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Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome

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Abstract

A set of 111,090 barley expressed sequence tags (ESTs) was searched for the presence of microsatellite motifs [simple sequence repeat (SSRs)] and yielded 2,823 non-redundant SSR-containing ESTs (SSR–ESTs). From this, a set of 754 primer pairs was designed of which 525 primer pairs yielded an amplicon and as a result, 185 EST-derived microsatellite loci (EST–SSRs) were placed onto a genetic map of barley. The markers show a uniform distribution along all seven linkage groups ranging from 21 (7H) to 35 (3H) markers. Polymorphism information content values ranged from of 0.24 to 0.78 (average 0.48). To further investigate the physical distribution of the EST–SSRs in the barley genome, a bacterial artificial chromosomes (BAC) library was screened. Out of 129 markers tested, BAC addresses were obtained for 127 EST–SSR markers. Twenty-seven BACs, forming eight contigs, were hit by two or three EST–SSRs each. This unexpectedly high incidence of EST–SSRs physically linked at the sub-megabase level provides additional evidence of an uneven distribution of genes and the segmentation of the barley genome in gene-rich and gene-poor regions.

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References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186

    Article  PubMed  CAS  Google Scholar 

  • Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    Article  PubMed  CAS  Google Scholar 

  • Barakat A, Carels N, Bernardi G (1997) The distribution of genes in the genomes of Gramineae. Proc Natl Acad Sci USA 94:6857–6861

    Article  PubMed  CAS  Google Scholar 

  • Bennett MD, Leitch IJ (2003) Angiosperm DNA C-values database (release 4.0, January 2003).

  • Carels N, Barakat A, Bernardi G (1995) The gene distribution of the maize genome. Proc Natl Acad Sci USA 92:11057–11060

    Article  PubMed  CAS  Google Scholar 

  • Erayman M, Sandhu D, Sidhu D, Dilbirligi M, Baenziger PS, Gill KS (2004) Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Res 32:3546–3565

    Article  PubMed  CAS  Google Scholar 

  • Gao LF, Jing RL,Hu NX, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ (2004) One hundred and one new microsatellite loci derived from ESTs (EST–SSRs) in bread wheat. Theor Appl Genet 108:1392–1400

    Article  PubMed  CAS  Google Scholar 

  • Gill KS (2004) Gene distribution in cereal genomes. In: Gupta PK, Varshney RK (eds) Cereal genomics. Kluwer, Dordrecht, pp 361–384

    Google Scholar 

  • Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71

    Article  CAS  Google Scholar 

  • Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5:246–251

    Article  PubMed  CAS  Google Scholar 

  • Kleinhofs A, Graner A (2001) An integrated map of the barley genome. In: Phillips RL, Vasil IK (eds) DNA markers in plants. Kluwer, Dordrecht, pp 187–199

    Google Scholar 

  • Kleinhofs A, Kilian A, Saghai-Maroof MA, Biyashev RM, Hayes PM (1993) A molecular, isozyme and morphological map of barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712

    Article  CAS  Google Scholar 

  • Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A (2003) Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Gen Genome 270:224–233

    Google Scholar 

  • Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412

    PubMed  Google Scholar 

  • Li JZ, Sjakste TG, Röder MS, Ganal MW (2003) Development and genetic mapping of 127 new microsatellite markers in barley. Theor Appl Genet 107:1021–1027

    Article  PubMed  CAS  Google Scholar 

  • Miller RT, Christoffels AG, Gopalkrishnan C, Burke J, Ptitsyn AA, Broveak TR, Hide WA (1999) A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res 9:1143–1155

    Article  PubMed  CAS  Google Scholar 

  • Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH (2002) Integration of cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12:795–807

    Article  PubMed  CAS  Google Scholar 

  • Perovic D, Stein N, Zhang H, Drescher A, Prasad M, Kota R, Kopahnke D, Graner A (2004) An integrated approach for comparative mapping in rice and barley based on genomic resources reveals a large number of syntenic markers but no candidate gene for the Rph16 resistance locus. Funct Integr Genomics 4:74–83

    Article  PubMed  CAS  Google Scholar 

  • Pillen K, Binder A, Kreuzkam B, Ramsay L, Waugh R, Förster J, Leon J (2000) Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars. Theor Appl Genet 101:652–660

