Grains from cereals contribute an important source of protein to human food, and grain protein content(GPC) is an important determinant of nutritional quality in cereals.Here we show that the quantitative trait locus (QTL) qPC1 in ricecontrols GPC by regulating the synthesis and accumulation of glutelins, prolamins, globulins, albumins and starch.qPC1, encodes a putative amino acid transporterOsAAP6, which functions as a positive regulator of GPC in rice, such that higher expression of OsAAP6is correlated with higher GPC.OsAAP6 greatly enhances root absorption of a range of amino acids and has effects on the distribution of various amino acids.Two common variations in the potential cis-regulatory elements of theOsAAP65-untranslated region seem to be associated with GPC diversity mainly in indica cultivars.Our results represent the first step toward unravelling the mechanism of regulation underlying natural variation of GPC in rice.