@article{fdi:010037624, title = {{SSR} mining in coffee tree {EST} databases: potential use of {EST}-{SSR}s as markers for the {C}offea genus}, author = {{P}oncet, {V}al{\'e}rie and {R}ondeau, {M}yriam and {T}ranchant, {C}hristine and {C}ayrel, {A}nne and {H}amon, {S}erge and {K}ochko, {A}lexandre de and {H}amon, {P}erla}, editor = {}, language = {{ENG}}, abstract = {{E}xpressed sequence tags ({EST}s) from {C}offea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats ({EST}-{SSR}s) with a motif length of 1-6 bp. {F}rom 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. {T}rinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. {T}he 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. {T}wenty-five {EST}-{SSR}s were developed and used to evaluate cross-species transferability in the {C}offea genus. {T}he orthology was supported by the amplicon sequence similarity and the amplification patterns. {T}he > 94% identity of flanking sequences revealed high sequence conservation across the {C}offea genus. {A} high level of polymorphic loci was obtained regardless of the species considered (from 75% for {C}. liberica to 86% for {C}. canephora). {M}oreover, the polymorphism revealed by {EST}-{SSR} was similar to that exposed by genomic {SSR}. {I}t is concluded that {C}offea {EST}s are a valuable resource for microsatellite mining. {EST}-{SSR} markers developed from {C}. canephora sequences can be easily transferred to other {C}offea species for which very little molecular information is available. {T}hey 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} ; {C}offea ; transferability ; genetic variation}, booktitle = {}, journal = {{M}olecular {G}enetics and {G}enomics}, volume = {276}, numero = {5}, pages = {436--449}, ISSN = {1617-4615}, year = {2006}, DOI = {10.1007/s00438-006-0153-5}, URL = {https://www.documentation.ird.fr/hor/fdi:010037624}, }