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Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz)

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Abstract

Single nucleotide polymorphisms (SNP) are the most abundant type of DNA polymorphism found in animal and plant genomes. They provide an important new source of molecular markers that are useful in genetic mapping, map-based positional cloning, quantitative trait locus mapping and the assessment of genetic distances between individuals. Very little is known on the frequency of SNPs in cassava. We have exploited the recently-developed collection of cassava expressed sequence tags (ESTs) to detect SNPs in the five cultivars of cassava used to generate the sequences. The frequency of intra-cultivar and inter-cultivar SNPs after analysis of 111 contigs was one polymorphism per 905 and one per 1,032 bp, respectively; totaling 1 each 509 bp. We have obtained further information on the frequency of SNPs in six cassava cultivars by analysis of 33 amplicons obtained from 3′ EST and BAC end sequences. Overall, about 11 kb of DNA sequence was obtained for each cultivar. A total of 186 SNPs (136 and 50 from ESTs and BAC ends, respectively) were identified. Among these, 146 were intra-cultivar polymorphisms, while 80 were inter-cultivar polymorphisms. Thus the total frequency of SNPs was one per 62 bp. This information will help to develop new strategies for EST mapping as well as their association with phenotypic characteristics.

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Acknowledgements

We are grateful to Chike Mba and Olivier Panaud for critically reading the manuscript. Thanks to Christel Llauro-Berger and Michèle Laudié for sequencing. All the sequencing was performed by the facilities of the Montpellier Languedoc Rousillon Genopole. Camilo Lopez was supported by a doctoral fellowship awarded by the IRD.

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Authors and Affiliations

  1. Laboratoire Génome et Développement des Plantes, UMR5096, CNRS-Université de Perpignan-Institut de Recherche pour le Développement, 52 Av Paul Alduy, 66860, Perpignan Cedex, France

    C. Lopez, B. Piégu, R. Cooke, M. Delseny & V. Verdier

  2. Biotechnology Research Unit Centro Internacional de Agricultura Tropical, 6713, Cali, Colombia

    J. Tohme & V. Verdier

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  1. C. Lopez
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  2. B. Piégu
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  3. R. Cooke
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  4. M. Delseny
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  5. J. Tohme
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  6. V. Verdier
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Corresponding author

Correspondence to V. Verdier.

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Communicated by E. Guiderdoni

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Lopez, C., Piégu, B., Cooke, R. et al. Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz). Theor Appl Genet 110, 425–431 (2005). https://doi.org/10.1007/s00122-004-1833-3

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  • DOI: https://doi.org/10.1007/s00122-004-1833-3

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