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

Abstract

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 full-sib 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.