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Genetic models for polyploid crop adaptation provide important information relevant for future breeding prospects. A well-suited model is  Brassica napus , a recent allopolyploid closely related to  Arabidopsis thaliana . Flowering time is a major adaptation trait determining life cycle synchronization with the environment. Here we unravel natural genetic variation in  B. napus  flowering time regulators and investigate associations with evolutionary diversification into different life cycle morphotypes. Deep sequencing of 35 flowering regulators was performed in 280 diverse  B. napus  genotypes. High sequencing depth enabled high-quality calling of single-nucleotide polymorphisms (SNPs), insertion-deletions (InDels) and copy number variants (CNVs). By combining these data with genotyping data from the Brassica 60 K Illumina® Infinium SNP array, we performed a genome-wide marker distribution analysis across the 4 ecogeographical morphotypes. Twelve haplotypes, including  Bna.FLC.A10, Bna.VIN3.A02  and the  Bna.FT  promoter on C02_random, were diagnostic for the diversification of winter and spring types. The subspecies split between oilseed/kale ( B. napus  ssp.  napus ) and swedes/rutabagas ( B. napus  ssp.  napobrassica ) was defined by 13 haplotypes, including genomic rearrangements encompassing copies of  Bna.FLC, Bna.PHYA  and  Bna.GA3ox1. De novo  variation in copies of important flowering-time genes in  B. napus  arose during allopolyploidisation, enabling sub-functionalisation that allowed different morphotypes to appropriately fine-tune their lifecycle.

Post-polyploidisation morphotype diversification associates with gene copy number variation