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Genetics. Nov 2001; 159(3): 1231–1242.
PMCID: PMC1461882

An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence.


The genome of the model plant species Arabidopsis thaliana has recently been sequenced. To accelerate its current genome research, we developed a whole-genome, BAC/BIBAC-based, integrated physical, genetic, and sequence map of the A. thaliana ecotype Columbia. This new map was constructed from the clones of a new plant-transformation-competent BIBAC library and is integrated with the existing sequence map. The clones were restriction fingerprinted by DNA sequencing gel-based electrophoresis, assembled into contigs, and anchored to an existing genetic map. The map consists of 194 BAC/BIBAC contigs, spanning 126 Mb of the 130-Mb Arabidopsis genome. A total of 120 contigs, spanning 114 Mb, were anchored to the chromosomes of Arabidopsis. Accuracy of the integrated map was verified using the existing physical and sequence maps and numerous DNA markers. Integration of the new map with the sequence map has enabled gap closure of the sequence map and will facilitate functional analysis of the genome sequence. The method used here has been demonstrated to be sufficient for whole-genome physical mapping from large-insert random bacterial clones and thus is applicable to rapid development of whole-genome physical maps for other species.

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Selected References

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  • Skeen LC, Due BR, Douglas FE. Neonatal sensory deprivation reduces tufted cell number in mouse olfactory bulbs. Neurosci Lett. 1986 Jan 2;63(1):5–10. [PubMed]
  • Liu YG, Mitsukawa N, Lister C, Dean C, Whittier RF. Isolation and mapping of a new set of 129 RFLP markers in Arabidopsis thaliana using recombinant inbred lines. Plant J. 1996 Oct;10(4):733–736. [PubMed]
  • Liu YG, Shirano Y, Fukaki H, Yanai Y, Tasaka M, Tabata S, Shibata D. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc Natl Acad Sci U S A. 1999 May 25;96(11):6535–6540. [PMC free article] [PubMed]
  • Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gund C, et al. zA map for sequence analysis of the Arabidopsis thaliana genome. Nat Genet. 1999 Jul;22(3):265–270. [PubMed]
  • Martienssen RA. Functional genomics: probing plant gene function and expression with transposons. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2021–2026. [PMC free article] [PubMed]
  • Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M. Arabidopsis thaliana: a model plant for genome analysis. Science. 1998 Oct 23;282(5389):662–682. [PubMed]
  • Mozo T, Fischer S, Shizuya H, Altmann T. Construction and characterization of the IGF Arabidopsis BAC library. Mol Gen Genet. 1998 Jun;258(5):562–570. [PubMed]
  • Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, et al. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet. 1999 Jul;22(3):271–275. [PubMed]
  • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796–815. [PubMed]
  • Azpiroz-Leehan R, Feldmann KA. T-DNA insertion mutagenesis in Arabidopsis: going back and forth. Trends Genet. 1997 Apr;13(4):152–156. [PubMed]
  • Ruan Y, Gilmore J, Conner T. Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 1998 Sep;15(6):821–833. [PubMed]
  • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467–470. [PubMed]
  • Bent AF, Kunkel BN, Dahlbeck D, Brown KL, Schmidt R, Giraudat J, Leung J, Staskawicz BJ. RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Science. 1994 Sep 23;265(5180):1856–1860. [PubMed]
  • Schmidt R, West J, Love K, Lenehan Z, Lister C, Thompson H, Bouchez D, Dean C. Physical map and organization of Arabidopsis thaliana chromosome 4. Science. 1995 Oct 20;270(5235):480–483. [PubMed]
  • Camilleri C, Lafleuriel J, Macadré C, Varoquaux F, Parmentier Y, Picard G, Caboche M, Bouchez D. A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J. 1998 Jun;14(5):633–642. [PubMed]
  • Soderlund C, Longden I, Mott R. FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci. 1997 Oct;13(5):523–535. [PubMed]
  • Somerville C, Dangl Genomics. Plant biology in 2010. Science. 2000 Dec 15;290(5499):2077–2078. [PubMed]
  • Stupar RM, Lilly JW, Town CD, Cheng Z, Kaul S, Buell CR, Jiang J. Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5099–5103. [PMC free article] [PubMed]
  • Desprez T, Amselem J, Caboche M, Höfte H. Differential gene expression in Arabidopsis monitored using cDNA arrays. Plant J. 1998 Jun;14(5):643–652. [PubMed]
  • Sulston J, Mallett F, Staden R, Durbin R, Horsnell T, Coulson A. Software for genome mapping by fingerprinting techniques. Comput Appl Biosci. 1988 Mar;4(1):125–132. [PubMed]
  • Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiol. 2000 Dec;124(4):1465–1467. [PMC free article] [PubMed]
  • Tao Q, Zhang HB. Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res. 1998 Nov 1;26(21):4901–4909. [PMC free article] [PubMed]
  • Hwang I, Kohchi T, Hauge BM, Goodman HM, Schmidt R, Cnops G, Dean C, Gibson S, Iba K, Lemieux B, et al. Identification and map position of YAC clones comprising one-third of the Arabidopsis genome. Plant J. 1991 Nov;1(3):367–374. [PubMed]
  • Jones JD, Shlumukov L, Carland F, English J, Scofield SR, Bishop GJ, Harrison K. Effective vectors for transformation, expression of heterologous genes, and assaying transposon excision in transgenic plants. Transgenic Res. 1992 Nov;1(6):285–297. [PubMed]
  • Wu Y, Tulsieram L, Tao Q, Zhang HB, Rothstein SJ. A binary vector-based large insert library for Brassica napus and identification of clones linked to a fertility restorer locus for Ogura cytoplasmic male sterility (CMS). Genome. 2000 Feb;43(1):102–109. [PubMed]
  • Klein M, Eckert-Ossenkopp U, Schmiedeberg I, Brandt P, Unseld M, Brennicke A, Schuster W. Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones. Plant J. 1994 Sep;6(3):447–455. [PubMed]
  • Zachgo EA, Wang ML, Dewdney J, Bouchez D, Camilleri C, Belmonte S, Huang L, Dolan M, Goodman HM. A physical map of chromosome 2 of Arabidopsis thaliana. Genome Res. 1996 Jan;6(1):19–25. [PubMed]
  • Koncz C, Martini N, Mayerhofer R, Koncz-Kalman Z, Körber H, Redei GP, Schell J. High-frequency T-DNA-mediated gene tagging in plants. Proc Natl Acad Sci U S A. 1989 Nov;86(21):8467–8471. [PMC free article] [PubMed]
  • Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature. 1999 Dec 16;402(6763):761–768. [PubMed]

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