A large genetic variability was observed in the shoot NO(3) (-) content of recombinant inbred lines (RILs) of Lotus japonicus. To determine the cause of this variability, we have studied some aspects of nitrate uptake and assimilation in the two parental ecotypes (Gifu and Funakura) and four representatives of the RILs population differing both in their shoot biomass and shoot NO(3) (-) content. Higher shoot NO(3) (-)content was mainly due to an increase in the uptake of the ion regardless of the plant biomass production. The positive correlation observed between the shoot NO(3) (-) content and the steady state level of mRNA encoding high affinity NO(3) (-) transporters suggests that the higher NO(3) (-) influx is due to enhanced expression of the transporters. In contrast, neither the level of nitrate reductase mRNA, nor the potential enzyme activity in vivo in the different lines was correlated with the shoot NO(3) (-) content. This indicates that NO(3) (-) transport in Lotus is one of the main checkpoints controlling shoot NO(3) (-) accumulation. In addition, this study shows that at least in Lotus, it is possible, through breeding strategies, to lower the NO(3) (-) content without affecting biomass production.