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Arabidopsis thaliana Full Genome Longmer Microarrays: A Powerful Gene Discovery Tool for Agriculture and Forestry

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Abstract

Sequenced plant genomes provide a large reservoir of known genes with potential for use in crop and tree improvement, but assignment of specific functions to annotated genes in sequenced plant genomes remains a challenge. Furthermore, most plant genes belong to families encoding proteins with related but distinct functions. In this commentary, we discuss our development of Arabidopsis spotted whole genome longmer oligonucleotide microarrays, and their use in global transcription profiling. We show that longmer array based transcriptome analysis in Arabidopsis can be used as an efficient and effective gene discovery and functional genomics tool, particularly for functional analyses of members of large gene families. We discuss experiments that focus on gene families involved in phenylpropanoid natural product biosynthesis and fiber differentiation. These analyses have helped to elucidate functions of individual gene family members, and have identified new candidate genes involved in fiber development and differentiation. Results obtained by these studies in Arabidopsis can be used as the basis for gene discovery in commercially important plants, and we have focused our attention on Populus trichocarpa (poplar), a species important in forestry and agroforestry for which complete genome sequence information is available.

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References

  • SF Altschul W Gish W Miller EW Myers DJ Lipman (1990) ArticleTitleBasic local alignment search tool J Mol Biol 215 403–410 Occurrence Handle10.1006/jmbi.1990.9999 Occurrence Handle2231712

    Article  PubMed  Google Scholar 

  • W Boerjan J Ralph M Baucher (2003) ArticleTitleLignin biosynthesis Ann Rev Plant Biol 54 519–546 Occurrence Handle10.1146/annurev.arplant.54.031902.134938

    Article  Google Scholar 

  • N Chaffey E Cholewa S Regan B Sundberg (2002) ArticleTitleSecondary xylem development in Arabidopsis: a model for wood formation Physiol Plant 114 594–600 Occurrence Handle11975734

    PubMed  Google Scholar 

  • MA Costa RE Collins AM Anterola FC Cochrane LB Davin NG Lewis (2003) ArticleTitleAn in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof Phytochem 64 1097–1112 Occurrence Handle10.1016/S0031-9422(03)00517-X

    Article  Google Scholar 

  • D Cukovic J Ehlting JA VanZiffle CJ Douglas (2001) ArticleTitleStructure and evolution of 4-coumarate: coenzyme A ligase (4CL) gene families Biol Chem 382 645–654 Occurrence Handle10.1515/BC.2001.076 Occurrence Handle11405227

    Article  PubMed  Google Scholar 

  • RA Dixon L Achnine P Kota C-J Liu MSS Reddy L Wang (2002) ArticleTitleThe phenylpropanoid pathway and plant defence-a genomics perspective Mol Plant Pathol 3 371–390 Occurrence Handle10.1046/j.1364-3703.2002.00131.x

    Article  Google Scholar 

  • J Ehlting D Büttner Q Wang CJ Douglas IE Somssich E Kombrink (1999) ArticleTitleThree 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms Plant J 19 9–20 Occurrence Handle10.1046/j.1365-313X.1999.00491.x Occurrence Handle10417722

    Article  PubMed  Google Scholar 

  • 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) ArticleTitleGlobal 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 Occurrence Handle10.1111/j.1365-313X.2005.02403.x Occurrence Handle15918878

    Article  PubMed  Google Scholar 

  • T Girke J Todd S Ruuska J White C Benning J Ohlrogge (2000) ArticleTitleMicroarray analysis of developing Arabidopsis seeds Plant Physiol 124 1570–1581 Occurrence Handle10.1104/pp.124.4.1570 Occurrence Handle11115875

    Article  PubMed  Google Scholar 

  • T Goujon R Sibout A Eudes J MacKay L Jouanin (2003) ArticleTitleGenes involvedikntthe biosynthesis of lignin precursors in Arabidopsis thaliana Plant Physiol Biochem 41 677–687 Occurrence Handle10.1016/S0981-9428(03)00095-0

