The cluster file for B. napus was generated at AAFC through analysis of 437 genotypes and at TraitGenetics through the analysis of 432 genotypes. The cluster files for B. oleracea and B. rapa were generated with 129 and 121 samples, respectively. In both laboratories, DNA was extracted from young leaf tissue of greenhouse grown plants using a cetyltrimethylammonium bromide (CTAB)-based method (Murray and Thompson 1980 (link)). DNA was quantified and 200 ng were hybridised to the Brassica 60 K Infinium array as described in the manufacturer’s protocol (Illumina Inc., San Diego, CA). The arrays were scanned using an Illumina HiScan or BeadArray Reader, and SNP data were analysed using the Genotyping module of the GenomeStudio software package with the setting for the No Call threshold set to 0.05.
Clarke W.E., Higgins E.E., Plieske J., Wieseke R., Sidebottom C., Khedikar Y., Batley J., Edwards D., Meng J., Li R., Lawley C.T., Pauquet J., Laga B., Cheung W., Iniguez-Luy F., Dyrszka E., Rae S., Stich B., Snowdon R.J., Sharpe A.G., Ganal M.W, & Parkin I.A. (2016). 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. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 129(10), 1887-1899.
Other organizations :
Agriculture and Agri-Food Canada, National Research Council Canada, University of Western Australia, Huazhong Agricultural University, Illumina (United States), Bayer (Belgium), Agriaquaculture Nutritional Genomic Center, Max Planck Institute for Plant Breeding Research, University of Giessen
Genotyping platform (Brassica 60 K Infinium array)
Scanning method (Illumina HiScan or BeadArray Reader)
SNP data analysis (GenomeStudio software, No Call threshold set to 0.05)
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