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.

The next generation sequencing (NGS) has been developed rapidly in recent years, paving ways of discovering vast sequence variations among germplasms. Whole-genome sequencing was performed on the genomic DNA of Milyang23 and Gihobyeo using NGS and developed new CAPS (cleaved amplified polymorphic sequence) markers based on the single nucleotide polymorphisms (SNPs) in coding sequence between these varieties. The NGS sequencing yielded sequences of 60x coverage of the Nipponbare reference genome on average. A molecular genetic map was constructed with the recombinant inbred population derived from Milyang23/Gihobyeo cross (MGRIL) integrating the newly developed 146 CAPS makers and previously reported 219 PCR-based DNA markers. This map was applied to the detection of quantitative trait loci (QTLs) for stem internode diameters, culm length and panicle length in rice with MGRIL population. A total of 4 new QTLs were detected for stem diameter traits including the first internode diameter (I1D), second internode diameter (I2D), third internode diameter (I3D), and fourth internode diameter (I4D). Among stem diameter QTLs, qI1D5 had relatively 6.09 LOD (likelihood of odds) score and explained 8.99% of total variation. Only very small portion of SNPs through re-sequencing were used in this study. Much more markers can be developed by using SNP information acquired in this study, which will enable construction of high-density genetic map and more accurate QTL analysis of important agronomical traits with MGRIL population.