    Article  CAS  Google Scholar 

  • Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Dubcovsky J et al (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701–712

    Article  PubMed  CAS  Google Scholar 

  • Rabinowicz PD, McCombie WR, Martienssen RA (2003) Gene enrichment in plant genomic shotgun libraries. Curr Opin Plant Biol 6:150–156

    Article  PubMed  CAS  Google Scholar 

  • Ramsay L, Macaulay M, Ivanissevich DS,MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997–2005

    PubMed  CAS  Google Scholar 

  • Rostoks N, Park YJ, Ramakrishna W, Ma J, Druka A, Shiloff BA, SanMiguel PJ, Jiang Z, Brueggeman R, Sandhu D, Gill K, Bennetzen JL, Kleinhofs A. (2002) Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley. Funct Integr Genomics 2:51–59

    Article  PubMed  CAS  Google Scholar 

  • Sasaki T, Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141

    Article  PubMed  CAS  Google Scholar 

  • Schulman AH, Gupta PK, Varshney RK (2004) Organization of retrotransposons and microsatellites in cereal genomes. In: Gupta PK, Varshney RK (eds) Cereal genomics. Kluwer, Dordrecht, pp 83–118

    Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114

    Article  PubMed  CAS  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–774

    Article  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546

    PubMed  CAS  Google Scholar 

  • Varshney RK, Korzun V, Börner A (2004) Molecular maps in cereals: methodology and progress. In: Gupta PK, Varshney RK (eds) Cereal genomics. Kluwer, Dordrecht, pp 35–82

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005a) Genic microsatellite markers in plants: features and applications. Trends Biotech 23:48–55

    Article  CAS  Google Scholar 

  • Varshney RK, Sigmund R, Borner A, Korzun V, Stein N, Sorrells ME, Langridge P, Graner A (2005b) Interspecific transferability and comparative mapping of barley EST–SSR markers in wheat, rye and rice. Plant Sci 168:195–202

    Article  CAS  Google Scholar 

  • Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B (2001) Analysis of a contigous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26:307–316

    Article  PubMed  CAS  Google Scholar 

  • Wicker T, Zimmermann W, Perovic D, Paterson AH, Ganal M, Graner A, Stein N (2005) A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eif4e locus: recombination, re-arrangements, and repeats. Plant J 41:184–194

    Article  PubMed  CAS  Google Scholar 

  • Yu Y, Tmkins JP, Waugh R, Frisch A, Kleinhofs A, Brueggeman 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

    Article  CAS  Google Scholar 

  • Zhang H, Sreenivasulu N, Weschke W, Stein N, Rudd S, Radchuk V, Potokina E, Scholz U, Schweizer P, Zierold U, Langridge P, Varshney R K, Wobus U, Graner A (2004). Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J 40:276–290

    Article  PubMed  Google Scholar 

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Acknowledgements

We are grateful to Timothy J. Close (University of California, Riverside, USA) for his valuable suggestions on the physical mapping data. We thank Uwe Scholz and Christian Künne (IPK) for performing cluster analysis of SSR-ESTs of IPK and non-IPK ESTs, and Paul Krapivsky (Boston University, Boston, USA), Stefan Posch (Martin Luther University Halle-Wittenberg, Halle, Germany) and Roland Schnee (IPK) for helpful discussions. We also thank Christine Künzel, Anita Czech, Brigitte Schmidt and Ingelore Dommers for technical assistance. The present work was funded by grants from the Grain Research and Development Corporation, Australia (GRDC, UA476), the Federal Ministry of Education and Research (BMBF, GABI-PLANT 312271A,B,C) and BMBF Bioinformatics Centre, Gatersleben/Halle 0312706A).

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Correspondence to A. Graner.

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Communicated by T.Sasaki

Primer sequences for developed SSR markers are available upon request from the corresponding author (A. Graner).

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Varshney, R.K., Grosse, I., Hähnel, U. et al. Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor Appl Genet 113, 239–250 (2006). https://doi.org/10.1007/s00122-006-0289-z

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  • DOI: https://doi.org/10.1007/s00122-006-0289-z

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