Molecular Breeding

, Volume 20, Issue 3, pp 189–208 | Cite as

Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross

  • Karine M. Oliveira
  • Luciana R. Pinto
  • Thiago G. Marconi
  • Gabriel R. A. Margarido
  • Maria Marta Pastina
  • Laura Helena M. Teixeira
  • Antônio V. Figueira
  • Eugênio César Ulian
  • Antônio Augusto F. Garcia
  • Anete Pereira Souza


The growing availability of ESTs provides a potentially valuable source of new DNA markers. The authors examined the SUCEST database and developed EST-derived markers. Thus to enhance the resolution of an existing linkage map and to identify putative functional polymorphic gene loci in a sugarcane commercial cross, 149 EST-SSRs and 10 EST-RFLPs were screened in the SP80-180  ×  SP80-4966 mapping population. With the markers already analyzed in the previous map, 2303 polymorphic markers were generated, of which 1669 (72.5%) were single-dose (SD) markers. Out of these 1669 SD markers, 664 (40%) were scattered onto 192 co-segregation groups (CGs) with a total estimated length of 6.261,1 cM. Using both genomic and EST-derived SSR and RFLP markers, 120 out of the 192 CGs were formed into fourteen putative homology groups (HGs). The EST-derived markers were subjected to BLASTX search in the SUCEST database, of which putative function was assigned to 113 EST-SSRs and six EST-RFLPs based on high nucleotide homology to previously studied genes. The integration of EST-derived markers improved the map, making it possible to consider additional fine mapping of the genome, and providing the means for developing ‘perfect markers’ associated with key QTL. To summarize, this paper deals with the construction of a genetic linkage map of sugarcane that is populated by functionally associated markers.


ESTs Functional map Mapping Polyploid SUCEST Sugarcane 



This work was supported by grants from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, 02/01167-1) and from CTC (Centro de Tecnologia Canavieira – Piracicaba/SP). K.M.O. and M.M.P. received Doctorate fellowships, respectively, from FAPESP (02/00197-4) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); K.M.O. also received PDEE fellowship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, 0181-05-6); L.H.M. received an MS fellowship from FAPESP (03/07960-6); TGM and GRAM received IC fellowships from FAPESP (04/10596-9 and 05/59268-6, respectively); L.R.P. received a Postdoctorate fellowship from FAPESP (01/14656); A.P.S., A.A.F.G. and A.F. received a research fellowship from CNPq. The authors would like to thank Dr. Angélique D’Hont (Centre de Coopération Internationale en Recherche Agronomique pour le Développement) for valuable discussions and anonymous reviewers for carefully reading the manuscript.


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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Karine M. Oliveira
    • 1
  • Luciana R. Pinto
    • 2
  • Thiago G. Marconi
    • 1
  • Gabriel R. A. Margarido
    • 3
  • Maria Marta Pastina
    • 3
  • Laura Helena M. Teixeira
    • 1
  • Antônio V. Figueira
    • 4
  • Eugênio César Ulian
    • 5
  • Antônio Augusto F. Garcia
    • 3
  • Anete Pereira Souza
    • 1
  1. 1.Centro de Biologia Molecular e Engenharia Genética (CBMEG), Departamento de Genética e Evolução, Instituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrasil
  2. 2.Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana - IAC/AptaRibeirao PretoBrasil
  3. 3.Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ)Universidade de São Paulo (USP)PiracicabaBrasil
  4. 4.Centro de Energia Nuclear na Agricultura (CENA)Universidade de São PauloPiracicabaBrasil
  5. 5.Centro de Tecnologia Canavieira - CTCPiracicabaBrasil

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