The tendency of global MHD models to overestimate the transpolar potential in simulations of strong geomagnetic storms and evidence of an adverse feedback of the ionospheric conductance on the potential suggest that these models lack important physics leading to the conductance enhancement. Farley-Buneman instability in the auroral ionosphere provides this lacking physics. This instability is believed to cause strong anomalous electron heating which affects the ionospheric conductivity. We use an earlier developed model of anomalous electron heating to estimate the ionospheric conductance disturbance as a function of the local electric field. This result is used to modify the ionospheric conductance in the LFM model to study its effect on the simulated transpolar potential. An idealized and a real-case simulations are accomplished. In both cases a considerable drop in the simulated transpolar potential is found. The latter is in a good agreement with AMIE model and DMSP data.