Open Access Research article

Comparative mapping in the Fagaceae and beyond with EST-SSRs

Catherine Bodénès12*, Emilie Chancerel12, Oliver Gailing113, Giovanni G Vendramin4, Francesca Bagnoli5, Jerome Durand12, Pablo G Goicoechea6, Carolina Soliani7, Fiorella Villani8, Claudia Mattioni8, Hans Peter Koelewijn9, Florent Murat10, Jerome Salse10, Guy Roussel12, Christophe Boury12, Florian Alberto12, Antoine Kremer12 and Christophe Plomion12

Author affiliations

1 INRA, UMR1202 BIOGECO, Cestas, F-33610, France

2 Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France

3 Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology Göttingen University, Büsgenweg 2, 37077, Göttingen, Germany

4 Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy

5 Plant Protection Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy

6 NEIKER-Tecnalia, Dpto Biotecnologia, PO Box 46, Vitoria-Gasteiz, 01080, Spain

7 Unidad de Genética Ecológica y Mejoramiento Forestal, INTA EEA Bariloche, Bariloche, CC277 8400, Argentina

8 CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy

9 ALTERRA Wageningen UR, PO Box 47, Wageningen, 6700 AA, The Netherlands

10 INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France

11 New address: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA

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Citation and License

BMC Plant Biology 2012, 12:153  doi:10.1186/1471-2229-12-153

Published: 29 August 2012



Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species.


We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype.


This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.