Quantitative Trait Locus Analysis for Quality-Related Traits Using the Recombinant Inbred Lines Derived from a Cross between “Boramchan” and “Pecos” Japonica Rice

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.