title: High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L.
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.
authors: INRA, UMR1349 IGEPP, BP35327, 35653, Le Rheu cedex, France. Regine.Delourme@rennes.inra.fr
authors: Régine
authors: R
authors: Delourme
authors: Cyril
authors: C
authors: Falentin
authors: Berline Fopa
authors: BF
authors: Fomeju
authors: Marie
authors: M
authors: Boillot
authors: Gilles
authors: G
authors: Lassalle
authors: Isabelle
authors: I
authors: André
authors: Jorge
authors: J
authors: Duarte
authors: Valérie
authors: V
authors: Gauthier
authors: Nicole
authors: N
authors: Lucante
authors: Amandine
authors: A
authors: Marty
authors: Maryline
authors: M
authors: Pauchon
authors: Jean-Philippe
authors: JP
authors: Pichon
authors: Nicolas
authors: N
authors: Ribière
authors: Gwenn
authors: G
authors: Trotoux
authors: Philippe
authors: P
authors: Blanchard
authors: Nathalie
authors: N
authors: Rivière
authors: Jean-Pierre
authors: JP
authors: Martinant
authors: Jérôme
authors: J
authors: Pauquet
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D002874:Chromosome Mapping; D008040:Genetic Linkage; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics