches

BMC Plant Biology

Volumn 9, Issue , 2009, Pages

  Robinson, Stephen J ^a   Tang, Lily H ^a   Mooney, Brent Ag ^a   McKay, Sheldon J ^a,b   Clarke, Wayne E ^a   Links, Matthew G ^a   Karcz, Steven ^a   Regan, Sharon ^c   Wu, Yun Yun ^c   Gruber, Margaret Y ^a   Cui, Dejun ^a   Yu, Min ^a   Parkin, Isobel Ap ^a  

^a SASKATOON RESEARCH CENTRE   (Canada)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c QUEEN S UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

BACTERIAL DNA; PLANT DNA; T DNA; T-DNA;

ARABIDOPSIS; ARTICLE; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GENOME;

ARABIDOPSIS; DNA MUTATIONAL ANALYSIS; DNA, BACTERIAL; DNA, PLANT; GENES, PLANT; GENOME, PLANT; GENOMICS; MUTAGENESIS, INSERTIONAL;

EID: 69549085007     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-9-101     Document Type: Article

References (58)

1. Prehistory and History of Arabidopsis Research. EM Meyerowitz, Plant Physiol 2001 125 1 15 19 10.1104/pp.125.1.15 11154286 (Pubitemid 32116716)
2. Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. X Zhang R Henriques S-S Lin Q-W Niu N-H Chua, Nat Protocols 2006 1 2 641 646 10.1038/nprot.2006.97
3. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. AGI, Nature 2007 408 6814 796 815 10.1038/35048692
4. A barley activation tagging system. MA Ayliffe M Pallotta P Langridge AJ Pryor, Plant Mol Biol 2007 64 3 329 347 10.1007/s11103-007-9157-8 17429742 (Pubitemid 46663199)
5. Generation and analysis of end sequence database for T-DNA tagging lines in rice. S An S Park DH Jeong DY Lee HG Kang JH Yu J Hur SR Kim YH Kim M Lee, Plant Physiol 2003 133 4 2040 2047 10.1104/pp.103.030478 14630961 (Pubitemid 38047330)
6. Establishment of a soybean (Glycine max Merr. L) transposon-based mutagenesis repository. M Mathieu EK Winters F Kong J Wan S Wang H Eckert D Luth M Paz C Donovan Z Zhang, Planta 2009 229 2 279 289 10.1007/s00425-008-0827-9 18855007
7. Establishing gene function by mutagenesis in Arabidopsis thaliana. L Ostergaard MF Yanofsky, Plant J 2004 39 5 682 696 10.1111/j.1365-313X.2004. 02149.x 15315632 (Pubitemid 39218778)
8. Spectrum of Chemically Induced Mutations From a Large-Scale Reverse-Genetic Screen in Arabidopsis. EA Greene CA Codomo NE Taylor JG Henikoff BJ Till SH Reynolds LC Enns C Burtner JE Johnson AR Odden, Genetics 2003 164 2 731 740 12807792
9. Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. V Sundaresan P Springer T Volpe S Haward JD Jones C Dean H Ma R Martienssen, Genes Dev 1995 9 14 1797 1810 10.1101/gad.9.14.1797 7622040
10. A fast neutron deletion mutagenesis-based reverse genetics system for plants. X Li Y Song K Century S Straight P Ronald X Dong M Lassner Y Zhang, Plant J 2001 27 3 235 242 10.1046/j.1365-313x.2001.01084.x 11532169 (Pubitemid 32778814)
11. Genome-wide insertional mutagenesis of Arabidopsis thaliana. JM Alonso AN Stepanova TJ Leisse CJ Kim H Chen P Shinn DK Stevenson J Zimmerman P Barajas R Cheuk, Science 2003 301 653 657 10.1126/science.1086391 12893945 (Pubitemid 36927950)
12. A high-throughput Arabidopsis reverse genetics system. A Sessions E Burke G Presting G Aux J McElver D Patton B Dietrich P Ho J Bacwaden C Ko, Plant Cell 2002 14 12 2985 2994 10.1105/tpc.004630 12468722 (Pubitemid 36029127)
