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Background   Brassica napus  is an important oilseed crop cultivated worldwide. During domestication and breeding of  B. napus , flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in  B. napus . An F 2  mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type.    Results  Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including  FLC .    Conclusions  These findings demonstrate the effectiveness of the ddRAD approach to sample the  B. napus  genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F 2  populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02756-y.

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus