Abstract
A BAC library to serve as a general tool for the physical mapping and positional cloning of rose genes has been constructed from Rosa rugosa DNA. With 27,264 clones the library contains 5.2 genome equivalents. The library was used to assemble a contig of BAC clones spanning Rdr1, a locus that confers resistance to blackspot. For this purpose fine-scale mapping of the target locus was achieved by bulked segregant analysis using 816 AFLP primer combinations. The target region around Rdr1 comprises about 400 kb and is covered by a minimum of six BAC clones. Furthermore, the detection of at least five resistance gene analogs of the TIR-NBS-LRR family on the contig indicates the presence of a cluster of resistance genes around Rdr1. These results will not only allow the isolation and identification of Rdr1 in the near future, but also provide the tools for the physical mapping and positional cloning of other horticulturally interesting genes in roses.
Similar content being viewed by others
References
Allouis S, Qi X, Lindup S, Gale MD, Devos KM (2001) Construction of a BAC library of pearl millet, Pennisetum glaucum. Theor Appl Genet 102:1200–1205
Ballvora A, Ercolano MR, Weiss J, Meksem K, Bormann CA, Oberhagemann P, Salamini F, Gebhardt C (2002) The R1 gene for potato resistance to late blight ( Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes. Plant J 30:361–372
Budiman MA, Mao L, Wood TC, Wing RA (2000) A deep-coverage tomato library and prospects toward development of an STC framework for genome sequencing. Genome Res 10:129–136
Cai L, Taylor JF, Wing RA, Gallagher DS, Woo SS, Davis SK (1995) Construction and characterization of a bovine artificial chromosome library. Genomics 29:413–425
Channelière S, Rivière S, Scalliet G, Jullien F, Szecsi J, Dolle C, Vergne P, Dumas C, Bendamahne M, Hugueney P, Cock M (2002) Analysis of gene expression in rose petals using expressed sequence tags. FEBS Lett 515:35–38
Choi S, Wing RA (1999) The construction of bacterial artificial chromosome (BAC) libraries. In: Gelvin S, Schilperoort R (eds) Plant molecular biology manual (2nd edn) Suppl IV. Kluwer Academic Publishers, Dordrecht, pp 1–32
Choi S, Creelman R, Mullet JE, Wing RA (1995) Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol Biol Rep 13:124–128
Clarke L, Carbon J (1976) A colony bank containing synthetic Col EI hybrid plasmids representative of the entire E. coli genome. Cell 9:91–99
Danesh D, Penuela S, Mudge J, Denny R, Nordstrom H, Martinez J, Young N (1998) A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene. Theor Appl Genet 96:196–202
Debener T (1999) Genetic analyses of important morphological and physiological characters in diploid roses. Gartenbauwissenschaft 64:14–20
Debener T, Mattiesch L (1999) Construction of a genetic linkage map for roses using RAPD and AFLP markers. Theor Appl Genet 99:891–899
Debener T, Drevez-Alvarez R, Rockstroh K (1998) Identification of five physiological races of blackspot, Diplocarpon rosae Wolf, on roses. Plant Breed 117:267–270
Dickson EE, Arumuganathan K, Kresovich S, Doyle JJ (1992) Nuclear DNA content variation within the Rosaceae. Am J Bot 79:1081–1086
Dirlewanger E, Pronier V, Parvery C, Rothan C, Guye A, Monet R (1998) Genetic linkage map of peach ( Prunus persica (L.) Batsch) using morphological and molecular markers. Theor Appl Genet 97:888–895
Dohm A, Ludwig C, Schilling D, Debener T (2001) Transformation of roses with genes for antifungal proteins. Acta Hort 547:27–34
Gindullis F, Dechyeva D, Schmidt T (2001) Construction and characterization of a BAC library for the molecular dissection of a single wild beet centromere and sugar beet ( Beta vulgaris) genome analysis. Genome 44:846–855
Gudin S (2000) Rose: genetics and breeding. Plant Breed Rev 17:159–189
Joobear T, Viruel M, de Vicente MC, Jauregni B, Ballester J, Dettori MT, Verde I, Messegner R, Truco MJ, Battle I, Suanzes M, Quarta R, Dirlewanger E, Aarus P (1998) Construction of a saturated linkage map with an almond x peach F2 progeny. Theor Appl Genet 97:1034–1041
Kim U-J, Birren BW, Slepak T, Mancino V, Boysen D, Kang H-L, Simon MI, Shizuya H (1996) Construction and characterization of a human bacterial artificial chromosome library. Genomics 34:213–218
Kitara K, Matsumoto S (2000) Rose MADS-box genes 'Masako C1 and D1' homologous to class C floral identity genes. Plant Sci 151:121–134
Lu ZX, Sosonski B, Reighard GL, Baird WV, Abbott AG (1998) Construction of a genetic linkage map and identification of AFLP markers for resistance to root-knot nematodes in peach rootstocks. Genome 41:199–207
Luo M, Wang Y-H, Frisch D, Joobeur T, Wing RA, Dean RA (2001) Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt ( Fom-2). Genome 44:154–162
Malek B, Debener T (1998) Genetic analysis of resistance to blackspot (Diplocarpon rosae) in tetraploid roses. Theor Appl Genet 96:228–231
Malek B, Weber WE, Debener T (2000) Identification of molecular markers linked to Rdr1, a gene conferring resistance to blackspot in roses. Theor Appl Genet 101:977–983
Maliepaard C, et al. (1998) Integrating male and female linkage maps of apple ( Malus domestica Borkh) using multi-allelic markers. Theor Appl Genet 97:60–73
