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

BMC Genomics High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L Rgine Delourme Cyril Falentin Berline Fopa Fomeju Marie Boillot Gilles Lassalle Isabelle Andr Jorge Duarte Valrie Gauthier Nicole Lucante Amandine Marty Maryline Pauchon Jean-Philippe Pichon Nicolas Ribire Gwenn Trotoux Philippe Blanchard Nathalie Rivire Jean-Pierre Martinant Jrme Pauquet 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. - Background Genetic linkage maps are highly valuable tools for comparative genome analyses and the identification of genomic regions carrying major genes and quantitative trait loci (QTL) controlling agronomical traits. They are a prerequisite for further map-based cloning or marker-assisted breeding programs. In recent years, the establishment of genetic maps have benefited from the development of new types of molecular markers which take advantage of automated sequencing and genotyping technologies. * Correspondence: 1INRA, UMR1349 IGEPP, BP35327, Le Rheu cedex 35653, France Full list of author information is available at the end of the article While the first marker-based genetic maps were built with restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs), dense genetic maps now include simple sequence repeats (SSRs) and more recently single nucleotide polymorphisms (SNPs). Dense genetic maps based on sequence-derived markers allow finer comparative genome analyses to be performed based on comparisons with sequenced related genomes and to accelerate the process of map-based cloning of major genes and QTL. They are also very useful tools to assist sequence assembly in whole de novo genome sequencing projects [1-3]. Moreover, by integrating genetic map data with genotyping data generated from collections of accessions/varieties linkage disequilibrium (LD) pattern along the genome of a given species can be investigated, which is a prerequisite for precise genome wide association studies (GWAS). GWAS performed with a large number of SNPs have been reported in a number of crop species such as maize [4,5], Arabidopsis [6], barley [7-11], and rice [12-15] The success of GWAS to locate genes responsible for complex traits depends on the extent of LD, the number, the distribution and the diversity of markers and the underlying structure in the studied collections. Since the diversity of markers and the extent of LD may vary depending on the history of the collections [7,15], they should be investigated prior to GWAS design. Oilseed rape (Brassica napus) is a prominent oilseed crop in most world continents including America, Europe, Australia and Asia and is cultivated for food (oil) and feed (meal) as well as for non-food uses such as biofuels or lubricants. It is the second world oil crop after soybean (http://faostat3.fao.org/home/index.html; May 2011) with a world production of more than 60 million tonnes per year. B. napus is an amphidiploid species (AC genome, n = 19) that arose from hybridization between B. rapa (A genome, n = 10) and B. oleracea (C genome, n = 9) diploid species [16] within the past 10,000 years [17]. B. napus includes spring and winter oilseed rape, rutabaga or swede, and some fodder crops. It likely originated from a few interspecific hybridization events [18] and has only a short domestication history of about 400500 years [17,19]. For these reasons, the genetic diversity within B. napus germplasm is rather low compared to that of its two progenitor species B. rapa and B. oleracea. Moreover, two bottlenecks have occurred during breeding of modern oilseed rape varieties through the selection for low erucic acid content in the oil and low glucosinolate content in the seeds, which reduced the genetic diversity in modern varieties [20]. Over the last 20 years, many genetic B. napus maps have been built, which have been progressively integrating various types of markers [21-27]. These maps have been used for genetic studies of various agronomical traits including development traits [28,29], seed quality [30-34], yield components [35-38] and disease resistance [39-44] as well as for genetic study of chromosome pairing [45]. The establishment of genetic maps of diploid and amphidiploid Brassica species, and their comparison and alignment to Arabidopsis genome sequence provided insights into Brassica genome organization and evolution after the different rounds of polyploidization and diploidization occurring in these species history. Extensive collinearity observed between A. thaliana and B. napus led to the description of a genomic block system determined by Parkin et al. [21], who demonstrated that the structure of the Brassica A and C genomes could be described with approximately 21 conserved blocks. A framework built of 24 genomic blocks (A-X) within the ancestral karyotype was then proposed that represents an extension of the above mentioned study [46]. This conserved block structure was then further investigated in related species such as B. juncea [47] or B. oleracea [48] and led to a block arrangement comparison in the A, B and C genomes [49]. It was also recently confirmed in B. napus using dense genetic maps with SSR [27], and SNP [50] markers. The availability of high numbers of markers now makes it possible to investigate more precisely genome wide diversity and the extent of LD in oilseed rape ( (...truncated)