Main conclusionDysfunctional mutation of OsNDPK4 resulted in severe defects in root development of rice. However, the resistance of Osndpk4 against bacterial blight was significantly enhanced.AbstractNucleoside diphosphate kinases (NDPKs) are an evolutionarily conserved family of important enzymes balancing the energy currency nucleoside triphosphates by catalyzing the transfer of their phosphate groups. The aim of this study was to elucidate the function of OsNDPK4 in rice. A dysfunctional rice mutant was employed to characterize the function of OsNDPK4. Its expression and subcellular localization were examined. The transcriptomic change in roots of Osndpk4 was analyzed by RNA-seq. The rice mutant Osndpk4 showed severe defects in root development from the early seedling stage. Further analysis revealed that meristematic activity and cell elongation were significantly inhibited in primary roots of Osndpk4, together with reduced accumulation of reactive oxygen species (ROS). Map-based cloning identified that the mutation occurred in the OsNDPK4 gene. OsNDPK4 was found to be expressed in a variety of tissues throughout the plant and OsNDPK4 was located in the cytosol. Osndpk4 showed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and up-regulation of pathogenesis-related marker genes. In addition, transcriptomic analysis showed that OsNDPK4 was significantly associated with a number of biological processes, including translation, protein modification, metabolism, biotic stress response, etc. Detailed analysis revealed that the dysfunction of OsNDPK4 might reorchestrate energy homeostasis and hormone metabolism and signalling, resulting in repression of translation, DNA replication and cell cycle progression, and priming of biotic stress defense. Our results demonstrate that OsNDPK4 plays important roles in energy homeostasis, development process, and defense responses in rice.