biostudies-literatureUnknown129(10)Clarke WE<h4>Key message</h4>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 mateTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik1887-99https://www.ebi.ac.uk/biostudies/studies/S-EPMC5025514biostudies-literatureA 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.PMC5025514Wieseke RSidebottom CPauquet JIniguez-Luy FStich BParkin IAClarke WELaga BGanal MWBatley JLawley CTSnowdon RJLi RSharpe AGPlieske JHiggins EECheung WEdwards DDyrszka ERae SMeng JKhedikar YfalseA 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.<h4>Key message</h4>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 mate2016-01-01T00:00:00Z2016 Oct2025-05-29T21:27:05.662Z2025-05-29T21:27:05.662ZS-EPMC50255142736491510.1007/s00122-016-2746-7