The genotype of the association panel was assayed using a Brassica 60K Illumina Infinium SNP array, according to the manufacturer's protocol (Infinium HD Assay Ultra Protocol Guide; Li et al., 2014 (link)). SNP alleles were called using GenomeStudio software v2011.1 (Illumina, Inc., San Diego, CA) with the Genotyping module (v1.9.4).
Only SNPs with a percentage of missing data of <10% across all genotypes and a minor allele frequency (MAF) of >0.05 were retained. From 52,157 SNPs in the array, 20,678 SNPs were filtered, and 31,839 were analyzed further. Physical localization of SNPs was assigned using BLASTN searches against the B. napus “Darmor-bzh” reference genome version 4.1, with an E-value cut-off of 1E-5 (Altschul et al., 1997 (link); Chalhoub et al., 2014 (link)). Only SNPs with a maximum bit-score were retained as unique SNPs, and subjected to further analysis.
Only SNPs with a percentage of missing data of <10% across all genotypes and a minor allele frequency (MAF) of >0.05 were retained. From 52,157 SNPs in the array, 20,678 SNPs were filtered, and 31,839 were analyzed further. Physical localization of SNPs was assigned using BLASTN searches against the B. napus “Darmor-bzh” reference genome version 4.1, with an E-value cut-off of 1E-5 (Altschul et al., 1997 (link); Chalhoub et al., 2014 (link)). Only SNPs with a maximum bit-score were retained as unique SNPs, and subjected to further analysis.
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