Arabidopsis thaliana full genome longmer microarrays: A powerful gene discovery tool for agriculture and forestry

Transgenic Research

Volumn 14, Issue 5, 2005, Pages 551-561

  Douglas, Carl J ^a   Ehlting, Jürgen ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b CNRS   (France)

Author keywords

Arabidopsis; Expression profiling; Fiber development; Phenylpropanoid metabolism; Populus; Shikimate pathway; Transcription factor

Indexed keywords

AGRICULTURE; ARABIDOPSIS; ASPEN; DNA MICROARRAY; FORESTRY; GENE EXPRESSION PROFILING; GENETIC PROCEDURES; GENETICS; GENOME; PLANT; REVIEW; TREE;

AGRICULTURE; ARABIDOPSIS; FORESTRY; GENE EXPRESSION PROFILING; GENETIC TECHNIQUES; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANTS, EDIBLE; POPULUS; TREES;

ARABIDOPSIS; ARABIDOPSIS THALIANA; POPULUS; POPULUS BALSAMIFERA SUBSP. TRICHOCARPA;

EID: 27144552583     PISSN: 09628819     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11248-005-8926-x     Document Type: Review

References (34)

1. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410
2. W Boerjan J Ralph M Baucher 2003 Lignin biosynthesis Ann Rev Plant Biol 54 519 546
3. N Chaffey E Cholewa S Regan B Sundberg 2002 Secondary xylem development in Arabidopsis: a model for wood formation Physiol Plant 114 594 600
4. MA Costa RE Collins AM Anterola FC Cochrane LB Davin NG Lewis 2003 An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof Phytochem 64 1097 1112
5. D Cukovic J Ehlting JA VanZiffle CJ Douglas 2001 Structure and evolution of 4-coumarate: coenzyme A ligase (4CL) gene families Biol Chem 382 645 654
6. RA Dixon L Achnine P Kota C-J Liu MSS Reddy L Wang 2002 The phenylpropanoid pathway and plant defence-a genomics perspective Mol Plant Pathol 3 371 390
7. J Ehlting D Büttner Q Wang CJ Douglas IE Somssich E Kombrink 1999 Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms Plant J 19 9 20
8. J Ehlting N Mattheus DS Aeschliman E Li B Hamberger IF Cullis J Zhuang M Kaneda SD Mansfield L Samuels K Ritland BE Ellis J Bohlmann CJ Douglas 2005 Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation Plant J 42 618 640
9. T Girke J Todd S Ruuska J White C Benning J Ohlrogge 2000 Microarray analysis of developing Arabidopsis seeds Plant Physiol 124 1570 1581
10. T Goujon R Sibout A Eudes J MacKay L Jouanin 2003 Genes involvedikntthe biosynthesis of lignin precursors in Arabidopsis thaliana Plant Physiol Biochem 41 677 687
11. AT Groover 2005 What makes a tree a tree? Trends Plant Biol 10 210 214
12. K Hahlbrock D Scheel 1989 Physiology and molecular biology of phenylpropanoid metabolism Ann Rev Plant Physiol Plant Mol Biol 40 347 469
13. P Hegde R Qi K Abernathy C Gay S Dharap R Gaspard JE Hughes E Snesrud N Lee J Quackenbush 2000 A concise guide to cDNA microarray analysis BioTechniques 29 548 562
14. JM Humphreys C Chapple 2002 Rewriting the lignin roadmap Curr Opin Plant Biol 5 224 229
15. MD Kane TA Jatkoe CR Stumpf J Lu JD Thomas SJ Madore 2000 Assessment of the sensitivity and specificity of oligonucleotide 50mer microarrays Nucl Acids Res 28 4552 4557
16. S-J Kim M-R Kim DL Bedger SGA Moinuddin CL Cardenas LB Davin CH Kang NG Lewis 2003 Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis Proc Nat Acad Sci USA 101 1455 1460
17. RJ Lipshutz SPA Fodor TR Gingeras DJ Lockhart 1999 High density synthetic oligonucleotide arrays Nature Genet 21 Supplement 20 24
18. CHA Little JE MacDonald O Olsson 2002 Involvement of indole-3-acetic acid in fascicular and interfascicular cambial growth and interfascicular extraxylary fiber differentiation in Arabidopsis thaliana inflorescence stems Int J Plant Sci 163 519 529
19. DJ Lockhart HL Dong MC Byrne MT Follettie MV Gallo MS Chee M Mittmann CW Wang M Kobayashi H Horton EL Brown 1996 Expression monitoring by hybridization to high-density oligonucleotide arrays Nature Biotech 14 1675 1680
20. B McGonigle SJ Keeler S-MC Lau MK Koeppe DP O'Keefe 2000 A genomics approach to the comprehensive analysis of the glutathione S-transferase gene family in soybean and maize Plant Physiol 124 1105 1120
21. BC Meyers DW Galbraith T Nelson V Agrawal 2004 Methods for transcriptional profiling in plants. Be fruitful and replicate Plant Physiol 135 637 652
22. M Mizutani D Ohta 1998 Two isoforms of NADPH: cytochrome P450 reductase in Arabidopsis thaliana. Gene structure, heterologous expression in insect cells, and differential regulation Plant Physiol 116 357 367
23. LJ Newman DE Perazza L Juda MM Campbell 2004 Involvement of the R2R3-MYB, AtMYB61, in the ectopic lignification and dark-photomorphogenic components of the det3 mutant phenotype Plant J 37 239 250
24. KM Nieminen L Kauppinen Y Helariutta 2004 A weed for wood? Arabidopsis as a genetic model for xylem development Plant Physiol 135 653 659
25. S Oh S Park K-H Han 2003 Transcriptional regulation of secondary growth in Arabidopsis thaliana J Exp Bot 54 2709 2722
26. A Patzlaff S McInnis A Courtenay C Surman LJ Newman C Smith MW Bevan S Mansfield RW Whetten RR Sederoff MM Campbell 2003 Characterisation of a pine MYB that regulates lignification Plant J 36 743 754
27. J Raes A Rohde JH Christensen Y van de Peer W Boerjan 2003 Genome-wide characterization of the lignification toolbox in Arabidopsis Plant Physiol 133 1051 1071
28. J Schrader K Baba ST May K Palme M Bennett RP Bhalerao G Sandberg 2003 Polar auxin transport in the wood-forming tissues of hybrid aspen is under simultaneous control of developmental and environmental signals Proc Nat Acad Sci USA 100 10096 10101
29. J Schrader J Nilsson E Mellerowicz A Berglund P Nilsson M Hertzberg G Sandberg 2004 A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity Plant Cell 16 2278 2292
30. JA Shockey MS Fulda J Browse 2003 Arabidopsis contains a large superfamily of acyl-activating enxymes. Phylogenetic and biochemical analysis reveals a new class of acyl-coezyme A synthases Plant Physiol 132 1065 1076
31. The Arabidopsis Genome Initiative 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796 815
32. HY Wang RL Malek AE Kwitek AS Green TV Luu B Bahbahani B Frank J Quackenbush NH Lee 2003 Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays Genome Biol 4 R5
33. JZ Zhang RA Creelman J-K Zhu 2004 From laboratory to field. Using information from Arabidopsis to engineer salt, cold, and drought tolerance in crops Plant Physiol 135 615 621
34. W Xu S Bak A Decker S Paquette R Feyereisen D Galbraith 2001 Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana Gene 272 61 74