Open Access Highly Accessed Research article

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Jérôme Durand12, Catherine Bodénès12, Emilie Chancerel12, Jean-Marc Frigerio12, Giovanni Vendramin3, Federico Sebastiani3, Anna Buonamici3, Oliver Gailing45, Hans-Peter Koelewijn6, Fiorella Villani7, Claudia Mattioni7, Marcello Cherubini7, Pablo G Goicoechea8, Ana Herrán8, Ziortza Ikaran8, Cyril Cabané9, Saneyoshi Ueno1102, Florian Alberto12, Pierre-Yves Dumoulin12, Erwan Guichoux12, Antoine de Daruvar9, Antoine Kremer12 and Christophe Plomion12*

Author Affiliations

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

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

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

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

5 School 07 Forest Resources and Environmental Science, Michigan Technological University, Houghton 49931, Michigan, USA

6 ALTERRA - Wageningen UR, PO Box 47, Wageningen, 6700 AA, The Netherlands

7 CNR Istituto di Biologia Agroambientale e Forestale, Porano (TR), 05010, Italy

8 NEIKER, Dpto Biotecnologia, Vitoria-Gasteiz, 01080, Spain

9 CBiB - Université Victor Segalen Bordeaux 2 146, rue Léo Saignat, 33076 Bordeaux, France

10 Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan

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BMC Genomics 2010, 11:570  doi:10.1186/1471-2164-11-570

Published: 15 October 2010

Additional files

Additional file 1:

Table S1. Occurrence of non-redundant SSRs in the oak unigene, according to the SSR motif and number of repeats.

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Additional file 2:

Table S1. Characteristics of the Quercus EST-SSRs.

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Additional file 3:

Table S1. SSR database.

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Additional file 4:

Table S1. Transferability of dinucleotide EST-SSRs from oak to chesnut.

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Additional file 5:

Table S1. Segregation, bin and map position of Quercus gSSRs and EST-SSRs.

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Additional file 6:

Figure S1. A macrosynteny map for oak based on 55 intercross SSRs. In black: framework markers (AFLP, RAPD), in red: EST-SSRs, in blue: gSSRs. Bold types indicate fully informative SSRs. Female linkage groups on the left (F), male linkage group on the right (M).

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Additional file 7:

Figure S1 Location of EST-SSRs based on FrameDP (a), ESTscan (b) and structural annotation (c) for a set of 4,664 poplar genes. Methods. 1. 4,664 full-length cDNA sequences of poplar, downloaded from Genbank. 2. SSRs searched using mreps program with default parameters. 3. Coding sequences estimated by FrameDP and ESTScan. A matrix based on Arabidopsis CDS was used for ESTScan. 4. SSR location (coding or non-coding) inferred by combining FrameDP and mreps results (Figure S1a) and ESTScan and mreps results (Figure S1b). SSR locations were also determined using mreps results and structural annotation for the corresponding cDNA (Figure S1c). Results. Figure S1a: SSR location based on the estimation by FrameDP. Figure S1b: SSR location based on the estimation by ESTScan. Figure S1c: SSR location based on structural annotation.

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Additional file 8:

Figure S1. Schematic representation of the bin mapping strategy.

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