%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Poncet, Valérie
%A Rondeau, Myriam
%A Tranchant, Christine
%A Cayrel, Anne
%A Hamon, Serge
%A Kochko, Alexandre de
%A Hamon, Perla
%T SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus
%D 2006
%L fdi:010037624
%G ENG
%J Molecular Genetics and Genomics
%@ 1617-4615
%K SSR mining ; EST SSR ; Coffea ; transferability ; genetic variation
%M CC:0002407986-0003
%N 5
%P 436-449
%R 10.1007/s00438-006-0153-5
%U https://www.documentation.ird.fr/hor/fdi:010037624
%> https://www.documentation.ird.fr/intranet/publi/2006/10/010037624.pdf
%V 276
%W Horizon (IRD)
%X 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.
%$ 076