title: A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome.
abstract: The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Wayne E
authors.initials: WE
authors.lastname: Clarke
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Erin E
authors.initials: EE
authors.lastname: Higgins
authors.affiliation: TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.
authors.forename: Joerg
authors.initials: J
authors.lastname: Plieske
authors.affiliation: TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Wieseke
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada.
authors.forename: Christine
authors.initials: C
authors.lastname: Sidebottom
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors.forename: Yogendra
authors.initials: Y
authors.lastname: Khedikar
authors.affiliation: School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.
authors.forename: Dave
authors.initials: D
authors.lastname: Edwards
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Ruiyuan
authors.initials: R
authors.lastname: Li
authors.affiliation: Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA, 92121, USA.
authors.forename: Cynthia Taylor
authors.initials: CT
authors.lastname: Lawley
authors.affiliation: BIOGEMMA 6, chemin des Panedautes, 31700, Mondonville, France.|SYNGENTA France SAS, 346, route des Pasquiers, 84260, Sarrians, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Pauquet
authors.affiliation: Bayer BioScience NV, 9052, Ghent, Belgium.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Laga
authors.affiliation: DNA Landmarks Inc, 84 Rue Richelieu, St-Jean-sur-Richelieu, QC, J3B 6X3, Canada.
authors.forename: Wing
authors.initials: W
authors.lastname: Cheung
authors.affiliation: Genomics and Bioinformatics Unit, Agri Aquaculture Nutritional Genomic Center (CGNA), Conicyt-Regional, Gore La Araucania, R10C1001, Temuco, Chile.
authors.forename: Federico
authors.initials: F
authors.lastname: Iniguez-Luy
authors.affiliation: Syngenta France SAS, 12 Chemin de l'hobit, B.P. 27, 31790, Saint-Sauveur, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Dyrszka
authors.affiliation: Bayer BioScience NV, 9052, Ghent, Belgium.
authors.forename: Stephen
authors.initials: S
authors.lastname: Rae
authors.affiliation: Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Stich
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
authors.forename: Rod J
authors.initials: RJ
authors.lastname: Snowdon
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
authors.affiliation: TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.
authors.forename: Martin W
authors.initials: MW
authors.lastname: Ganal
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. isobel.parkin@agr.gc.ca.
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D004171:Diploidy; D005819:Genetic Markers; D018745:Genome, Plant; D060005:Genotyping Techniques; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D057891:Tetraploidy
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers