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To investigate the effect of low light (LL, 50% natural light) during grain filling (GF) stage on rice transamination, amino acid (AA) accumulation, nutritional value, and cooking quality in three different rice genotypes, transaminase activities and AA levels in grains during GF stage and the traits that significantly affected rice quality (physical appearance, cooking quality, and nutritional value) were analyzed. LL did not disturb transamination in rice grains during GF stage, as minimal impact was found on alanine and aspartate transaminase activities. Nevertheless, most AAs in caryopses, including lysine and threonine, increased in response to LL, except for sulfur-containing AAs. These results suggest that AA metabolism and accumulation in rice grains were rarely suppressed by LL during GF stage. Rice nutritional ingredients at harvest, such as major protein components including glutelin and most important essential amino acids (EAAs) including lysine and threonine, increased significantly in response to LL, whereas most protein and EAA ratios were rarely affected. However, LL markedly affected physical appearance of rice grains by reducing brown rice rate, milled rice rate, and 1000-grain weight and increasing the chalkiness rate. In addition, cooking qualities decreased in response to LL, while breakdown values and amylose levels decreased and setback values increased. We concluded that LL during GF stage decreased the cooking quality of rice, but could potentially improve the nutritional value of rice. [ABSTRACT FROM AUTHOR]