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

Published: 29 August 2012

Additional files

Additional file 1:

Description of SSR markers (locus name, forward and reverse primers, EST sequences, accessions number).

Format: XLSX Size: 96KB Download file

Open Data

Additional file 2:

Description of location of the Q. robur and Q. petraea individuals used for diversity analyses.

Format: DOCX Size: 13KB Download file

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Additional file 3:

Map of the populations location of Q. faginea and Q; pyrenaica used for the diversity analyses.

Format: JPEG Size: 57KB Download file

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Additional file 4:

Description of the SSCP method implemented on a Licor DNA sequencer.

Format: DOCX Size: 12KB Download file

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Additional file 5:

Comparison of Gene Ontology classification between the four sets of sequences containing EST-SSRs (CR: Coding Region, NCR: Non Coding Region, 5’UTR: 5’ Un-Transcribed Region, 3’UTR: 3’ Un-Transcribed Region. The relative frequencies of GO hits for oak sequences are assigned to the GO functional categories (Cellular Compounds, Molecular Function and Biological Process.

Format: DOCX Size: 18KB Download file

Open Data

Additional file 6:

Clustering of Blast2GO categories using the four sets of sequences containing EST (CR: Coding Region, NCR: Non Coding Region, 5’UTR: 5’ Un-Transcribed Region, 3’UTR: 3’ Un-Transcribed Region).

Format: DOCX Size: 198KB Download file

Open Data

Additional file 7:

Number of loci per LG for the five pedigrees (in () data for two partial linkage group, acc: accessory markers, tot: total number of markers).

Format: DOCX Size: 19KB Download file

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Additional file 8:

Map length in cM of the ten parental maps (in () are written the values obtained for two partial linkage groups).

Format: DOCX Size: 20KB Download file

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Additional file 9:

Estimation of genome length in cM for LOD score ranging from 3 to 5.

Format: DOCX Size: 13KB Download file

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Additional file 10:

Transferability results for EST-SSR loci tested on Castanea sativa, Fagus sylvatica, Quercus faginea, Q. pyrenaica, Q. ilex, Q. suber, Nothofagus pumilio and N. antartica.

Format: XLSX Size: 25KB Download file

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Additional file 11:

Linkage groups homology between Castanea and Quercus.

Format: PDF Size: 263KB Download file

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Additional file 12:

Diversity results for Quercus robur , Q. petraea; Q. faginea and Q. pyrenaica (LG: Linkage group, AR: allelic richness, Ho: observed heterozygosity, He: expected heterozygosity).

Format: XLSX Size: 38KB Download file

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Additional file 13:

List of the all mapped SNPs, annotation and map location.

Format: XLSX Size: 31KB Download file

Open Data