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Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers

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Abstract

Microsatellite [simple-sequence repeat (SSR)] markers were developed and positioned on the genetic map of tetraploid cotton. Three hundred and ninety-two unique microsatellite sequences, all but two containing a (CA/GT) repeat, were isolated, and the deduced primers were used to screen for polymorphism between the Gossypium hirsutum and G. barbadense parents of the mapping population analyzed in our laboratory. The observed rate of polymorphism was 56%. The 204 polymorphic SSRs revealed 261 segregating bands, which ultimately gave rise to 233 mapped loci. The updated status of our genetic map is now of 1,160 loci and 5,519 cM, with an average distance between two loci of 4.8 cM. The presence of a total of 466 microsatellite loci, with an average distance of 12 cM between two SSR loci, now provides wide coverage of the genome of tetraploid cotton and thus represents a powerful means for the production of a consensus map and for the effective tracking of QTLs.

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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 

  • Billotte N, Lagoda PJ, Risterucci A-M, Baurens F-C (1999) Microsatellite-enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–288

    CAS  Google Scholar 

  • Brubaker CL, Wendel JF (2001) RFLP diversity in cotton. In: Jenkins JN, Saha S (eds) Genetic improvement of cotton, emerging technologies. Science, Enfield, N.H., USA, pp 81–101

  • Brubaker CL, Cantrell RG, Giband M, Lyon BR, Wilkins TA (2000) Letter to Journal of Cotton Science community: formation of the International Cotton Genome Initiative, ICGI. J Cotton Sci 4:149

    Google Scholar 

  • Cone KC, McMullen MD, Bi IV, Davis GL, Yim YS, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA, Coe EH Jr (2002) Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol 4:1598–1605

    Article  Google Scholar 

  • Connell JP, Pammi S, Iqbal MJ, Huizinga T, Reddy AS (1998) A high throughput procedure for capturing microsatellites from complex plant genomes. Plant Mol Biol Rep 16:341–349

    CAS  Google Scholar 

  • Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE (1999) An integrated genetic linkage map of the soybean genome. Crop Sci 39:1464–1490

    CAS  Google Scholar 

  • Danin-Poleg Y, Reis N, Baudrasso-Arnas S, Pitrat M, Staub JE, Oliver M, Arus P, deVicente CM, Katzir N (2000) Simple sequence repeats in Cucumis mapping and map merging. Genome 43:963–974

    Article  CAS  PubMed  Google Scholar 

  • Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758–760

    CAS  PubMed  Google Scholar 

  • Endrizzi JE, Turcotte EL, Kohel RJ (1985) Genetics, cytology and evolution of Gossypium. Adv Genet 23:271–375

    Google Scholar 

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

    CAS  Google Scholar 

  • Jones ES, Dupal MP, Kölliker R, Drayton MC, Forster JW (2001) Development and characterization of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102:405–415

    CAS  Google Scholar 

  • Kijas JMH, Fowler JCS, Garbett CA, Thomas MR (1994) Enrichment of microsatellites from the Citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. Biotechniques 16:656–662

    CAS  PubMed  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Kumpatla SP, Horne EC, Shah MR, Gupta M, Thompson SA (2002) Development of SSR markers: towards genetic mapping in cotton (Gossypium hirsutum L.). Abstract communication at the 3rd international cotton genome initiative workshop, Nanjing, China. Cotton Sci 14 [Suppl]:28

  • Lacape J-M, Nguyen TB, Thibivilliers S, Courtois B, Bojinov BM, Cantrell RG, Burr B, Hau B (2003) A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum × Gossypium barbadense backcross population. Genome 46:612–626

    Google Scholar 

  • Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115

    CAS  PubMed  Google Scholar 

  • Lander E, Green P, Abrahamson J, Barlow A, Daley M, Lincoln S, Newburg L (1987) MapMaker: an interactive computer package for constructing primary linkage maps of experimental and natural populations. Genomics 1:174–181

    CAS  PubMed  Google Scholar 

  • Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604–610

    CAS  PubMed  Google Scholar 

  • Mace ES, Godwin ID (2002) Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta). Genome 45:823–832

    Article  CAS  PubMed  Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, MW, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerk G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    CAS  PubMed  Google Scholar 

  • Reddy OUK, Pepper AE, Abdurakhmonov I, Saha S, Jenkins JN, Brooks T, Bolek Y, El-Zik KM (2001) New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. J Cotton Sci 5:103–113

    Google Scholar 

  • Reinish A, Dong J-M, Brubaker CL, Stelly DM, Paterson AH (1994) A detailed RFLP map of cotton, Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829–847

    CAS  PubMed  Google Scholar 

  • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana, Totowa, N.J., pp 365–386

  • Ruiz C, Asins MJ (2003) Comparison between Ponsirus and Citrus linkage maps. Theor Appl Genet 106:826–836

    CAS  PubMed  Google Scholar 

  • Saha S, Karaca M, Jenkins JN, Zipf A, Reddy OUK, Kantety RV (2003) Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130:355–364

    Article  CAS  Google Scholar 

  • Schoot J van der, Popiskova M, Vosman B, Smulders MJM (2000) Development and characterization of microsatellite markers in black poplar (Populus nigra L.). Theor Appl Genet 101:317–322

    Article  Google Scholar 

  • Shappley Z, Jenkins JN, Meredith W, McCartty JCJ (1998) An RFLP linkage map of upland cotton, Gossypium hirsutum L. Theor Appl Genet 97:756–761

    CAS  Google Scholar 

  • Tatineni V, Cantrell RG, Davis DD (1996) Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPDs. Crop Sci 36:186–192

    Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    CAS  PubMed  Google Scholar 

  • Ulloa M, Meredith W, Shappley Z, Kahler A (2002) RFLP genetic linkage maps from four F2.3 populations and a JoinMap of Gossypium hirsutum L. Theor Appl Genet 104:200–208

    Article  Google Scholar 

  • Yu J, Kohel RJ (2001) Cotton genome research in the United States. In: Jenkins JN, Saha S (eds) Genetic improvement of cotton. Emerging technologies. Science, Enfield, N.H., USA, pp 103–122

  • Zhang J, Guo W, Zhang T (2002) Molecular linkage map of allotetraploid cotton (Gossypium hirsutum L. × Gossypium barbadense L.) with a haploid population. Theor Appl Genet 105:1166–1174

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. UMR1096, TA 70/03, Centre International en Recherche Agronomique pour le Développement (CIRAD), Avenue Agropolis, 34398 , Montpellier , Cedex 5, France

    T.-B. Nguyen, M. Giband, A.-M. Risterucci & J.-M. Lacape

  2. Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux CP 5706, 91057 , Evry , Cedex, France

    P. Brottier

Authors
  1. T.-B. Nguyen
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  2. M. Giband
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  3. P. Brottier
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  4. A.-M. Risterucci
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  5. J.-M. Lacape
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Correspondence to J.-M. Lacape.

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Communicated by C. Möllers

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Nguyen, TB., Giband, M., Brottier, P. et al. Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theor Appl Genet 109, 167–175 (2004). https://doi.org/10.1007/s00122-004-1612-1

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  • DOI: https://doi.org/10.1007/s00122-004-1612-1

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