Comparative mapping in the Fagaceae and beyond with EST-SSRs

Oliver Gailing,Emilie Chancerel,Giovanni G Vendramin,Carolina Soliani,Guy Roussel,Jerome Salse,Fiorella Villani,Christophe Plomion,Hans Peter Koelewijn,Antoine Kremer,Jerome Durand,Florent Murat,Francesca Bagnoli,Pablo G Goicoechea,Catherine Bodénès,Florian Alberto,Claudia Mattioni,Christophe Boury

doi:10.1186/1471-2229-12-153

Abstract

BackgroundGenetic 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.ResultsWe 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.ConclusionsThis 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.

Highlights

Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning
Functional annotation of EST-Simple sequence repeats (SSRs) We identified more than 52,834 EST-SSRs among the Quercus ESTs [33]
We identified 35, 7 and 19 gene categories, at “level 3”, within the biological process (BP), cell compound (CC) and molecular function (MF) classes, respectively (Additional file 4)

Summary

Introduction

Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. Genetic linkage maps constitute an ideal framework for studies of the genetic architecture of quantitative traits [1,2] and genome evolution [3,4] They are a prerequisite for map-based gene cloning [5,6,7] and for the ordering of physical scaffolds in genome sequencing projects [8]. Simple sequence repeats (SSRs) are the markers of choice, because they are reproducible, abundant in the genome and they provide highly polymorphic information and are readily transferable between phylogenetically related species [10]. SSRs are easy to handle and, once developed, are cost-effective markers for high-throughput genotyping

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