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Construction of two BAC libraries from cucumber (Cucumis sativus L.) and identification of clones linked to yield component quantitative trait loci

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Abstract

Two bacterial artificial chromosome (BAC) libraries were constructed from an inbred line derived from a cultivar of cucumber (Cucumis sativus L.). Intact nuclei were isolated and embedded in agarose plugs, and high-molecular-weight DNA was subsequently partially digested with BamHI or EcoRI. Ligation of double size-selected DNA fragments with the pECBAC1 vector yielded two libraries containing 23,040 BamHI and 18,432 EcoRI clones. The average BamHI and EcoRI insert sizes were estimated to be 107.0 kb and 100.8 kb, respectively, and BAC clones lacking inserts were 1.3% and 14.5% in the BamHI and EcoRI libraries, respectively. The two libraries together represent approximately 10.8 haploid cucumber genomes. Hybridization with a C0t-1 DNA probe revealed that approximately 36% of BAC clones likely carried repetitive sequence-enriched DNA. The frequencies of BAC clones that carry chloroplast or mitochondrial DNA range from 0.20% to 0.47%. Four sequence-characterized amplified region (SCAR), four simple sequence repeat, and an randomly amplified polymorphic DNA marker linked with yield component quantitative trait loci were used either as probes to hybridize high-density colony filters prepared from both libraries or as primers to screen an ordered array of pooled BAC DNA prepared from the BamHI library. Positive BAC clones were identified in predicted numbers, as screening by polymerase chain reaction amplification effectively overcame the problems associated with an overabundance of positives from hybridization with two SCAR markers. The BAC clones identified herein that are linked to the de (determinate habit) and F (gynoecy) locus will be useful for positional cloning of these economically important genes. These BAC libraries will also facilitate physical mapping of the cucumber genome and comparative genome analyses with other plant species.

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References

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    CAS  Google Scholar 

  • Bradeen JM, Staub JE, Wye C, Antonise R, Peleman J (2001) Towards an expanded and integrated linkage map of cucumber (Cucumis sativus L.). Genome 44:111–119

    Article  CAS  PubMed  Google Scholar 

  • Budiman MA, Mao L, Wood TC, Wing RA (2000) A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res 10:129–136

    CAS  PubMed  Google Scholar 

  • Burke DT, Carle GF, Olson MV (1987) Cloning of large fragments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236:801–811

    Google Scholar 

  • Cantliffe DJ (1981) Alteration of sex expression in cucumber due to changes in temperature, light intensity, and photoperiod. J Am Soc Hort Sci 106:133–136

    Google Scholar 

  • Carpin S, Crevecoeur M, Greppin H, Penel C (1999) Molecular cloning and tissue-specific expression of an anionic peroxidase in zucchini. Plant Physiol 120:799–810

    Article  CAS  PubMed  Google Scholar 

  • Chang Y-L, Tao Q, Scheuring C, Meksem K, Zhang H-B (2001) An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics 159:1231–1242

    CAS  PubMed  Google Scholar 

  • Chen Q, Sun S, Ye Q, McCuine S, Huff E, Zhang H-B (2004) Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum, and the identification of clones near the late blight and Colorado potato beetle resistance loci. Theor Appl Genet 108:1002–1009

    Article  CAS  PubMed  Google Scholar 

  • Choi S, Creelman RA, Mullet JE, Wing RA (1995) Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol Biol Rep 13:124–128

    Google Scholar 

  • Cregan PB, Mudge J, Fickus EW, Marek LF, Danesh D, Denny R, Shoemaker RC, Matthews BF, Jarvik T, Young ND (1999) Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919–928

    Article  CAS  Google Scholar 

  • Dane F (1991) Cytogenetics in the genus Cucumis. In: Tsuchiya T, Gupta PK (eds) Chromosome engineering in plants: genetics, breeding, and evolution. Elsevier, Amsterdam, pp 201–214

    Google Scholar 

  • Danesh D, Penuela S, Mudge J, Denny RL, Nordstorm H, Martinez JP, Young ND (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

    Article  CAS  Google Scholar 

  • FAO (1993) Year book production 1992. Food and Agriculture Organization of the United Nations, Rome, Italy

  • Fazio G, Staub JE, Chung S-M (2002) Development and characterization of PCR markers in cucumber. J Am Soc Hort Sci 127:545–557

    CAS  Google Scholar 

  • Fazio G, Chung SM, Staub JE (2003a) Comparative analysis of response to phenotypic and marker-assisted selection for multiple lateral branching in cucumber (Cucumis sativus L.). Theor Appl Genet 107:875–883

    Article  CAS  PubMed  Google Scholar 

  • Fazio G, Staub JE, Stevens MR (2003b) Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Theor Appl Genet 107:864–874

