Genetic dissection of the mechanism of flowering time based on an environmentally stable and specific QTL in Brassica napus

•Dissecting QTLs for flowering time of rapeseed in multiple environments, including the winter, the semi-winter and the spring rape area.•Fifty-five consensus QTLs were identified after combining phenotype and genomic data, including 12 environment-stable QTLs and 43 environment-specific QTLs. Importantly, six major QTLs for flowering time were identified, of which two were considered environment-specific QTLs in spring ecological condition and four were considered environment-stable QTLs in winter and semi-winter ecological conditions.•A putative flowering regulatory network was constructed, including the photoperiod, circadian clock, vernalization, autonomous and gibberellin pathways.•Multiple copies of genes led to functional difference among the different copies of homologous genes, which also increased the complexity of the flowering regulatory networks.