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High-density SNP genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns population structure and linkage disequilibrium (LD).In this study we used the Brassica 60kSNP Illumina consortium array to assess the genetic diversity,population structure and the extent of LD and haplotype blocks in a diverse panel of 203 Chinese semi-winter rapeseed inbred lines.