Genotyping Brassica F2 Lines with Illumina 60K SNP Array

The Illumina Infinium Brassica 60K SNP Array (Clarke et al., 2016 (link)) was used for genotyping 190 F₂ lines and two parental lines (Supplementary Table 2). Total genomic DNA was extracted using DP321-03 DNA extraction kits (Tiangen, Beijing, China). SNP genotyping was performed in the National Key Laboratory of Crop Genetic Improvement, National Subcenter of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China, according to the Infinium HD Assay Ultra manual protocols. Illumina HiSCAN scanner was used for imaging the hybridized chips. GenomeStudio v2011 (Illumina, Inc.) genotyping software was used for allele calling. SNP markers were named using the SNP plus index numbers assigned by GenomeStudio from the chip information (Clarke et al., 2016 (link)), followed by chromosome number. SNP positions were obtained by BLAST search (e ≤ 1e−50) against the B. napus genome reference Darmor v4.1 (Chalhoub et al., 2014 (link)).