Understanding how crops interact with their environments is increasingly important in breeding program, especially in light of highly anticipated climate changes. A total of 150 recombinant inbred lines (RILs) of F12 generation derived from Dasanbyeo (Indica) x TR22183 (Japonica) were evaluated at Suwon 2010, Shanghai 2010, IRRI 2010 wet season, Suwon 2011, Shanghai 2011, IRRI 2011 dry season, and IRRI 2011 wet season as a total of seven diverse environments. Traits evaluation included eight important agronomical traits such as days to heading (DTH), culm length (CL), panicle length (PL), panicle number per plant (PN), spikelet number per panicle (SN), spikelet fertility (SF), 100-grain weight (GW), and grain yield (GY). As a result of genotyping using 384-plex GoldenGate oligo pool assay (OPA) set (RiceOPA3.1), the linkage map for 235 SNP markers covering a total of 926.53 cM with an average interval of 4.01 cM was constructed and a total of 44 main-effect quantitative trait loci (QTL)s and 35 QTLs by environment interaction (QEI) were detected for all eight traits using single environment and multi-environments analysis, respectively. Of these, fourteen putative QTLs for DTH, CL, PN, SN, GW and GY found in single environment analysis had the similar position to QEI for those traits, suggesting that these same QTLs from both single-and multi-environments are major and stable for certain traits. To the best of our knowledge, 12 QTLs consisted of four QTLs for CL (qCL2, qCL8.1, qCL8.2, and qCL8.3), six QTLs for GW (qGW3.1, qGW3.2, qGW7, qGW8, qGW10.1, and qGW10.2), one QTL for GY (qGY3) and one for SF (qSF4) out of 44 QTLs obtained from single environment analysis were considered to be novel since no overlapping QTL was reported from previous studies. In addition, 12 out of 35 QTLs obtained from multi-environments analysis were also novel.

Rice eating quality is considered to be one of the top priorities in determining the agronomical value of rice. Thus the rapid evaluation of eating quality at early breeding generations in breeding programs for better eating quality is of great importance. However, it has been limited due to the complex nature of eating quality and the absence of standard evaluation method. In our previous study, we developed a evaluation method with a set of DNA markers that allows to predict the eating quality for japonica rices. Here we successfully developed another marker set for the eating quality of indica rices. We used multiple regression analysis to test 54 markers, which were preselected for their possible association with eating quality, using 24 indica varieties with different palatability scores. Of these markers, eighteen markers were found to be significantly associated with palatability according to sensory evaluation. Accordingly, a marker set in the model regression equation with a high R2 (0.997) was formulated to estimate indica rice palatability. Validation suggests that markers and the statistical parameters formulated by the equation could be a potential tool to predict the palatability of cooked Indonesian indica rice and could be reliable in developing country-dependent model equations for eating quality. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.

The architecture of rice panicle is primarily determined by the arrangement of branches and spikelets, and it directly affects grain yield. We identified a mutant for panicle apical abortion from a japonica cultivar Hwacheongbyeo treated with N-methyl-N-nitrosourea. Under normal growth conditions, the mutant had multiple abnormal phenotypes, such as a slight reduction in plant height, narrow and dark green leaf blades, and small erect panicles with clear panicle apical abortion compared to the wild-type plants. Genetic analysis revealed that the panicle apical abortion was controlled by a single recessive gene, which is tentatively designated as paa. The paa gene was fine mapped at an interval of 71 kb flanked by STS markers aptn3 and S6685-1 at the long arm of chromosome 4. Sequence analysis of the candidate genes within the delimited region showed a single base-pair change corresponding to an amino acid substitution from glycine to glutamic acid. We expect that the paa gene will be a clue to uncover the molecular mechanism of panicle apical abortion and to maintain the panicle identity for grain yield in rice breeding programs.

Two sugary mutants, Hwacheong sugary-1 (Hsu1) and Hwacheong sugary-2 (Hsu2) were obtained by chemical mutagenesis from japonica cultivar, Hwacheongbyeo. Sugary mutants exhibited wrinkled and translucent grain with high soluble sugar content. In addition, amber-colored endosperm of sugary mutants was loosely packed due to abnormal starch granules compared to densely packed wild-type. Especially, the grain of Hsu2 mutant was less wrinkled than that of Hsu1, thus Hsu2 can be polished easily. Previous studies reveal that su1 mutant was resulted from mutation in gene for a debranching enzyme, isoamylase but the sequence of the mutated gene has not been identified. To identify the sequence of sugary genes, the map-based cloning strategy was applied. The genetic study revealed that the phenotype of Hsu2 mutant was controlled by two recessive genes. Interestingly, one of the genes was located on chromosome 8 at the position of isoamylase which was known as su-1. This indicates that mutation in isoamylase gene causes sugary endosperm characteristics. However we found different mutation points between the Hsu1 and Hsu2. The point mutation in Hsu1 was occurred at 10th exon whereas the other mutation related with Hsu2 was occurred at 15th exon. As mentioned above, the Hsu2 mutant has less wrinkled shape and less soluble sugar content than the Hsu1 mutant. Thus, we hypothesize that the other gene controlling Hsu2 mutant phenotype may have a role in weakening the effect of the su-1. Further study on the other gene associated with the Hsu2 phenotype is in progress.