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

Valérie Poncet 1 Myriam Rondeau 1 Christine Tranchant 1 Anne Cayrel 1 Serge Hamon 1 Alexandre De Kochko 1 Perla Hamon 1
1 UMR DIADE - Diversité, adaptation, développement des plantes
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 : genetic variation Coffea transferability SSR mining EST SSR
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Valérie Poncet, Myriam Rondeau, Christine Tranchant, Anne Cayrel, Serge Hamon, et al.. SSR mining in coffee tree EST databases : potential use of EST-SSRs as markers for the Coffea genus. Molecular Genetics and Genomics, Springer Verlag, 2006, 276 (5), pp.436-449. ⟨ird-01223821⟩

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