Flowering is a critical step in plant development. It is induced by various signals produced in response to environmental and endogenous cues, such as photoperiod, temperature or plant age. A master flowering signal is the FLOWERING LOCUS T (FT) protein, which is produced in the leaves and transported through the phloem toward the shoot apical meristem, where it triggers the morphogenesis switch. The biological question examined in this thesis is whether the systemic effect of FT encompasses the roots, coordinating their growth with the aerial part. We used the model species Arabidopsis thaliana (L.) Heynh., where FT shares its function with a paralog, TWIN SISTER OF FT (TSF). In the first part of our work, we designed a hydroponic rhizotron device suitable for growing adult plants of Arabidopsis: Rhizoponics. Using this setup, we observed that a photoperiodic treatment that induces flowering of Col-0 wild type plants also promotes development of the root system. However, this increase also occurs in ft-10 tsf-1 double mutant, thus independently of FT and TSF proteins. In the second part of our work, we analyzed the organization and maintenance of the root apical meristem, and the branching of primary root. Experiments were performed with ft-10 tsf-1 and 35S:FT seedlings grown in vitro, using several reporter genes to study auxin signaling and transport. We observed a higher number of distal stem cell layers in primary root columella of the ft-10 tsf-1 mutant and an increased branching of the primary root in the 35S:FT line. These results suggest that FT/TSF promote cell differentiation at root tip and priming of lateral roots, two processes that are regulated by auxin. We confirmed, using pDR5:GUS and pDR5:GFP reporter genes, that FT/TSF interfere with auxin homeostasis at the primary root tip. The most intriguing result is the absence of the auxin efflux carrier PIN3 in the columella of the primary root in the ft- 10 tsf-1 mutant. This phenotype could not be explained neither by transcriptional repression of PIN3 nor by protein endocytosis. We analyzed different processes where PIN3 modulates auxin flux to induce tissue differential growth, such as gravitropism, phototropism and apical hook development. We observed that the responses of the 35S:FT seedlings were slightly accentuated compared to Col-0, suggesting PIN3 activation by FT.All together, our results indicate that the systemic proteins FT/TSF have an effect on auxin signaling in root tip and could stimulate root branching at floral transition.