Large-scale motions (LSMs) with length scale greater than 3h (h is water depth) in turbulent open-channel flows (OCFs) have been found in flume experiments and play an essential role in understanding sediment dynamics. A recently developed DNS solver called CP3d was employed to study LSMs in rough-bed OCFs. Turbulence-sediment interactions are handled by DNS-DEM-IBM coupling method. The computational domain is 2 m long and 0.02 m high, which is discretized by 8.4 billion uniform grids. The flow slope is 0.38%, and bulk Reynolds number is around 7,400. The roughness bed is formed by 2.2 million spherical particles with a diameter 1 mm. When the roughness is fixed, compared with the smooth bed cases, the total velocity fluctuation intensities nearly unchanged far away from the bed, while the intensities are redistributed among different scales: the intensities near the peak of very-large-scale motion (around 20h) are damped, while the fluctuations of wavelength larger than 30h are slightly strengthened. Besides, LSMs contribute more than 65% of the total particle torque fluctuation and 50% of the particle streamwise force fluctuation, which implies the non-local feature of the fluid-induced forces. After bed particles are released, the general flat rough bed develops gradually into a ripple-like bedform. The pre-multiplied spectra profiles of streamwise and wall-normal velocities show peaks near the mean wavelength of ripples, and the fluctuation intensities with wavelengths within 10h to 30h are further decreased. It is concluded that rough bed alters the LSMs and LSMs in turn obviously impact the development of bedforms.