Molecular Genetics and Genomics

, Volume 276, Issue 5, pp 436–449

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

  • Valérie Poncet
  • Myriam Rondeau
  • Christine Tranchant
  • Anne Cayrel
  • Serge Hamon
  • Alexandre de Kochko
  • Perla Hamon
Original Paper

DOI: 10.1007/s00438-006-0153-5

Cite this article as:
Poncet, V., Rondeau, M., Tranchant, C. et al. Mol Genet Genomics (2006) 276: 436. doi:10.1007/s00438-006-0153-5

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.

Keywords

SSR mining EST–SSR Coffea Transferability Genetic variation 

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Valérie Poncet
    • 1
  • Myriam Rondeau
    • 1
  • Christine Tranchant
    • 1
  • Anne Cayrel
    • 1
  • Serge Hamon
    • 1
  • Alexandre de Kochko
    • 1
  • Perla Hamon
    • 1
  1. 1.UMR 1097 Diversité et Génomes des Plantes Cultivées (DGPC)IRD, Institut de Recherche pour le DéveloppementMontpellier Cedex 5France

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