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

Régine Delourme (1) , Cyril Falentin (1) , Berline Fopa Fomeju (1) , Marie Boillot (2) , Gilles Lassalle , Isabelle André (3) , Jorge Duarte (3) , Valérie Gauthier (4) , Nicole Lucate (3) , Amandine Marty (2) , Maryline Pauchon (4) , Jean-Philippe Pichon (3) , Nicolas Ribière (3) , Gwenn Trotoux (1) , Philippe Blanchard (2) , Nathalie Rivière (3) , Jean-Pierre Martinant (4) , Jérôme Pauquet (3)

1 IGEPP - Institut de Génétique, Environnement et Protection des Plantes
2 Euralis Semences
3 BIOGEMMA
4 Limagrain

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. 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 2250cM, 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.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

Mots clés: Colza; carte génétique; marqueurs SNP; brassica napus

Domaines: Sciences agricoles; Biologie végétale

Régine Delourme, Cyril Falentin, Berline Fopa Fomeju, Marie Boillot, Gilles Lassalle, et al.. High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics, 2013, 14, pp.120. ⟨10.1186/1471-2164-14-120⟩. ⟨hal-01208606⟩