13. FLAGdb++: a database for the functional analysis of the Arabidopsis genome. F Samson V Brunaud S Duchene Y De Oliveira M Caboche A Lecharny S Aubourg, Nucleic Acids Res 2004 32 Database D347 350 10.1093/nar/gkh134 14681431
14. GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. Y Li MG Rosso P Viehoever B Weisshaar, Nucleic Acids Res 2007 35 Database D874 878 10.1093/nar/gkl753 17062622 (Pubitemid 46056325)
15. Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions. Y Li MG Rosso B Ulker B Weisshaar, Genomics 2006 87 5 645 652 10.1016/j.ygeno.2005.12.010 16488113
16. Gene Traps: Tools for Plant Development and Genomics. PS Springer, Plant Cell 2000 12 7 1007 1020 10.1105/tpc.12.7.1007 10899970 (Pubitemid 30622708)
17. Activation tagging in plants: a tool for gene discovery. H Tani X Chen P Nurmberg JJ Grant M SantaMaria A Chini E Gilroy PR Birch GJ Loake, Funct Integr Genomics 2004 4 4 258 266 10.1007/s10142-004-0112-3 15156357 (Pubitemid 41166573)
18. Activation tagging in Arabidopsis. D Weigel JH Ahn MA Blazquez JO Borevitz SK Christensen C Fankhauser C Ferrandiz I Kardailsky EJ Malancharuvil MM Neff, Plant Physiol 2000 122 4 1003 1013 10.1104/pp.122.4.1003 10759496
19. Identification of plant stress-responsive determinants in Arabidopsis by large-scale forward genetic screens. H Koiwa RA Bressan PM Hasegawa, J Exp Bot 2006 57 5 1119 1128 10.1093/jxb/erj093 16513815
20. Getting the most out of publicly available T-DNA insertion lines. B Ulker E Peiter DP Dixon C Moffat R Capper N Bouche R Edwards D Sanders H Knight MR Knight, Plant J 2008 56 4 665 677 10.1111/j.1365-313X.2008.03608.x 18644000
21. Insertional mutagenesis of genes required for seed development in Arabidopsis thaliana. J McElver I Tzafrir G Aux R Rogers C Ashby K Smith C Thomas A Schetter Q Zhou MA Cushman, Genetics 2001 159 4 1751 1763 11779812
22. A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization. T Singer Y Fan HS Chang T Zhu SP Hazen SP Briggs, PLoS Genet 2006 2 9 e144 10.1371/journal.pgen.0020144 17044735 (Pubitemid 44504787)
23. T-DNA-mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants. B Ulker Y Li MG Rosso E Logemann IE Somssich B Weisshaar, Nat Biotechnol 2008 26 9 1015 1017 10.1038/nbt.1491 18758448
24. The generic genome browser: a building block for a model organism system database. LD Stein C Mungall S Shu M Caudy M Mangone A Day E Nickerson JE Stajich TW Harris A Arva, Genome Res 2002 12 10 1599 1610 10.1101/gr.403602 12368253 (Pubitemid 35175099)
25. Bridging the Gene-to-Function Knowledge Gap Through Functional Genomics. SJ Robinson IAP Parkin, Plant Genomics 2009 153 173
26. Characterization of a weak allele of the GL1 gene of Arabidopsis thaliana. JJ Esch DG Oppenheimer MD Marks, Plant Mol Biol 1994 24 1 203 207 10.1007/BF00040586 8111017
27. The GLABRA2 gene encodes a homeo domain protein required for normal trichome development in Arabidopsis. WG Rerie KA Feldmann MD Marks, Genes Dev 1994 8 12 1388 1399 10.1101/gad.8.12.1388 7926739
