The main objective of this research was to identify quantitative trait loci associated with rice qualities to provide reliable information for marker-assisted selection and development of new varieties. In total, 120 doubled haploid (DH) lines developed by another culture from the F₁ hybrid of a cross between “Cheongcheong”, a Tongil variety, and “Nagdong”, a japonica variety, were used. A microsatellite linkage map of 222 markers spanned 2082.4 centimorgans (cM) and covered 12 rice chromosomes with an average interval of 9.4cM between markers. Eight quantitative trait loci (QTLs) were associated with rice quality, consisting of two QTLs on chromosomes 1 and 9 for amylose content; three QTLs on chromosomes 8, 9, and 10 for protein content; and three QTLs on chromosomes 2, 3, and 6 for lipid content. PCR expression levels measured using the SSR markers RM23914 for proteins and RM6266 for lipids, and RM586 showed a higher degree of amplification. The present study should be useful for improving the nutritional quality of rice by means of marker-assisted selection.