Marchant R, Davey MR, Lucas JA, Lamb CJ, Dixon RA, Power JB (1998) Expression of a chitinase transgene in rose ( Rosa hybrida L.) reduces development of blackspot disease ( Diplocarpon rosae Wolf.) Mol Breed 4:187–194
Marek LF, Shoemaker RC (1997) BAC contig development by fingerprint analysis in soybean. Genome 40:420–427
Matallana E, Bell CJ, Dunn PJ, Lu M, Ecker JR (1992) Genetic and physical linkage of the Arabidopsis genome: methods for anchoring Yeast Artificial Chromosomes. In: Koncz C, Chua N-H, Schell J (eds) Methods in Arabidopsis research. World Scientific, Singapore, pp 145–169
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832
Mozo T, Fischer S, Shizuya H, Altmann T (1998) Construction and characterization of the IGF Arabidopsis BAC library. Mol Gen Genet 258:562–570
Nakamura S, Asakawa S, Ohmido N, Fukui K, Shimizu N, Kawasaki S (1997) Construction of an 800-kb contig in the near centromeric region of the rice blast resistance gene Pi-ta 2 using a highly representative rice BAC library. Mol Gen Genet 254:611–620
O'Sullivan DM, Ripoll PJ, Rodgers M, Edwards KJ (2001) A maize bacterial artificial chromosome (BAC) library from the European flint inbred line F2. Theor Appl Genet 103:425–432
Pan Q, Liu Y-S, Budai-Hadrian O, Sela M, Carmel-Goren L, Zamir D, Fluhr R (2000) Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologs in the genome of two dicotyledons: tomato and Arabidopsis. Genetics 155:309–322
Patocchi A, Vinatzer BA, Gianfrancesci L, Tartarini S, Zhang H-B, Sansavini S, Gessler C (1999) Construction of a 550-kb BAC contig spanning the genomic region containing the apple scab resistance gene Vf. Mol Gen Genet 262:884–891
Rajapakse S, Byrne DH, Zhang L, Anderson N, Arumuganathan K, Ballard RE (2001) Two genetic linkage maps of tetraploid roses. Theor Appl Genet 103:575–583
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual (2nd edn). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
Slabaugh MB, Huestis GM, Leonard J, Holloway JL, Rosato C, Hongtrakul V, Martini N, Toepfer R, Voetz M, Schell J, Knapp SJ (1997) Sequence-based genetic markers for genes and gene families: single-strand conformational polymorphisms for the fatty acid synthesis genes of Cuphea. Theor Appl Genet 94:400–408
Song W-Y, Wang G-L, Chen L-L, Kim H-S, Pi L-Y, Holsten T, Gardner J, Wang B, Zhai W-X, Zhu L-H, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806
Strong SJ, Ohta Y, Litman GW, Amemiya CT (1997) Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res 25:3959–3961
Vinatzer BA, Zhang H-B, Sansavini S (1998) Construction and characterization of a bacterial artificial chromosome library of apple. Theor Appl Genet 97:1183–1190
Wang G-L, Holsten TE, Song W-Y, Wang H-P, Ronald P (1995) Construction of a rice bacterial artificial chromosome library and identification of clones linked to the Xa-21 disease resistance locus. Plant J 7:525–533
Wang Q, Zhang K, Qu X, Jia J, Shi J, Jin D, Wang B (2001) Construction and characterization of a bacterial artificial chromosome library of peach. Theor Appl Genet 103:1174–1179
Wang W, Zhai W, Luo M, Jiang G, Chen X, Li X, Wing RA, Zhu L (2001) Chromosome landing at the bacterial blight resistance gene Xa4 locus using a deep coverage rice BAC library. Mol Genet Genomics 265:118–125
Woo S-S, Jiang J, Gill BS, Patterson AH, Wing RA (1994) Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22:4922–4931
Xu ML, Song JQ, Cheng ZK, Jiang JM, Korban SS (2001) A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf. Genome 44:1104–1113
Yang D, Sanchez A, Khush GS, Zhu Y, Huang N (1998) Construction of a BAC contig containing the xa5 locus in rice. Theor Appl Genet 97:1120–1124
Yokoya K, Roberts AV, Mottley J, Lewis R, Brandham PE (2000) Nuclear DNA amounts in roses. Ann Bot 85:557–561
Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggemann RS, Muehlbauer GJ, Wise RP, Wing RA (2000) A bacterial artificial chromosome library for barley ( Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101:1093–1099
Zhang H-B, Zhao X, Ding X, Paterson AH, Wing RA (1995) Preparation of megabase-size DNA from plant nuclei. Plant J 7:175–184
Zhang H-B, Choi S, Woo S-S, Li Z, Wing RA (1996) Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Mol Breed 2:11–24
Acknowledgements
We thank M. Schreiber and G. Bräcker for technical assistance, and Dr. A. Dohm for providing the colchicine-treated R. rugosa clone C5-23. We also thank Prof. A. Roberts and Dr. T. Lahaye for their critical review of this manuscript. The project was supported in part by grants from the Bundesanstalt für Landwirtschaft und Ernährung (No. 97HS043). All experiments described in this paper comply with current laws governing genetic experimentation in Germany
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by R. Hagemann
Rights and permissions
About this article
Cite this article
Kaufmann, H., Mattiesch, L., Lörz, H. et al. Construction of a BAC library of Rosa rugosa Thunb. and assembly of a contig spanning Rdr1, a gene that confers resistance to blackspot. Mol Gen Genomics 268, 666–674 (2003). https://doi.org/10.1007/s00438-002-0784-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00438-002-0784-0