Abstract: Vacuolar H⁺-ATPases (V-ATPase) is a multi-subunit enzyme complex found in the tonoplast of eukaryotes. V-ATPase subunitA(VHA) encoded by OsVHA-A1 gene is crucial in the development and tolerance to environmental stress of rice. This study applied a wild type and a purified mutant rice with a single cytosine deletion from its OsVHA-A1 gene to compare the differences of their phenotypes during the entire growth period. The mutant rice senesced at late-growth stage resulting a significant yield reduction as compared to the wild type. The activities of antioxidant enzymes including SOD, POD and CAT of the two isogene rice lines showed differential temporal patterns.The senescence-induced increases on O₂^- production as well as H₂O₂ and MDA contents in the leaves and roots of the mutant rice after booting stage were generally higher than those of the wild type.The performance of the roots tended to be poorer than that of the leaves in the mutant type in comparison with that of the wild type. OsVHA-A1 was significantly down-regulated and the V-ATPase activity significantly declined at grain-filling stage after senescence from seeding stage before senescence for both lines. But the down-regulated OsVHA-A1 expression and reduced V-ATPase activity in the roots and leaves were greater in the mutant rice than those in the wild type. It appeared that OsVHA-A1 played a crucial role in regulating rice senescence.Aside from genetic changes, environmental factors also contributed to the heightened root senescence, as the 16S rDNA sequencing showed that the pathogenic fungi population in the rhizosphere soil increased significantly when the mutant type at its grain-filling stage. In the soil, HPLC analysis identified 5 phenolic acids, i.e., phydroxybenzoic, vanillin, syringate, pcoumaric acid, and ferulic acid. The contents of phydroxybenzoic and pcoumaric acid were extremely significantly lower associated with the mutant than the wild type. It suggested that the pathogens might participate in the process of root senescence. Furthermore, the declined root activity was found correlating with the chlorophyll or photosynthesis decrease in the isogen rice lines after booting stage.It was concluded that the absence of functional OsVHA-A1 directly affected the senescence, whereas the altered underground microbial community further hastened the aging process of the rice plant.