To diversify the grain quality characteristics of Korean varieties of japonica rice (Oryza sativa japonica), recombinant inbred lines were developed from a cross between the Korean cultivar “Boramchan” and the tropical japonica cultivar “Pecos” from the United States. Quantitative trait locus (QTL) analysis was performed to investigate the traits related to grain quality. Sixteen traits were evaluated, including five related to grain appearance, six associated with pasting properties and glossiness of cooked rice, and four related to eating texture. QTLs were detected on chromosomes 3, 5, 6, and 10, and candidate genes, including Hd1, qLTG3-1, GW5, and qGS10 were identified. The heading date-related gene Hd1 was associated with the following traits: head rice (HR), opaque rice (OR), damaged rice, pasting temperature, peak viscosity (PV), breakdown viscosity (BD), and glossiness. Most quality-related traits were influenced by allelic variation at Hd1, and the Hd1⁺ allele from “Boramchan”, which delays heading, positively affected both grain appearance and eating quality. The low-temperature germinability gene qLTG3-1 was identified as a candidate gene for broken rice and several pasting properties, including trough, final, and breakdown viscosities, and was shown to influence pasting characteristics depending on allelic variation. The grain shape gene GW5 was a candidate gene for HR and whiteness, whereas qGS10 was associated with OR, PV, BD, and setback viscosity. The GW5⁺ and qGS10^P alleles, derived from the slender grain shape of “Pecos,” contributed positively to both grain appearance and eating quality, indicating their potential as favorable alleles for improving grain shape and diversifying quality traits in Korean japonica rice. The results of this study demonstrate that key agronomic trait-related genes, such as heading and grain shape, significantly affect various quality-related traits, highlighting the potential of introducing and combining novel alleles to enhance grain quality in Korean japonica rice.

‘Chamdongjin’ is a rice cultivar with a distinctively large grain size and good palatability, similar to ‘Sindongjin,’ which is a mega-cultivar in Korea. ‘Younghojinmi’ is a rice cultivar known for having the highest taste value among premium quality cultivars. In this study, we conducted quantitative trait loci (QTL) analysis of quality-related traits using recombinant inbred lines (RILs) derived from a cross between ‘Chamdongjin’ and ‘Younghojinmi’ to elucidate their genetic interactions. We analyzed 20 traits, including protein content, amylose content, glossiness of cooked rice, 7 traits related to grain appearance, 6 traits related to pasting properties, and 4 traits related to texture. Quality-related QTL were primarily detected on chromosome 3. In particular, GS3, one of the candidate genes for QTL, significantly influenced quality by affecting 14 different traits, including appearance traits such as head rice and the texture of cooked rice. Furthermore, RILs with the gs3 allele, which exhibited the large grains of ‘Chamdongjin,’ showed a lower protein content and higher amylose content than RILs with the GS3 allele. These lines also had lower head rice percentages and higher percentages of whiteness, opacity, and broken rice, indicating an inferior appearance quality. In terms of pasting properties, RILs with the gs3 allele showed a lower pasting temperature, peak viscosity, and breakdown, but a higher setback than RILs with the GS3 allele. Although the gs3 allele did not affect the glossiness, hardness, or toughness of the cooked rice, it resulted in higher adhesiveness and stickiness. Allelic alteration of the preharvest sprouting gene qLTG3-1 was found to affect seven quality-related traits, including pasting properties. Genes related to heading date (Hd18), culm length (SD1), and tiller number (OsTB1) were also associated with quality-related QTL. Alterations in the alleles of these genes caused variations in quality-related traits. Our identification of the association between quality-related traits and key agronomic genes is expected to support the effective development of rice cultivars with improved quality.