Brassica 60k array

The KN DH population was genotyped using the Brassica 60K array (Illumina Inc., USA) following the manufacturer’s protocol [53 (link)]. The genotyping data were scanned and exported by the Genome Studio software (Illumina Inc., USA). All SNP probe sequences were subject to BLAST analysis against the ZS11 reference genome [25 (link)]. Subsequently, SNP probe sequences were screened with the following criteria: (1) filter out the sequences with lengths of less than 50 bp; (2) only include the cases where the sequence identification values were 100%; (3) remove uncertain chromosome SNPs; (4) polymorphic SNPs were used for genotyping.

The genotyping data from the Illumina Brassica 60K array were visualized using Genome Studio V2011.1 (Illumina, Inc., San Diego, CA), and processed with a manually adapted cluster file. The positions on the B. napus chromosomes of the SNP markers present on the array were obtained by blasting the 52,157 sequence contexts against the B. napus cv. Darmor reference genome sequence assembly (version 4.1: Chalhoub et al. 2014 (link)). Only the BLAST hits with a minimum of 90% global overlap and 90% identity were retained. Subsequently, only markers presenting no more than one BLAST hit on each subgenome were kept, enabling SNPs with the potential to hybridize at paralogous regions to be discarded.