Chromosome walking with YAC clones in Arabidopsis: isolation of 1700 kb of contiguous DNA on chromosome 5, including a 300 kb region containing the flowering-time gene CO
Tóm tắt
The co mutation of Arabidopsis thaliana causes a late-flowering phenotype that is insensitive to day-ength. The mutation was mapped previously to the upper arm of chromosome 5, approximately 1.6 cM from the chalcone synthase gene (CHS). We were provided with five yeast artificial chromosome (YAC) libraries and used these to perform a chromosome walk from CHS to the CO gene. In this paper we report the isolation of 1700 kb of contiguous Arabidopsis DNA, which represents approximately 1%–2% of the genome, inserted in YACs. This required the detailed analysis of 67 YACs, from which 87 end probes were isolated and examined in hybridisation experiments. This analysis showed that approximately 40% of the YACs presented problems in chromosome walking experiments because they contained repetitive sequence at one of their termini, were chimaeric or because part of the plant DNA was deleted. DNA fragments isolated from YACs were used as restriction fragment length polymorphism (RFLP) markers to localize CO to a 300 kb region within the cloned DNA. We compare the physical distance between CHS and CO with the genetic distance and find that in this region 1 cM is equivalent to approximately 200 kb.
Tài liệu tham khảo
Argumanathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1988) Current protocols in molecular biology, vol 2. John Wiley and Sons, pp 13.1.2
Bancroft I, Wolk CP (1988) Pulsed homogeneous orthoganal field gel electrophoresis (PHOGE) Nucleic Acids Res 16:7405–7418
Bender W, Spierer P, Hogness DS (1983) Chromosome walking and jumping to isolate DNA from the Ace and rosy loci and Bithorax complex in Drosophila melanogaster. J Mol Biol 168:17–33
Brown J, Sundaresan V (1991) A recombination hotspot in the maize A1 intragenic region. Theor Appl Genet 81:185–188
Burke DT, Carle GF, Olson MV (1987) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236:806–812
Chang C, Bowman JL, DeJohn AW, Lander ES, Meyerowitz EM (1988) Restriction fragment length polymorphism map for Arabidopsis thaliana. Proc Natl Acad Sci USA 85:6856–6860
Coulson A, Waterston R, Kiff J, Sulston J, Kohara Y (1988) Genome linking with yeast artificial chromosomes. Nature 335:184–186
Dooner H (1986) Genetic fine structure of the Bronze locus in maize. Genetics 113:1021–1036
Ecker JR (1990) PFGE and YAC analysis of the Arabidopsis genome. Methods 1:186–194
Ewens WJ, Bell CJ, Donnelly PJ, Dunn P, Matallana E, Ecker JR (1991) Genomic mapping with anchored clones: theoretical aspects. Genomics 11:799–805
Feinbaum RL, Ausubel FM (1988) Transcriptional regulation of the Arabidopsis thaliana chalcone synthase gene. Mol Cell Biol 8:1985–1992
Feinberg AP, Vogelstein B (1983) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132:6–13 Addendum (1984) 137:266–267
Feldmann KA, Marks MD, Christianson ML, Quatrano RS (1989) A dwarf mutant of Arabidopsis generated by T-DNA insertion mutagenesis. Science 243:1351–1354
Ganal MW, Young ND, Tanksley SD (1989) Pulsed field gel electrophoresis and physical mapping of large DNA fragments in the Tm-2a region of chromosome 9 in tomato. Mol Gen Genet 215:395–400
Gibson S, Somerville C (1992) Chromosome walking in Arabidopsis thaliana using yeast artificial chromosomes. In: Koncz C, Chua N-H, Schell J (eds) Methods in Arabidopsis research. World Scientific, Singapore, pp 119–143
Green ED, Riethman HC, Dutchik JE, Olson MV (1991) Detection and characterization of chimeric yeast artificial-chromosome clones. Genomics 11:658–669
Grill E, Somerville C (1991) Construction and characterization of a yeast artificial chromosome library of Arabidopsis which is suitable for chromosome walking. Mol Gen Genet 226:484–490
Guzman P, Ecker JR (1988) Development of large DNA methods for plants: Molecular cloning of large segments of Arabidopsis and carrot DNA into yeast. Nucleic Acids Res 16:11091–11105
Hauge BM, Goodman HM (1992) Genome mapping in Arabidopsis. In: Koncz C, Chua N-H, Schell J (eds) Methods in Arabidopsis research. World Scientific, Singapore, pp 191–224
Hauge BM, Hanley S, Giraudat J, Goodman H (1991) Mapping the Arabidopsis genome. In: Jenkins GI, Schuch W (eds) Molecular biology of plant development Company of Biologists, Cambridge, pp 45–56
Heard E, Davies B, Feo S, Fried M (1989) An improved method for the screening of YAC libraries. Nucleic Acids Res 17:5861
Hwang I, Takayuki K, Hauge BM, Goodman HM, Schmidt R, Cnops G, Dean C, Gibson S, Iba K, Lemieux B, Arondel V, Danhoff L, Somerville C (1991) Identification and map position of YAC clones comprising one-third of the Arabidopsis genome. Plant J 1:367–374
