Infinium 60k snp array

DNA was isolated from the leaves of 480 individuals (~10 individuals per family) according to the protocols of Porebsky et al. [92 (link)] and Doyle and Doyle [93 ]. Genotyping was carried out using the Illumina Infinium 60K SNP array (Illumina, CA, USA). The markers with a call rate <90% and with a minor allele frequency (MAF) <0.05 were discarded from the genotypic data matrix. Missing data were imputed using the LD-kNNi method in TASSEL v.5.2 [94 (link)]. A total of 3879 SNPs were retained and subsequently used for the GWAS and pleiotropy studies.

An Illumina Infinium 60k SNP array developed for B. napus (http://www.illumina.com), carrying 52,157 SNPs across the 19 A- and C-genome chromosomes, was used for genotyping. Hybridization protocols were run as per manufacturer’s specifications for all samples in the population and controls (parent species). The chips were scanned using Illumina HiScanSQ. Genotypic data were visualized using Genome Studio v.2011.1 (Illumina, Inc., San Diego, CA). Single nucleotide polymorphisms were filtered in Genome Studio to retain genome-specic SNPs. Polymorphic SNP markers were distributed evenly across all 19 B. napus chromosomes. SNPs that did not show three clear genotype clusters (AA, AB, BB) in the population were removed. As the available SNP chip was designed for A- and C-genomes it could not be used directly to score B-genome chromatin substitutions. All SNPs giving >20% hetero calls (AB), >10% no calls (NC), or cross-amplifying the B-genome of B. nigra/B. carinata were removed. Finally, 1458 A-genome and 1936 C-genome SNPs (a total of 3394) were retained. NCs were recorded for many SNPs in several regions of ILs. Strings of NCs ≥3 Mb were color coded and treated as B-genome introgressions. All the preexisting A–C translocations in recipient B. napus genotypes were not included in the introgression count.