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Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases

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Abstract

Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars (‘SP80-180’ × ‘SP80-4966’) using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane.

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Acknowledgments

This work was supported by a grant from “Conselho Nacional de Desenvolvimento Científico e Tecnológico” (CNPq)-PADCT (SBIO 62.0020/99-7) and “Fundação de Amparo à Pesquisa do Estado de São Paulo” (FAPESP 00/05718-7 and 02/01167-1). A.P.S., A.A.F.G. and A.F. receive a research fellowship from “Conselho Nacional de Desenvolvimento Científico e Tecnológico” (CNPq); E.A.K. and H.M.B.S. were recipient of fellowships from “Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); A.N.M and L.R.P. were recipients of graduate and post-doctoral fellowships, respectively from FAPESP (00/05718-7; 01/14656-8) and C.S.L. and M.M.P were recipients of undergraduate fellowships from CNPq and FAPESP, respectively. The authors thank G.R.A. Margarido and M. Mollinari for help with the OneMap software development.

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Authors and Affiliations

  1. Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970, Piracicaba-SP, Brazil

    A. A. F. Garcia & M. M. Pastina

  2. Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil

    E. A. Kido, H. M. B. Souza & A. Figueira

  3. Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária “Zeferino Vaz”, CP 6010, 13083-970, Campinas-SP, Brazil

    A. N. Meza, L. R. Pinto, C. S. Leite & A. P. Souza

  4. Texas Agricultural Experiment Station, Weslaco Center, Texas A and M University, 2415 E. Hwy. 83, Weslaco, TX, 78596, USA

    J. A. G. da Silva

  5. Copersucar Technology Center, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brazil

    E. C. Ulian

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  1. A. A. F. Garcia
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  2. E. A. Kido
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  3. A. N. Meza
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  4. H. M. B. Souza
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  5. L. R. Pinto
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  7. C. S. Leite
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  8. J. A. G. da Silva
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  9. E. C. Ulian
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  10. A. Figueira
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  11. A. P. Souza
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Correspondence to A. A. F. Garcia.

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Communicated by A. Charcosset

E.A. Kido, A.N. Meza and H.M.B. Souza contributed equally to this work.

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Garcia, A., Kido, E., Meza, A. et al. Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theor Appl Genet 112, 298–314 (2006). https://doi.org/10.1007/s00122-005-0129-6

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