Brassica 60k infinium hd assay snp arrays

Genotyping of the 521 accessions was performed with Brassica 60K Illumina Infinium^® HD Assay SNP arrays (Illumina Inc., San Diego, CA) in accordance with the manufacturer’s protocol. For quality control, SNPs with an AA or BB frequency equal to zero, a missing rate >0.2, a heterozygous rate >0.2 and a MAF ≤ 0.05 were excluded. For the physical localization of SNP markers, the probe sequences of 52 157 SNPs were used to perform a BlastN (Altschul et al., 1990) query against the B. napus ‘Darmor‐bzh’ reference genome version 4.1 (Chalhoub et al., 2014). Only, the top BLAST hits in accordance with an e‐value threshold of e‐10 were considered mapped in the genome. SNPs with multiple or unknown chromosomal locations were also excluded. After the filtering process was performed, 521 accessions with 23 168 SNPs and 366 accessions with 23 426 SNPs remained for further analysis.

The young leaves from the representative plants of all accessions were collected, and extracted their genomic DNAs using a modified cetyltrimethyl ammonium bromide (CTAB, Murray and Thompson, 1980 (link)) method. SNP genotyping of 472 accessions was performed using Brassica 60K Illumina Infinium^® HD Assay SNP arrays by Emei Tongde, Co. (Beijing) according to the manufacturer’s protocol². The quality control process of SNP array genotyping data was the same to our previous study (Li et al., 2014 (link)). The LD was calculated using the software TASSEL3.0 (Bradbury et al., 2007 (link)). The principal component analysis (PCA), population structure and kinship were analyzed by Li et al. (2014) (link). To confirm the physical position of each SNP, the probe sequences of 26,841 high-quality SNPs previously selected (Li et al., 2014 (link)) were used to perform a BlastN search against the B. napus (Darmor-bzh) reference genome by Li et al. (2016) (link). Only the top blast hits were considered to be mapped in the genome with an E-value threshold of 1E–15, and blast matches to multiple loci with the same top E-value were not considered to be mapped successfully. Totally, 19,945 SNPs were assigned to B. napus chromosomes.