Leaf size is closely related to photosynthesis and greatly affects rice productivity. Therefore, the search for quantitative trait Locus (QTL) that regulates leaf size is important for improving productivity through rice breeding. The F₉ recombinant inbred line (RIL) population from the cross between ‘Unbong 40’ (large leaves) and ‘Odae’ (ordinary size leaves) was grown in a test field, and the size traits of the flag leaves and 2nd leaves, along with stem and panicle length, were measured. Through QTL analysis of these traits, we detected 20 QTLs on chromosomes 1, 3, 6, 9, 11, and 12. In particular, the flag leaf length QTL qFLL3, the flag leaf area QTL qFLA3, the 2nd leaf length QTL q2LL3-2, and the 2nd leaf area QTL q2LA3 were clustered in the 149.0-161.6 cM region of chromosome 3, indicating that one QTL gene in this region may have pleiotropic effects that regulate the flag leaf length, flag leaf area, 2nd leaf length, and 2nd leaf area. In addition, the flag leaf width QTL qFLW9 and 2nd leaf width QTL q2LW9 were clustered in the 2.1-22.86 cM region on chromosome 9, which suggests that one QTL gene in this region may have pleiotropic effects that regulate both the flag leaf width and 2nd leaf width. These results serve as a valuable reference for breeding programs aiming to increase photosynthesis and yield by identifying QTLs for leaf size traits in Korean japonica rice.

The rice recombinant inbred lines derived from Milyang23 and Gihobyeo cross were used in genetic mapping and QTL analysis studies. In this study, we developed a new 101 CAPS markers based on the SNPs in the whole genome region between these varieties. As a result, the total genetic distance and average distances were 1,696.97 cM and 3.64 cM, respectively. In comparison to the distance of the previous genetic map constructed based on 365 DNA markers, the new genetic map was found to have a decreased distance. The map was applied for the detection of QTLs on all seven traits relevant to diameter of stem internode, length of culms, length of panicles and the number of panicles including the correlation analysis between each trait. The QTLs results were similar to the report in previous studies, whereas the distance between the markers was narrowed and accuracy increased with the addition of 101 CAPS markers. A total of 9 new QTLs were detected for stem internode traits. Among them, qI1D-6 had higher LOD of 5.1 and phenotype variation of 50.92%. In this experiment, a molecular map was constructed with CAPS markers using next generation sequencing showing high accuracy for markers and QTLs. In the future, developing more accurate QTL information on stem internode diameters with various agriculturally important traits will be possible for further rice breeding.