SummaryA simple protocol for in vitro mass propagation of apple rootstock M.9 EMLA has been developed using an automated, low-cost bioreactor system. Comparative studies between semi-solid agar and bioreactor culture (continuous immersion with net and temporary immersion in liquid media using ebb and flood, with and without air exchanges inside the bioreactor chamber) revealed that shoot multiplication and growth were more efficient in continuous immersion (with net) bioreactor culture. Although the multiplication rate was highest in continuous immersion culture, a large number of micropropagated apple shoots showed symptoms of hyperhydricity. In case of temporary immersion culture (ebb and flood system) hyperhydricity was reduced as compared with continuous immersion. The percentage of shoots with hyperhydric leaves could be further reduced by air exchanges made over the culture period in a temporary immersion culture (ebb and flood) in air-lift-balloon type bubble bioreactor (BTBB). In vitro nodal cuttings of apple rootstock M.9 EMLA from bioreactor culture were hydroponically cultured for 30 d and more than 90% plants were rooted and acclimatized successfully. To assess the genetic fidelity of plantlets regenerated from nodal explants during bioreactor culture, the RAPD patterns were compared with that of greenhouse grown control plantlet and revealed genetic uniformity of the regenerants.