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

BMC Genomics

Research Article

Hans-Peter Koelewijn¹  Antoine de Daruvar²  Cyril Cabané²  Marcello Cherubini³  Claudia Mattioni³  Fiorella Villani³  Oliver Gailing⁴  Florian Alberto⁵  Pierre-Yves Dumoulin⁵  Jérôme Durand⁵  Catherine Bodénès⁵  Erwan Guichoux⁵  Antoine Kremer⁵  Christophe Plomion⁵  Jean-Marc Frigerio⁵  Emilie Chancerel⁵  Saneyoshi Ueno⁶  Ana Herrán⁷  Ziortza Ikaran⁷  Pablo G Goicoechea⁷  Anna Buonamici⁸  Federico Sebastiani⁸  Giovanni Vendramin⁸ 

[1] ALTERRA - Wageningen UR, PO Box 47, 6700, Wageningen, AA, The Netherlands;CBiB - Université Victor Segalen Bordeaux 2 146, rue Léo Saignat, 33076, Bordeaux, France;CNR Istituto di Biologia Agroambientale e Forestale, Porano (TR), 05010, Italy;Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology Göttingen University, Büsgenweg 2, 37077, Göttingen, Germany;School 07 Forest Resources and Environmental Science, Michigan Technological University, 49931, Houghton, Michigan, USA;INRA, UMR1202 BIOGECO, F-33610, Cestas, France;Université de Bordeaux, UMR1202 BIOGECO, F-33610, Cestas, France;INRA, UMR1202 BIOGECO, F-33610, Cestas, France;Université de Bordeaux, UMR1202 BIOGECO, F-33610, Cestas, France;Department of Forest Genetics, Tree Genetics Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, 305-8687, Tsukuba, Ibaraki, Japan;NEIKER, Dpto Biotecnologia, 01080, Vitoria-Gasteiz, Spain;Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy;

关键词: Amplify Fragment Length Polymorphism;    Genomic SSRs;    Amplify Fragment Length Polymorphism Marker;    Trimeric SSRs;    Dimeric SSRs;   

DOI  :  10.1186/1471-2164-11-570

 received in 2009-12-07, accepted in 2010-10-15,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundExpressed 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).ResultsA 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.ConclusionWe 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.

【 授权许可】

Unknown   
© Durand et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.