In order to find out better cultivation practices for the environmentally-friendly agriculture, an experiment with four fertilizer levels and one cultivar, Boseokchalbyeo, and three lines, GG-05-03, GG-05-04, and GG-05-07 was carried out. Those lines had selected from native green-kerneled glutinous rice during last five years (2004~2008). The tillering number of both GG-05-03 and GG-05-04 line was similar, but GG-05-07 was less than those. In the plant height, both GG-05-04 and GG-05-07 were higher than Boseokchalbyeo, while GG-05-03 was similar to it. Grain weight and grain number of ear not markedly showed the difference of quantitative character among three lines. 1000-grain weight of all three lines were slightly light as compare with Boseokchalbyeo cultivar. Head rice yield of both GG-05-03 and GG-05-07 lines were less than Boseokchalbyeo, but GG-05-04 line was similar to it. total lipid of all composition of brown rice Only slightly showed different rate as compared with Boseokchalbyeo. In study to evaluate putative changes of genetic diversity and relationships of rice, the primers based on AG and GA, ATG repeats were informative. Out of 4 lines selected for screening, ISSR loci showed 47.5% and 81.2% polymorphism as tested with UBC112 and UBC864 primers. The mRNA level of alanine aminotransferase gene in the leaves of Bosekchalbyeo and GG-05-03, GG-05-04, GG-05-07 were determined by RT-PCR. The mRNA levels of 3g 07570 and 3g 21960, 7g 42600, 9g 26360, 10g 25130 showed different patterns in the leaves of four lines. The level of catalase (CAT) and superperoxide dismutase (SOD), ascrobate peroxidase (APX) mRNA expression were determined by RT-PCR. Further studies on the developmental changes of mRNA levels showed that CAT-b decreased and CAT-C increased in leaves of Boseokchalbyeo and GG-05-07. In Boseokchalbyeo expression of cSOD and tAPX showed the aspect of all increasement. These results suggest that Boseokchalbyeo and GG-05-03, GG-05-04 and GG-05-07 line may differently affect the activity and synthesis of AlaAT and ROS enzyme. These results are summaried as GG-05-07 line was showed better than both GG-05-03 and GG-05-04 line for the environmentally-friendly agriculture practices.