    Article  CAS  PubMed  Google Scholar 

  • Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    Article  CAS  PubMed  Google Scholar 

  • Frijters ACJ, Zhang Z, van Damme M, Wang G-L, Roland PC, Michelmore RW (1997) Construction of a bacterial chromosome library containing large EcoRI and HindIII genomic fragments of lettuce. Theor Appl Genet 94:390–399

    Article  CAS  Google Scholar 

  • Grant S, Houben A, Vyskot B, Siroky J, Pan WH, Macas J, Saedler H (1994) Genetics of sex determination in flowering plants. Dev Genet 15:214–230

    Google Scholar 

  • Jeffrey C (1980) A review of the Cucurbitaceae. Bot J Linn Soc 81:233–247

    Google Scholar 

  • Kamachi S, Mizusawa H, Matsuura S, Sakai S (2000) Expression of two 1-aminocyclopropane-1-carboxylate synthase genes, CS-ACS1 and CS-ACS2, correlated with sex phenotypes in cucumber plants (Cucumis sativus L.). Plant Biotechnol 17:69–74

    CAS  Google Scholar 

  • Kieber JJ, Rothenberg M, Roman G, Feldmann KA, Ecker JR (1993) CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell 72:427–441

    Article  CAS  PubMed  Google Scholar 

  • van Leeuwen H, Monfort A, Zhang H-B, Puigdoménech P (2003) Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana. Plant Mol Biol 51:703–718

    Article  PubMed  Google Scholar 

  • Li J, Nagpal P, Vitart V, MacMorris TC, Chory J (1996) A role for brassinosteroids in light-dependent development of Arabidopsis. Science 272:398–401

    CAS  PubMed  Google Scholar 

  • Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang H-B (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 110:492–510

    Article  CAS  PubMed  Google Scholar 

  • Lower RL, Edwards MD (1986) Cucumber breeding. In: Bassett MJ (ed) Breeding vegetable crops. AVI, Westport

    Google Scholar 

  • Luo M, Wang Y, Frisch D, Joobeur T, Wing RA, Dean RA (2001) Melon bacterial artificial chromosome (BAC) library construction using an improved method and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2). Genome 44:154–162

    Article  CAS  PubMed  Google Scholar 

  • Malepszy S, Niemirowicz-Szczytt K (1991) Sex determination in cucumber (Cucumis sativus) as a model system for molecular biology. Plant Sci 80:39–47

    Article  Google Scholar 

  • Mibus H, Tatlioglu T (2004) Molecular characterization and isolation of the F/f gene for femaleness in cucumber (Cucumis sativus L.) Theor Appl Genet 109:1669–1676

    Article  CAS  PubMed  Google Scholar 

  • Michaels SD, Amasino RM (1998) A robust method for detecting single nucleotide changes as polymorphic markers by PCR. Plant J 14:381–385

    Article  CAS  PubMed  Google Scholar 

  • Mozo T, Fischer S, Shizuya H, Altmann T (1998) Construction and characterization of the IGF Arabidopsis BAC library. Mol Gen Genet 258:562–570

    Article  CAS  PubMed  Google Scholar 

  • Nam YW, Penmetsa RV, Endre G, Uribe P, Kim D, Cook DR (1999) Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene-response genes. Theor Appl Genet 98:638–646

    Article  CAS  Google Scholar 

  • Serquen FC, Bacher J, Staub JE (1997a) Genetic analysis of yield components in cucumber at low plant density. J Am Soc Hort Sci 122:522–528

    Google Scholar 

  • Serquen FC, Bacher J, Staub JE (1997b) Mapping and QTL analysis of horticultural traits in a narrow cross in cucumber (Cucumis sativus L.) using random-amplified polymorphic DNA markers. Mol Breed 3:257–268

    Article  CAS  Google Scholar 

  • Shizuya H, Birren B, Kim U-J, Mancino V, Slepak T, Tachini Y, Simon M (1992) Cloning and stable maintenance of 300 kilo base pair fragment of human DNA in Escherichia coli using an F-factor based vector. Proc Natl Acad Sci USA 89:8794–8797

    CAS  PubMed  Google Scholar 

  • Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Franquet C, Ronald PC (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806

    CAS  PubMed  Google Scholar 

  • Staub JE, Serquen FC, Gupta M (1996) Genetic markers, map construction, and their application in plant breeding. Hort Sci 31:729–741

    CAS  Google Scholar 

  • Tao Q, Zhang H-B (1998) Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res 26:4901–4909

    Article  CAS  PubMed  Google Scholar 

  • Tao Q, Wang A, Zhang H-B (2002) One large-insert plant-transformation-competent BIBAC library and three BAC libraries of Japonica rice for genome research in rice and other grasses. Theor Appl Genet 105:1058–1066