Koncz C, Mayerhofer R, Koncz-Kalman Zs, Nawrath C, Reiss B, Redei GP, Schell J (1990) Isolation of a gene encoding a novel chloroplast protein by T-DNA tagging in Arabidopsis thaliana. EMBO J 9:1337–1346
Koornneef M (1990) Linkage map of Arabidopsis thaliana (2n=10) In: O'Brien SJ (ed) Genetic maps, 5th edn, book VI. Cold Spring Harbor Laboratory Press, New York, pp 95–99
Koornneef M, Stam P (1992) Genetic analysis. In: Koncz C, Chua N-H, Schell J (eds) Methods in Arabidopsis research. World Scientific, Singapore, pp 83–99
Koornneef M, van Eden J, Hanhart CJ, Stam P, Braaksma FJ, Feenstra WJ (1983) Linkage map of Arabidopsis thaliana. J Hered 74:265–272
Koornneef M, Hanhart CJ, van der Veen JH (1991) A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 229:57–66
Laibach F (1951) Über sommer- und winterannuelle Rassen von Arabidopsis thaliana L Heynh. Ein Beitrag zur Aetiologie der Blütenbildung. Beitr Biol Pflanzen 28:173–210
Lazo GR, Stein PA, Ludwig RA (1991) A DNA transformationcompetent Arabidopsis genomic library in Agrobacterium. Bio/Technology 9:963–967
Leutwiler LS, Hough-Evans BR, Meyerowitz EM (1984) The DNA of Arabidopsis thaliana. Mol Gen Genet 194:15–23
Little RD, Pilia G, Johnson S, D'Urso M, Schlessinger D (1992) Yeast artificial chromosomes spanning 8 megabases and 10–15 centimorgans of human cytogenetic band Xg26. Proc Natl Acad Sci USA 89:177–181
Ma H, Yanofsky MF, Meyerowitz EM (1991) AGL1–AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes Dev 5:484–495
Ma H, Yanofsky MF, Klee HJ, Bowman JL, Meyerowitz EM (1992) Vectors for plant transformation and cosmid libraries. Gene 117:161–167
Martinez-Zapater JM, Somerville CR (1990) Effect of light quality and vernalization on late-flowering mutants of Arabidopsis thaliana. Plant Physiol 92:770–776
Meyerowitz EM (1989) Arabidopsis, a useful weed. Cell 56:263–269
Nam HG, Giraudat J, den Boer B, Moonan F, Loos W, Hauge B, Goodman HM (1989) Restriction fragment length polymorphism linkage map of Arabidopsis thaliana. Plant Cell 1:699–705
Ochmann H, Gerber AS, Hard DL (1988) Genetic application of an inverse polymerase chain reaction. Genetics 120:621
Oliver SG, van der Aart QJM, Agastoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, Antoine G, Anwar R et al. (1992) The complete DNA sequence of yeast chromosome III. Nature 357:38–46
Olszewski N, Ausubel FM (1988) Specialized binary vector for plant transformation: expression of Arabidopsis thaliana AHAS gene in Nicotiana tabacum. Nucleic Acids Res 16:10765–10782
Papp A, Rougvie AE, Ambros V (1991) Molecular cloning of lin-29, a heterochronic gene required for the differentiation of hypodermal cells and the cessation of molting in C. elegans. Nucleic Acids Res 19:623–630
Patton DA, Franzmann LH, Meinke DW (1991) Mapping genes essential for embryo development in Arabidopsis thaliana. Mol Gen Genet 227:337–347
Rédei GP (1962) Supervital mutants of Arabidopsis. Genetics 47:443–460
Rédei GP, Acedo G, Gavazzi G (1974) Flower differentiation in Arabidopsis. Stadler Symp 6:135–168
Reiter RS, Williams JGK, Feldmann KA, Rafalski JA, Tingey SV, Scolnik PA (1992) Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc Natl Acad Sci USA 89:1477–1481
Relichová J (1976) Some new mutants. Arabidopsis Inf Serv 13:25–28
Schlessinger D (1990) Yeast artificial chromosomes: Tools for mapping and analysis of complex genomes. Trends Genet 6:248–259
Schmidt R, Dean C (1992) Physical mapping of the Arabidopsis thaliana genome. Genome analysis, vol 4. Strategies for physical mapping. Cold Spring Harbor Laboratory Press, New York, pp 71–98
Schmidt R, Cnops G, Bancroft I, Dean C (1992) Construction of an overlapping YAC library of the Arabidopsis thaliana genome. Aust J Plant Physiol 19:341–351
Segal G, Sarfatti M, Schaffer MA, Ori N, Zamir D, Fluhr R (1992) Correlation of genetic and physical structure in the region surrounding the I2 Fusarium oxysporum resistance locus in tomato. Mol Gen Genet 231:179–185
Somerville CR (1989) Arabidopsis blooms. Plant Cell 1:1131–1135
Sun T, Goodman HM, Ausubel FM (1992) Cloning the Arabidopsis GA1 locus by genomic subtraction. Plant Cell 4:119–128
Tai T, Tanksley S (1991) A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue. Plant Mol Biol Rep 8:297–303
Valvekens D, Van Montagu M, Van Lijsebettens M (1988) Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc Natl Acad Sci USA 85:5536–5540
Ward ER, Jen JC (1990) Isolation of single-copy-sequence clones from a yeast artificial chromosome library of randomly sheared Arabidopsis thaliana DNA. Plant Mol Biol 14:561–568
Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz E (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell 69:843–859
Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, Meyerowitz EM (1990) The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346:35–39