Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to
develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea
provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying
adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based
linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as
well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position.
We also compared the level of polymorphism between genomic and EST-derived SSRs and address the
transferability of EST-SSRs in Castanea sativa (chestnut).
Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented
one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed
for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference fullsib
pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin
mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage
maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected
based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with
an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and
their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than
genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.
Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step
toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting
complex traits of ecological importance.