28. GL3 encodes a bHLH protein that regulates trichome development in arabidopsis through interaction with GL1 and TTG1. CT Payne F Zhang AM Lloyd, Genetics 2000 156 3 1349 1362 11063707
29. The Arabidopsis KAKTUS gene encodes a HECT protein and controls the number of endoreduplication cycles. A El Refy D Perazza L Zekraoui JG Valay N Bechtold S Brown M Hulskamp M Herzog JM Bonneville, Mol Genet Genomics 2003 270 5 403 414 10.1007/s00438-003-0932-1 14530964 (Pubitemid 38085125)
30. The actin cytoskeleton is required to elaborate and maintain spatial patterning during trichome cell morphogenesis in Arabidopsis thaliana. J Mathur P Spielhofer B Kost N Chua, Development 1999 126 24 5559 5568 10572033
31. Actin control over microtubules suggested by DISTORTED2 encoding the Arabidopsis ARPC2 subunit homolog. R Saedler N Mathur BP Srinivas B Kernebeck M Hulskamp J Mathur, Plant Cell Physiol 2004 45 7 813 822 10.1093/pcp/pch103 15295064 (Pubitemid 39123394)
32. A mutant of Arabidopsis thaliana displaying altered patterns of cellulose deposition. T Potikha DP Delmer, Plant J 1995 7 3 453 460 10.1046/j.1365-313X. 1995.7030453.x
33. The Arabidopsis STICHEL gene is a regulator of trichome branch number and encodes a novel protein. H Ilgenfritz D Bouyer A Schnittger J Mathur V Kirik B Schwab NH Chua G Jurgens M Hulskamp, Plant Physiol 2003 131 2 643 655 10.1104/pp.014209 12586888 (Pubitemid 36219526)
34. Essential role of a kinesin-like protein in Arabidopsis trichome morphogenesis. DG Oppenheimer MA Pollock J Vacik DB Szymanski B Ericson K Feldmann MD Marks, Proc Natl Acad Sci USA 1997 94 12 6261 6266 10.1073/pnas.94.12.6261 9177205 (Pubitemid 27270672)
35. GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana. Y Li MG Rosso N Strizhov P Viehoever B Weisshaar, Bioinformatics 2003 19 11 1441 1442 10.1093/bioinformatics/btg170 12874060 (Pubitemid 36939826)
36. RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. T Sakurai M Satou K Akiyama K Iida M Seki T Kuromori T Ito A Konagaya T Toyoda K Shinozaki, Nucleic Acids Res 2005 33 Database D647 650 15608280
37. A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. K Hanada X Zhang JO Borevitz WH Li SH Shiu, Genome Res 2007 17 5 632 640 10.1101/gr.5836207 17395691 (Pubitemid 46715514)
38. Discovery and revision of Arabidopsis genes by proteogenomics. NE Castellana SH Payne Z Shen M Stanke V Bafna SP Briggs, Proc Natl Acad Sci USA 2008 105 52 21034 21038 10.1073/pnas.0811066106 19098097
39. Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. P Nacry C Camilleri B Courtial M Caboche D Bouchez, Genetics 1998 149 2 641 650 9611180
40. A chromosomal paracentric inversion associated with T-DNA integration in Arabidopsis. P Laufs D Autran J Traas, Plant J 1999 18 2 131 139 10.1046/j.1365-313X.1999.00436.x 10363366 (Pubitemid 29223275)
41. T-DNA-associated duplication/translocations in Arabidopsis. Implications for mutant analysis and functional genomics. FE Tax DM Vernon, Plant physiology 2001 126 4 1527 1538 10.1104/pp.126.4.1527 11500551 (Pubitemid 32752381)
42. Identification and biochemical characterization of mutants in the proanthocyanidin pathway in Arabidopsis. S Abrahams GJ Tanner PJ Larkin AR Ashton, Plant Physiol 2002 130 2 561 576 10.1104/pp.006189 12376625 (Pubitemid 35224766)
