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Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop

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Abstract.

Cassava (Manihot esculenta) is an allogamous, vegetatively propagated, Neotropical crop that is also widely grown in tropical Africa and Southeast Asia. To elucidate genetic diversity and differentiation in the crop's primary and secondary centers of diversity, and the forces shaping them, SSR marker variation was assessed at 67 loci in 283 accessions of cassava landraces from Africa (Tanzania and Nigeria) and the Neotropics (Brazil, Colombia, Peru, Venezuela, Guatemala, Mexico and Argentina). Average gene diversity (i.e., genetic diversity) was high in all countries, with an average heterozygosity of 0.5358 ± 0.1184. Although the highest was found in Brazilian and Colombian accessions, genetic diversity in Neotropical and African materials is comparable. Despite the low level of differentiation [Fst(theta) = 0.091 ± 0.005] found among country samples, sufficient genetic distance (1-proportion of shared alleles) existed between individual genotypes to separate African from Neotropical accessions and to reveal a more pronounced substructure in the African landraces. Forces shaping differences in allele frequency at SSR loci and possibly counterbalancing successive founder effects involve probably spontaneous recombination, as assessed by parent-offspring relationships, and farmer-selection for adaptation.

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Acknowledgements.

We thank Eric Minch, and Xavier Vekemans (Université Libre de Bruxelles, Brussels, Belgium) for their assistance with the computer packages "microsat" and GEN-SURVEY, and for their helpful suggestions. We acknowledge the useful comments from Joe Tohme and Paul Chavariagga-Aguirre (CIAT), Luigi Guarino (IPGRI), Ken Olsen (North Carolina State University), Ryohei Terauchi (Iwate Biotechnology Research Center, Kitakami, Japan) and two anonymous reviewers. We also thank Matthew Raya of the Agricultural Research Institute at Naliendele, Tanzania, for his assistance with field collection. This work was supported in part by the International Program for the Chemical Sciences, Uppsala University, Sweden, and we are grateful to its director Malin Akerbolm for her abiding faith in our application of chemistry to unravel genetic diversity issues.

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Authors and Affiliations

  1. Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia

    M. A. Fregene & M. Suarez

  2. Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden

    J. Mkumbira & U. Gullberg

  3. Agricultural Research Institute (ARI), Ukiguru, Mwanza, Tanzania

    H. Kulembeka

  4. Rural Integrated Project Support (RIPS) Programme, Mtwara, Tanzania

    E. Ndedya

  5. Agricultural Research Institute (ARI), Mikocheni, Dar es Salaam, Tanzania

    A. Kulaya

  6. Division of International Health, Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden

    H. Rosling

  7. International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria

    S. Mitchel & A. G. O. Dixon

  8. Institute for Genomic Diversity (IGD), Cornell University, Ithaca, NY, USA

    S. Kresovich

  9. Plant Genetic Research Consortium, University of Georgia at Griffin, USA

    R. Dean

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  1. M. A. Fregene
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  2. M. Suarez
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  3. J. Mkumbira
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  4. H. Kulembeka
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  5. E. Ndedya
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  6. A. Kulaya
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  7. S. Mitchel
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  8. U. Gullberg
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  9. H. Rosling
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  10. A. G. O. Dixon
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  11. R. Dean
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  12. S. Kresovich
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Correspondence to M. A. Fregene.

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Communicated by H.C. Becker

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Fregene, M.A., Suarez, M., Mkumbira, J. et al. Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop. Theor Appl Genet 107, 1083–1093 (2003). https://doi.org/10.1007/s00122-003-1348-3

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  • DOI: https://doi.org/10.1007/s00122-003-1348-3

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