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SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus

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Abstract

Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST–SSRs) with a motif length of 1–6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST–SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST–SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies.

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Acknowledgments

This work was partly supported by EU grant No. ICA4-CT-2001-10068. The authors wish to thank I. Mougenot, C. Fizames, B. Piegu, A. Wissocq, F. Lechauve, F. Moreews, X. Argout, F. Chevalier, and many Genetrop researchers for their involvement in the development of ESTdb, and M. Lorieux for his help in developing the SSR script (http://www.mpl.ird.fr/bioinfo/). Thank to Dr. Santiago C.González-Martínez for his valuable comments on the manuscript.

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  1. UMR 1097 Diversité et Génomes des Plantes Cultivées (DGPC), IRD, Institut de Recherche pour le Développement, 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France

    Valérie Poncet, Myriam Rondeau, Christine Tranchant, Anne Cayrel, Serge Hamon, Alexandre de Kochko & Perla Hamon

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  1. Valérie Poncet
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Correspondence to Valérie Poncet.

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Poncet, V., Rondeau, M., Tranchant, C. et al. SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus. Mol Genet Genomics 276, 436–449 (2006). https://doi.org/10.1007/s00438-006-0153-5

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