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Background  Some broccoli ( Brassica oleracea  L.  italic ) accessions have purple sepals and cold weather would deepen the purple color, while the sepals of other broccoli lines are always green even in cold winter. The related locus or gene is still unknown. In this study, a high-density genetic map was constructed based on specific locus amplified fragment (SLAF) sequencing in a doubled-haploid segregation population with 127 individuals. And mapping of the purple sepal trait in flower heads based on phenotypic data collected during three seasons was performed.    Results  A genetic map was constructed, which contained 6694 SLAF markers with an average sequencing depth of 81.37-fold in the maternal line, 84-fold in the paternal line, and 15.76-fold in each individual population studied. In all of the annual data recorded, three quantitative trait loci (QTLs) were identified that were all distributed within the linkage group (LG) 1. Among them, a major locus,  qPH.C01–2 , located at 36.393 cM LG1, was consistently detected in all analysis. Besides this locus, another two minor loci,  qPH.C01–4  and  qPH.C01–5 , were identified near  qPH.C01–2 , based on the phenotypic data from spring of 2018.    Conclusion  The purple sepal trait could be controlled by a major single locus and two minor loci .  The genetic map and location of the purple sepal trait of flower heads provide an important foundation for mapping other compound traits and the identification of the genes related to purple sepal trait in broccoli.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1831-x) contains supplementary material, which is available to authorized users.

Construction of a high-density genetic map and identification of loci controlling purple sepal trait of flower head in Brassica oleracea L. italica