To analyze the function of SYNC1, an Arabidopsis asparaginyl-tRNA synthetase gene, the FOX-hunting system using super-growing roots (SR) from the legume species Lotus corniculatus was employed. One transformed line, FSL#121, was compared to parental SR and to an SR line harboring the empty vector (Control), all of which were grown in vivo using vermiculite pots. The level of several free amino acids was higher in FSL#121 than SR. Concomitantly, FSL#121 had a distinct phenotype of greater shoot length, stem diameter and shoot fresh weight compared with SR. Also, the root length, root diameter and fresh root weight were greater in FSL#121 than SR. Furthermore, the greater number of nodules in FSL#121 increased the nitrogen fixation activity per whole plant. Therefore, SYNC1 overexpression caused distinct changes in plant growth, increased the number of root nodules, and may be involved in increasing the amount of free amino acids, especially asparagine.