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Open Access Highly Accessed Research article

High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L

Régine Delourme1*, Cyril Falentin1, Berline Fopa Fomeju1, Marie Boillot2, Gilles Lassalle1, Isabelle André4, Jorge Duarte4, Valérie Gauthier3, Nicole Lucante4, Amandine Marty2, Maryline Pauchon3, Jean-Philippe Pichon4, Nicolas Ribière4, Gwenn Trotoux1, Philippe Blanchard2, Nathalie Rivière4, Jean-Pierre Martinant3 and Jérôme Pauquet4

Author Affiliations

1 INRA, UMR1349 IGEPP, BP35327, 35653, Le Rheu cedex, France

2 Euralis Semences, Domaine de Sandreau, 31700, Mondonville, France

3 Limagrain Europe, Route d’Ennezat, CS3911, 63920, Chappes, France

4 BIOGEMMA, Domaine de Sandreau, 31700, Mondonville, France

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BMC Genomics 2013, 14:120  doi:10.1186/1471-2164-14-120

Published: 22 February 2013

Abstract

Background

High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern.

Results

We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in “00” winter oilseed rape types but this was shown to vary greatly along the linkage groups.

Conclusions

Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.