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

Key messageTheBrassica napusIllumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploidB. napusand its progenitor diploid genomes.AbstractA 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.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2746-7) contains supplementary material, which is available to authorized users.

Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata

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Single R Gene Introgression Lines for Accurate Dissection of the Brassica - Leptosphaeria Pathosystem

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Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

“…Total genomic DNA was extracted from 200 mg leaf material of young leaves of mapping parents and DH lines, using the Qiagen BioSprint 96 DNA Plant Kit (Qiagen GmbH, Hilden, Germany). All samples were subjected to high-density, genomewide SNP genotyping using the Brassica Illumina 60K SNP genotyping array (Clarke et al, 2016). Genotyping was outsourced to TraitGenetics GmbH (Gatersleben, Germany).…”