    Article  Google Scholar 

  • AT Groover (2005) ArticleTitleWhat makes a tree a tree? Trends Plant Biol 10 210–214 Occurrence Handle10.1016/j.tplants.2005.03.001

    Article  Google Scholar 

  • K Hahlbrock D Scheel (1989) ArticleTitlePhysiology and molecular biology of phenylpropanoid metabolism Ann Rev Plant Physiol Plant Mol Biol 40 347–469 Occurrence Handle10.1146/annurev.pp.40.060189.002023

    Article  Google Scholar 

  • P Hegde R Qi K Abernathy C Gay S Dharap R Gaspard JE Hughes E Snesrud N Lee J Quackenbush (2000) ArticleTitleA concise guide to cDNA microarray analysis BioTechniques 29 548–562 Occurrence Handle10997270

    PubMed  Google Scholar 

  • JM Humphreys C Chapple (2002) ArticleTitleRewriting the lignin roadmap Curr Opin Plant Biol 5 224–229 Occurrence Handle10.1016/S1369-5266(02)00257-1 Occurrence Handle11960740

    Article  PubMed  Google Scholar 

  • MD Kane TA Jatkoe CR Stumpf J Lu JD Thomas SJ Madore (2000) ArticleTitleAssessment of the sensitivity and specificity of oligonucleotide 50mer microarrays Nucl Acids Res 28 4552–4557 Occurrence Handle10.1093/nar/28.22.4552 Occurrence Handle11071945

    Article  PubMed  Google Scholar 

  • S-J Kim M-R Kim DL Bedger SGA Moinuddin CL Cardenas LB Davin CH Kang NG Lewis (2003) ArticleTitleFunctional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis Proc Nat Acad Sci USA 101 1455–1460 Occurrence Handle10.1073/pnas.0307987100

    Article  Google Scholar 

  • RJ Lipshutz SPA Fodor TR Gingeras DJ Lockhart (1999) ArticleTitleHigh density synthetic oligonucleotide arrays Nature Genet 21 Supplement 20–24 Occurrence Handle10.1038/4447

    Article  Google Scholar 

  • CHA Little JE MacDonald O Olsson (2002) ArticleTitleInvolvement 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 Occurrence Handle10.1086/339642

    Article  Google Scholar 

  • DJ Lockhart HL Dong MC Byrne MT Follettie MV Gallo MS Chee M Mittmann CW Wang M Kobayashi H Horton EL Brown (1996) ArticleTitleExpression monitoring by hybridization to high-density oligonucleotide arrays Nature Biotech 14 1675–1680 Occurrence Handle10.1038/nbt1296-1675

    Article  Google Scholar 

  • B McGonigle SJ Keeler S-MC Lau MK Koeppe DP O′Keefe (2000) ArticleTitleA genomics approach to the comprehensive analysis of the glutathione S-transferase gene family in soybean and maize Plant Physiol 124 1105–1120 Occurrence Handle10.1104/pp.124.3.1105 Occurrence Handle11080288

    Article  PubMed  Google Scholar 

  • BC Meyers DW Galbraith T Nelson V Agrawal (2004) ArticleTitleMethods for transcriptional profiling in plants. Be fruitful and replicate Plant Physiol 135 637–652 Occurrence Handle10.1104/pp.104.040840 Occurrence Handle15173570

    Article  PubMed  Google Scholar 

  • M Mizutani D Ohta (1998) ArticleTitleTwo isoforms of NADPH: cytochrome P450 reductase in Arabidopsis thaliana. Gene structure, heterologous expression in insect cells, and differential regulation Plant Physiol 116 357–367 Occurrence Handle10.1104/pp.116.1.357 Occurrence Handle9449848

    Article  PubMed  Google Scholar 

  • LJ Newman DE Perazza L Juda MM Campbell (2004) ArticleTitleInvolvement of the R2R3-MYB, AtMYB61, in the ectopic lignification and dark-photomorphogenic components of the det3 mutant phenotype Plant J 37 239–250 Occurrence Handle14690508

