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Elongation of seminal and lateral roots of rice seedlings was markedly inhibited by high ammonium levels in growth medium. However, high exogenous nitrate concentrations had little inhibitory effect on root growth. The objective of this study was to elucidate the relationship between inhibition of rice root growth induced by high ammonium conditions and ammonium assimilation in the seedlings. Activity of glutamine synthetase (GS) was kept at a low level in the seminal roots of the seedlings grown under high nitrate levels. In contrast, high ammonium levels significantly enhanced the GS activity in the roots, so that Gln abundantly accumulated in the shoots. These results indicate that ammonium assimilation may be activated in the seminal roots under high ammonium conditions. Application of methionine sulfoximine (MSO), an inhibitor of GS, relieved the repression of the seminal root elongation induced by high ammonium concentrations. However, the elongation of lateral roots remained inhibited even under the same condition. Furthermore, MSO drastically increased ammonium level and remarkably decreased Gln level in the shoots grown under high ammonium conditions. These results show that, for rice seedlings, an assimilatory product of ammonium, and not ammonium itself, may serve as an endogenous indicator of the nitrogen status involved in the inhibition of seminal root elongation induced by high levels of exogenous ammonium.