In the rice inflorescence development, timing of inflorescent meristem abortion, conversion of the rachis branch meristem to the terminal spikelet meristem and shift to lateral meristem identity determine the overall architecture of the rice panicle (keda-Kawakatsu et al. 2009). Cheng et al. (2011) reported that quantitative trait loci (QTLs) have major effects on panicle apical abortion in rice. However, there have been very few reports about panicle tip mutants. Therefore, this research is conducted to fine map mutant gene and perform functional analysis of mutant gen. Hwacheongbyeo (japonica rice) seed was treated with ethyl methane sulfonate (EMS) for inducing mutation. Two F2 population (Japanica mutant crossed with wild type and Japanica mutant crossed with Milyang 23, Indica type) were established for Phenotyping and genomic analysis. STS markers in crop molecular Breeding laboratory. Additional STS markers for fine mapping were developed based on the Nipponbare genome sequence (http://rgp.dna.affrc.go.jp/blast/runblast.html). All F2 generations showed the segregation of normal plants and mutant following a ratio of 3:1 suggesting the mutant phenotype is caused by a single recessive gene. Initial BSA test made using STS markers confirmed the mutant gene is found in the long arm of chromosome 8. Panicle tip mutant gene, pnt has pleotropic effect which has been manifested in significant reduction of tiller development starting from late stage of vegetative growth and pronounced effect on possession of stay green nature of the rice during the vegetative stage of development. The only significant difference observed within panicle traits is the number of spikelet on primary branch and spikelet fertility. The first primary branch which contain aborted spikelet and elongated distance between spikelet is the most affected structure in the panicle.

Banaue Rice Terraces in the Philippines has been a rich source of genetic diversity of untapped rice landraces in the mountainous region of Cordillera. Although some may have been included into modern breeding programs, significant indica-japonica differentiation among landraces cultivated in the region is not well known. Thus, Cordillera landraces differentiation across different altitude gradient (458 m to 1830 m) will provide great opportunities for improvement on rice genetics. We analyzed the genetic variation among 166 accessions collected in 17 towns in 6 provinces across different altitudes using Subspecies Specific Sequence Tagged Site (SS-STS) and Insertion-Deletion (InDel) markers. Subspecies Prototype Index (SPI) degree of each landrace was used to calculate the genomic inclination of each variety towards subspecies. The 50 molecular markers (24 SS-STS and 26 InDel) that assayed variation in 166 accessions revealed 116 alleles. Gene diversity ranged from 0.04 (R3M23) to 0.50 (S04058) with an average of 0.40. Polymorphism information content (PIC) ranged from 0.04 (R3M23) to 0.37 (S12030, S07047, R10M40, S10001, S04058 and S09040B) with an average of 0.31. Using the control varieties to assign groups, the larger group of 114 Cordillera landraces corresponds to 71% japonica type while the smaller group of 42 corresponds to 26% indica and 3% intermediates. A total of 7 (4%) indica and 9 (6%) japonica type accessions were found above 1500 m. Results of this study suggested that majority of japonica type rice landraces were grown in high altitudes of Banaue Rice Terraces and nearby provinces, and interestingly, indica type rice landraces were cultivated in areas at much higher altitudes (>1500 m) than those categorized by the traditional methods.

The world population has been continuously increasing and has led to the growing demand for rice. It is therefore important to pay as much attention to the enhancement of grain yield as well as grain quality. Grain size is one of the major factors determining grain yield and quality. A large number of genes are known to be involved in regulation of grain size. However, the influence of their haplotype combination is still largely unknown. Of the previously characterized genes, we especially focused on the six genes (GS3, GS5, GS6, GW2, qSW5/GW5, and GW8/OsSPL16) to expand our understanding of regulation of grain size and to develop a regression equation model that can be used for molecular rice breeding. A total of 215 rice germplasms, which originated or developed from 28 rice-consuming countries, were used in this study. The genotyping analysis revealed that different alleles of the six genes were widely distributed in our germplasm collection and also showed significant associations with the differences in grain size. Interestingly, we found that the relatively small number of haplotype combinations preserved in diverse rice germplasms and showed significant associations with the differences in grain size. In addition, we also found that a single gene-specific allelic variation plays an important role in regulation of grain size in the presence of a certain type of haplotype combination. Based on these results, we developed a regression equation model for prediction of rice grain size. We expect that our model can be used for rice molecular breeding to develop new rice varieties having a grain size in a particular range.

Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yielding rice variety derived from a three-way cross between indica and japonica. Tongil contributed to staple food self-sufficiency of Korea, an achievement that was termed the ‘Korean Green Revolution’. In this study, we analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated from Tongil rice. Three parental accessions, two indica and one japonica types, of Tongil rice were also sequenced for approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare; the average SNP frequency of Tongil was 5.77 per kb. Genome composition based on the SNP data by comparing with the three parental genome sequences on sliding window of Nipponbare genome sequence revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent, different from the theoretical expectation in a three-way cross, i.e., 75% indica and 25% japonica parental origins on average. Copy number of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, yield-related QTLs or gene locations, and polymorphic transposon insertions were also comparatively analyzed between Tongil and parents using sequence-based tools. The results indicated that each genetic factor was transferred from parents into Tongil in proportion to the whole-genome composition. The Tongil rice is the first successful superior cultivar derived from indica × japonica hybridization in Korea. Defining of genome structure demonstrates that the Tongil genome is composed mostly of the indica genome with a small proportion of japonica genome introgression. 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 early senescence mutant was isolated from the japonica rice Koshihikari through Ethyl-methane-sulfonate (EMS) mutagenesis. The early senescence phenotype was controlled by a single recessive gene, tentatively symbolized as es-k. Using an F2 population derived from a cross between the mutant and Milyang23 and molecular markers, we mapped the es-k locus to the long arm of chromosome 7 between STS markers 147-1 and 147-2 with a physical distance of 66-kb. The symptom of early senescence appeared even before heading, while appeared during ripening in wild-type. Physiological characteristics of the es-k mutant before initiation of senescence was similar to the wild-type. However, after heading, es-k mutants started to exhibit a significant decrease in chlorophyll and soluble protein content compared to the wild-type. The wild-type leaf color appeared normal irrespective of temperature treatment, while the leaf of es-k mutant appeared pale-green at the low temperature and dark-green at the high temperature. During dark-induced senescence, mutant did not show significant differences compared to normal type. The results show that es-k is sensitive to temperature but not to light.

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.

Hybrid sterility is one of the major barrier to the application of wide crosses in plant breeding and is commonly encountered in crosses between indica and japonica rice varieties. Ten mapping populations comprised of two reciprocal F2 and eight BC1F1 populations generated from the cross between Ilpumbyeo (japonica) and Dasanbyeo (indica) were used to identify QTLs and to interpret the gametophytic factors involved in hybrid fertility or sterility between two subspecies. Frame maps were constructed using a total of 107 and 144 STS markers covering 12 rice chromosomes in two reciprocal F2 and eight BC1F1 populations, respectively. A total of 15 main-effect QTLs and 17 significant digenic- epistatic interactions controlling spikelet fertility (SF) were resolved in the the entire genome map of F2 BC1F1 populations . Among detected QTLs responsible for hybrid ferility, four QTLs, qSF5.1 and and qS F5.2 on chromosome 5, qSF6.2 on chromosome 6, and qSF12.2 on chromosome 12 were identified as major QTLs since they were located at corresponding position in at least three mapping populations. Loci qSF5.1, qSF6.1 and qSF6.2 were responsible for both female and male sterility, whereas qSF3.1, qSF7 and qSF 12.2 affected the spikelet fertility only through embryosac factors, and qSF9.1 did through pollen factors. Five new QTLs identified in this study will be helpful for understanding the hybrid sterility and for breeding programs via inter-subspecific hybridization.

Hybrid sterility is one of the major barrier to the application of wide crosses in plant breeding and is commonly encountered in crosses between indica and japonica rice varieties. Ten mapping populations comprised of two reciprocal F2 and eight BC1F1 populations generated from the cross between Ilpumbyeo (japonica) and Dasanbyeo (indica) were used to identify QTLs and to interpret the gametophytic factors involved in hybrid fertility or sterility between two subspecies. Frame maps were constructed using a total of 107 and 144 STS markers covering 12 rice chromosomes in two reciprocal F2 and eight BC1F1 populations, respectively. A total of 15 main-effect QTLs and 17 significant digenic- epistatic interactions controlling spikelet fertility (SF) were resolved in the the entire genome map of F2 BC1F1 populations . Among detected QTLs responsible for hybrid ferility, four QTLs, qSF5.1 and and qS F5.2 on chromosome 5, qSF6.2 on chromosome 6, and qSF12.2 on chromosome 12 were identified as major QTLs since they were located at corresponding position in at least three mapping populations. Loci qSF5.1, qSF6.1 and qSF6.2 were responsible for both female and male sterility, whereas qSF3.1, qSF7 and qSF 12.2 affected the spikelet fertility only through embryosac factors, and qSF9.1 did through pollen factors. Five new QTLs identified in this study will be helpful for understanding the hybrid sterility and for breeding programs via inter-subspecific hybridization.