43. Mutations affecting the testa colour in Arabidopsis. M Koornneef, Arabidopsis Information Service 1990 27 1 4
44. Mutation rate and novel tt mutants of Arabidopsis thaliana induced by carbon ions. N Shikazono Y Yokota S Kitamura C Suzuki H Watanabe S Tano A Tanaka, Genetics 2003 163 4 1449 1455 12702688
45. Analysis of Arabidopsis mutants deficient in flavonoid biosynthesis. BW Shirley WL Kubasek G Storz E Bruggemann M Koornneef FM Ausubel HM Goodman, Plant J 1995 8 5 659 671 10.1046/j.1365-313X.1995.08050659.x 8528278
46. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. B Winkel-Shirley, Plant Physiol 2001 126 2 485 493 10.1104/pp.126.2.485 11402179 (Pubitemid 32566604)
47. New perspectives on proanthocyanidin biochemistry and molecular regulation. MA Marles H Ray MY Gruber, Phytochem 2003 64 2 367 383 10.1016/S0031-9422(03)00377-7 (Pubitemid 37168954)
48. A plasma membrane H+-ATPase is required for the formation of proanthocyanidins in the seed coat endothelium of Arabidopsis thaliana. IR Baxter JC Young G Armstrong N Foster N Bogenschutz T Cordova WA Peer SP Hazen AS Murphy JF Harper, Proc Natl Acad Sci USA 2005 102 7 2649 2654 10.1073/pnas.0406377102 15695592 (Pubitemid 40279431)
49. TRANSPARENT TESTA 19 is involved in the accumulation of both anthocyanins and proanthocyanidins in Arabidopsis. S Kitamura N Shikazono A Tanaka, Plant J 2004 37 1 104 114 10.1046/j.1365-313X.2003.01943.x 14675436 (Pubitemid 38078269)
50. The Arabidopsis MATE transporter TT12 acts as a vacuolar flavonoid/H+ -antiporter active in proanthocyanidin-accumulating cells of the seed coat. K Marinova L Pourcel B Weder M Schwarz D Barron JM Routaboul I Debeaujon M Klein, Plant Cell 2007 19 6 2023 2038 10.1105/tpc.106.046029 17601828 (Pubitemid 47218856)
51. TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat. L Pourcel JM Routaboul L Kerhoas M Caboche L Lepiniec I Debeaujon, Plant Cell 2005 17 11 2966 2980 10.1105/tpc.105.035154 16243908
52. A Genetic Regulatory Network in the Development of Trichomes and Root Hairs. T Ishida T Kurata K Okada T Wada, Ann Rev Plant Biol 2008 59 1 365 386 10.1146/annurev.arplant.59.032607.092949 (Pubitemid 351813035)
53. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. SJ Clough AF Bent, Plant J 1998 16 6 735 743 10.1046/j.1365-313x.1998.00343.x 10069079 (Pubitemid 29083518)
54. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
55. Arabidopsis ovule is the target for Agrobacterium in planta vacuum infiltration transformation. G-N Ye D Stone S-Z Pang W Creely K Gonzalez M Hinchee, Plant J 1999 19 3 249 257 10.1046/j.1365-313X.1999.00520.x 10476072 (Pubitemid 29405178)
56. Efficient tests for normality, homoscedasticity and serial independence of regression residuals. CM Jarque AK Bera, Econom Letts 1980 6 3 255 259 10.1016/0165-1765(80)90024-5
57. Practical Nonparametric statistics. WC Conover, New York John Wiley & Sons 2 1980
58. The DMACA-HCl Protocol and the Threshold Proanthocyanidin Content for Bloat Safety in Forage Legumes. Y Li G Tanner P Larkin, J Sci Food Agri 1996 70 1 89 101 10.1002/(SICI)1097-0010(199601)70:1<89::AID-JSFA470>3.0.CO;2-N