Genotyping and Genetic Diversity Analysis of Brassica napus

The Brassica 60 K Illumina^® Infinium consortium SNP array [82 (link)] (http://www.illumina.com/technology/beadarray-technology/infinium-hd-assay.html) was used for accessions genotype. SNP data were analyzed using Illumina BeadStudio genotyping software (http://www.illumina.com/) with parameters set as a missing rate ≤ 0.2, heterozygous rate ≤ 0.2, and minor allele frequency (MAF) > 0.05. BLAST was performed to search the probe sequences of these SNPs against the B.napus Darmor-bzh reference genome [34 (link)] with an threshold of e⁻¹⁰. SNPs with merely one matched position in reference genome were used for further analysis. The population structure and relative kinship of the 280 B. napus accessions were analyzed using STRUCTURE v. 2.3.4 and SPAGeDi software, respectively [83 (link)]. The linkage disequilibrium (LD) decay between all SNPs was assessed by TASSEL 4.0 [84 ]. The trait–SNP association was analyzed using mixed linear model (MLM) for both the single repetition and the BLUP [85 (link)]. Marker haplotypes at each associated locus were identified using the four-gamete rule with Haploview software [86 (link)].