    Article  CAS  PubMed  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Google Scholar 

  • Trebitsh T, Staub JE, O’Neill SD (1997) Identification of a 1-aminocyclopropane-1-carboxylic acid synthase gene linked to the Female (F) locus that enhances female sex expression in cucumber. Plant Physiol 113:987–995

    Article  CAS  PubMed  Google Scholar 

  • USDA-NASS (1999) Vegetables: final estimates by States, 1992–97. US Department of Agriculture, Agricultural Statistics Service, Statistical Bulletin No. 946c

  • Venter JC, Smith HO, Hood L (1996) A new strategy for genome sequencing. Nature 381:364–366

    Article  CAS  PubMed  Google Scholar 

  • Woo S-S, Jiang J, Grill BS, Paterson AH, Wing RA (1994) Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22:4922–4931

    CAS  PubMed  Google Scholar 

  • Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, Zhang H-B (2004a) Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor Appl Genet 109:1041–1050

    Article  CAS  PubMed  Google Scholar 

  • Wu C, Sun S, Padmavathi N, Santos FA, Springman R, Meksem K, Lightfoot D, Zhang H-B (2004b) A BAC and BIBAC-based physical map of the soybean genome. Genome Res 14:319–326

    Article  CAS  PubMed  Google Scholar 

  • Xu ZY, Sun S, Covaleda L, Ding K, Zhang A, Scheuring C, Zhang H-B (2004) Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage and contig map quality. Genomics 84:941–951

    Article  CAS  PubMed  Google Scholar 

  • Yamagami T, Tsuchisaka A, Yamada K, Haddon WF, Harden LA, Theologis A (2003) Biochemical diversity among the 1-amino-cyclopropane-1-carboxylate synthase isozymes encoded by the Arabidopsis gene family. J Biol Chem 278:49102–49112

    Article  CAS  PubMed  Google Scholar 

  • Yoo EY, Kim S, Kim YH, Lee CJ, Kim B-D (2003) Construction of a deep coverage BAC library from Capsicum annuum, ‘CM334’. Theor Appl Genet 107:540–543

    Article  CAS  PubMed  Google Scholar 

  • Zhang H-B (2000) Construction and manipulation of large-insert bacterial clone libraries manual. Texas A&M University, College Station (available at http://hbz.tamu.edu)

  • Zhang H-B, Zhao X, Ding X, Peterson AH, Wing RA (1995) Preparation of megabase-size DNA from plant nuclei. Plant J 7:175–184

    Article  CAS  Google Scholar 

  • Zhang H-B, Woo S-S, Wing RA (1996) BAC, YAC and cosmid library construction. In: Foster G, Twell D (eds) Plant gene isolation: principles and practices. Wiley, UK, pp 75–99

    Google Scholar 

  • Zhang H-B, Wu C (2001) BAC as tools for genome sequencing. Plant Physiol Biochem 39:195–209

    Article  CAS  Google Scholar 

  • Zwick MS, Hanson RE, McKnight TD, Islam-Faridi MN, Stelly DM, Wing RA, Price HJ (1997) A rapid procedure for the isolation of C0t-1 DNA from plants. Genome 40:138–142

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Dr. Claude Penel (University of Geneva), Dr. Minkyun Kim (Seoul National University), and Dr. Shinje Kim (FnP) for gene-specific probes. This work was supported by a grant from Korea Research Foundation (KRF-2000-DP0401) to Y.-W.N. and a grant from Korea Science and Engineering Foundation (KOSEF) to the Agricultural Plant Stress Research Center (APSRC) at Chonnam National University (Y.-W.N.). Purchase of key experimental equipment and software programs was supported by Sogang University Research Grants (20021508 and 20041037).

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Authors and Affiliations

  1. Department of Life Science, Sogang University, Shinsoo-dong, Mapo-gu, Seoul 121-742, Korea

    Y.-W. Nam, J.-R. Lee & K.-H. Song

  2. Department of Soil and Crop Sciences, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843-2123, USA

    M.-K. Lee & H.-B. Zhang

  3. Department of Horticulture and the United States Department of Agriculture, Agricultural Research Service, University of Wisconsin, Madison, WI, 53706-1590, USA

    M. D. Robbins, S.-M. Chung & J. E. Staub

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  1. Y.-W. Nam
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Correspondence to Y.-W. Nam.

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Communicated by I. Paran

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Nam, YW., Lee, JR., Song, KH. et al. Construction of two BAC libraries from cucumber (Cucumis sativus L.) and identification of clones linked to yield component quantitative trait loci. Theor Appl Genet 111, 150–161 (2005). https://doi.org/10.1007/s00122-005-2007-7

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