The earth has been facing a rapid warming during past several decades. To figure out the impact of high temperature on agronomic performance of rice especially on yield, we cultivated 89 rice varieties of various origin in Suwon Korea, Shanghai China and IRRI Philippines(Wet season and Dry season). Days to heading, culm length, panicle length, panicle number, spikelet number, spikelet fertility, grain weight and grain yield were comparatively investigated. Overall grain yield displayed significantly lower values in Shanghai and IRRI(wet and dry) compared with in Suwon. Meanwhile minimum values were much lower in Shanghai and IRRI than in Suwon. However, some varieties such as Keunseom, Taichung178 showed similar performance for grain yield in both Suwon and IRRI(wet season), and some varieties such as Hangangchal, Dasan showed similar performance for grain yield in Suwon, Shanghai and IRRI(wet season), Nampung showed very high yield in Suwon comparing to other two locations. For most varieties, grain yield was the highest in Suwon and followed by in Shanghai and at IRRI(wet season). However, in dry season at IRRI, yield trend was quite different from the expectation. Further studies are in progress to find out the genotype by environment interactions in order to obtain basic information for breeding high temperature tolerant rice.

In plant, senescence is associated with various aspects of the final stage of leaf development, nutrient relocation from leaves to reproducing seeds and stress resistance, and yield which is the most important trait in crops. Thus, the increase of knowledge on the regulatory processes of plant senescence will allow us to manipulate senescence for agronomic benefit in the future. of genetic studies have been conducted with mutants, where most of studies were focused on the delayed senescence mutants which are associated with positive factors on senescence by treating EMS to Koshikari, we induced a mutant showing early senescence phenotype, which possibly enable us to identify a negative factor of senescence. The appearance of the mutant is identical before booting stage and then the mutant showed senescence phenotype rignt before booting stage whereas Koshikari have health green leaves. The clumn length of the mutant is 98cm and the panicle length is 23cm as same as those of Koshikari. The chlorophyl contents of the mutant leaves, measured by SPAD, decreased during senescence. The soluble protein contents in the mutant leaves also decreased but no differences in the constitution reolved 1D-SDS-PAGE was detected. However, an additional shotgun proteomic approach to detect the differences of the protein constitutions during the senescence in the mutant leaves will be conducted.

Grain size is one of the most important trait determining yield in cereal crops, apart from number of grains per panicle, number of panicles per plant and 1000 seed weight. Other than grain characteristics, plant architecture is another very important factor influencing yield by affecting the amount plant surface area directly exposed to the sun light. Erect panicle is important morphological characteristic which helps in enhancing the yield by allowing sun light to fall directly on leaves unlike curved panicle which blocks sunlight and consequently reduce photosynthesis. A small round grain and erect panicle mutant was obtained by treating Hwacheong rice (japonica) with MNU (N-methyl-N-nitrosourea) chemical mutagen. Through bulked segregant analysis (BSA) using STS (Sequence-Tagged Sites) and SS-STS (Sub-species Specific Sequence-Tagged Site) markers we located the mutated gene on the long arm of chromosome 7 and narrowed down candidate region to 168.75kbp through fine mapping. Mutant manifested characteristics like reduced grain size and plant height, dense and erect panicle and relatively erect plant compared to the wild type. When we crossed the mutant with its parent (Hwacheong), F1 panicle and grain characteristics showed intermediate phenotype, therefore, we concluded that wild type allele of this gene shows incomplete dominance. Scanning electron microscopy(SEM) result shows that increase in width of mutant grain, which changes its shape, is due to increase in width of glume cells. Phenotypic examination shows that dense and erect panicle phenotype is result of reduction in length of rachis, primary and secondary branch.