The grain size and shape have a significant impact on the grain quality and yield of rice. Additionally, due to the globalization of the rice market, there is a demand for rice varieties of various sizes. In this study, we analyzed quantitative trait loci (QTL) associated with grain length (GL), grain width (GW), grain thickness (GT) and ratio of length-to-width (RLW) using 149 F₂ plants obtained from a cross between Hopum and Basmati 370. To construct a linkage map, we utilized 89 Fluidigm SNP markers, which covered a span of 1,116 cM of F₂ population. Nine QTLs associated with four traits were identified on chromosomes 2, 3, 5, and 7. One major QTL on chromosome 3 accounted for 43.2% of the phenotypic variation in GL. Additionally, QTLs named qGW2 and qGW5 on chromosomes 2 and 5 were detected for GW, explaining 10.4% and 18.6% of the phenotypic variation, respectively. Three QTLs for GT were found on chromosomes 2, 5, and 7, explaining 9.9%, 12.9%, and 9.9% of phenotypic variation, respectively. These QTLs offer potential applications in breeding programs using Basmati 370 to develop long and slender grain japonica varieties.

Submergence is becoming a major problem in decreasing rice production. This study conducted a QTL analysis for submergence tolerance on germination stage using 165 recombinant inbred lines (RILs) derived from crosses between ‘Milyang 23’ and ‘Tong 88-7’. An integrated genetic linkage map consisting of 1,313 SNPs was constructed, which covered a total length of 1,254.59 cM, with an average distance of 0.96 cM between adjacent markers. Four QTLs were detected on chromosomes 1, 3, 4, and 7. In qSUB1 and qSUB3, the allele of ‘Tong88-7’ improved survival rates, while in qSUB4 and qSUB7 the allele of ‘Milyang 23’ improved the same. Phenotypic variance explanations for qSUB1, qSUB3, qSUB4, and qSUB7 were 9.44%, 14.62%, 9.74%, and 7.09%, respectively. The average survival rate of the lines with all four QTLs was 93.33±6.67%.

Interspecific and intersubspecific crosses have been an important strategy for rice breeding programs to obtain useful characters by expanding genetic diversity. However, the wide cross routinely causes undesirable characters in rice, such as spikelet sterility and poor quality. In this study, we developed near-isogenic lines of R-gene (Xa4+xa5+Xa21+Pi40+Bph18) introgression population to investigate the genetic relationship between the occurrence of poor characters and R-genes induced by MAS. The ANOVA analysis revealed that Pi40, Bph18, and Xa4 were associated with spikelet fertility (SF), ratio of ripened grain (RRG), third internode length (TIL), panicle extraction (PE), and protein content (Pro), whereas others showed no association with the 14 traits tested. In the three-way ANOVA, the impact of two R-genes (Pi40 and Bph18) on the poor characters was independent, with no interaction with others. Quantitative trait locus (QTL) analysis identified QTLs for PE and TIL traits near Pi40, and in particular, QTLs for five traits (SF, RRG, TIL, PE, and Pro) were negatively affected around Bph18. The occurrence of a poor character in R-gene pyramiding lines could be associated with linkage drag caused by the Bph18 gene. We speculate that the development of DNA markers that effectively eliminate poor characters will not only improve breeding efficiency using MAS, but will also help improve traits of japonica rice through wide crossing.

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.