Brassica species are characterized by their tremendous intraspecific diversity, exemplified by leafy vegetables, oilseeds, and crops with enlarged inflorescences or above ground storage organs. In contrast to potato tubers that are edible storage organs storing energy as starch and are the vegetative propagation modules, the storage organs of turnips, grown from true seed, are swollen hypocotyls with varying degrees of root and stem that mainly store glucose and fructose. To highlight their anatomical origin, we use the term “hypocotyl-tuber” for these turnip vegetative storage organs. We combined cytological, physiological, genetic and transcriptomic approaches, aiming to identify the initial stages, molecular pathways and regulatory genes for hypocotyl-tuber induction in turnips (B. rapa subsp. rapa). We first studied the development of the hypocotyl zone of turnip and Pak choi and found that 16 days after sowing (DAS) morphological changes occurred in the xylem which indicated the early tuberization stage. Tissue culture experiments showed a clear effect of auxin on hypocotyl-tuber growth. Differentially expressed genes between 1 and 6 weeks after sowing in turnip hypocotyls, located in genomic regions involved in tuber initiation and/or tuber growth defined by QTL and selective sweeps for tuber formation, were identified as candidate genes that were studied in more detail for their role in hypocotyl-tuber formation. This included a Bra-FLOR1 paralogue with increased expression 16 DAS, when the hypocotyl starts swelling, suggesting dual roles for duplicated flowering time genes in flowering and hypocotyl-tuber induction. Bra-CYP735A2 was identified for its possible role in tuber growth via trans-zeatin. Weigthed Co-expression Network Analysis (WGCNA) identified 59 modules of co-expressed genes. Bra-FLOR1 and Bra-CYP735A2 were grouped in a module that included several genes involved in carbohydrate transport and metabolism, cell-wall growth, auxin regulation and secondary metabolism that serve as starting points to illuminate the transcriptional regulation of hypocotyl-tuber formation and development., Turnips: “Neeps” show early differences from non-tuber–forming relative Turnips show physiological and molecular signs of hypocotyl-tuber development as early as 16 days after sowing, a finding that could help farmers improve the performance of this important food and feed crop. A team led by Guusje Bonnema from Wageningen University and Research in the Netherlands compared the early anatomy of turnips and another closely related subspecies of Brassica rapa, the non-tuber–forming pak choi. They documented differences in the cellular organization of the xylem by day-16 after seed planting. Gene expression profiling between 1–6 weeks after sowing revealed many genes involved in hypocotyl-tuber initiation and growth. These genes affect a range of biological processes, from carbohydrate transport and metabolism to cell-wall growth to hormone regulation. Tissue culture experiments also showed that auxin, a plant growth hormone, promoted early hypocotyl-tuber development.