    PubMed  Google Scholar 

  • KM Nieminen L Kauppinen Y Helariutta (2004) ArticleTitleA weed for wood? Arabidopsis as a genetic model for xylem development Plant Physiol 135 653–659 Occurrence Handle10.1104/pp.104.040212 Occurrence Handle15208411

    Article  PubMed  Google Scholar 

  • S Oh S Park K-H Han (2003) ArticleTitleTranscriptional regulation of secondary growth in Arabidopsis thaliana J Exp Bot 54 2709–2722 Occurrence Handle10.1093/jxb/erg304 Occurrence Handle14585825

    Article  PubMed  Google Scholar 

  • A Patzlaff S McInnis A Courtenay C Surman LJ Newman C Smith MW Bevan S Mansfield RW Whetten RR Sederoff MM Campbell (2003) ArticleTitleCharacterisation of a pine MYB that regulates lignification Plant J 36 743–754 Occurrence Handle10.1046/j.1365-313X.2003.01916.x Occurrence Handle14675440

    Article  PubMed  Google Scholar 

  • J Raes A Rohde JH Christensen Y Peer Particlevan de W Boerjan (2003) ArticleTitleGenome-wide characterization of the lignification toolbox in Arabidopsis Plant Physiol 133 1051–1071 Occurrence Handle10.1104/pp.103.026484 Occurrence Handle14612585

    Article  PubMed  Google Scholar 

  • J Schrader K Baba ST May K Palme M Bennett RP Bhalerao G Sandberg (2003) ArticleTitlePolar 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 Occurrence Handle10.1073/pnas.1633693100 Occurrence Handle12909722

    Article  PubMed  Google Scholar 

  • J Schrader J Nilsson E Mellerowicz A Berglund P Nilsson M Hertzberg G Sandberg (2004) ArticleTitleA high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity Plant Cell 16 2278–2292 Occurrence Handle10.1105/tpc.104.024190 Occurrence Handle15316113

    Article  PubMed  Google Scholar 

  • JA Shockey MS Fulda J Browse (2003) ArticleTitleArabidopsis 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 Occurrence Handle10.1104/pp.103.020552 Occurrence Handle12805634

    Article  PubMed  Google Scholar 

  • InstitutionalAuthorNameThe Arabidopsis Genome Initiative (2000) ArticleTitleAnalysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796–815

    Google Scholar 

  • HY Wang RL Malek AE Kwitek AS Green TV Luu B Bahbahani B Frank J Quackenbush NH Lee (2003) ArticleTitleAssessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays Genome Biol 4 R5 Occurrence Handle10.1186/gb-2003-4-1-r5 Occurrence Handle12540297

    Article  PubMed  Google Scholar 

  • JZ Zhang RA Creelman J-K Zhu (2004) ArticleTitleFrom laboratory to field. Using information from Arabidopsis to engineer salt, cold, and drought tolerance in crops Plant Physiol 135 615–621 Occurrence Handle10.1104/pp.104.040295 Occurrence Handle15173567

    Article  PubMed  Google Scholar 

  • W Xu S Bak A Decker S Paquette R Feyereisen D Galbraith (2001) ArticleTitleMicroarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana Gene 272 61–74 Occurrence Handle10.1016/S0378-1119(01)00516-9 Occurrence Handle11470511

    Article  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Botany, University of British Columbia, BC V6T 1Z4, Vancouver, Canada

    Carl J. Douglas

  2. Institute for Plant Molecular Biology, Centre National de la Recherche Scientifique, 67000, Strasbourg, France

    Jürgen Ehlting

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  1. Carl J. Douglas
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  2. Jürgen Ehlting
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Correspondence to Carl J. Douglas.

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Douglas, C.J., Ehlting, J. Arabidopsis thaliana Full Genome Longmer Microarrays: A Powerful Gene Discovery Tool for Agriculture and Forestry. Transgenic Res 14, 551–561 (2005). https://doi.org/10.1007/s11248-005-8926-x

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  • DOI: https://doi.org/10.1007/s11248-005-8926-x

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