벼의 잎은 광합성을 위한 주요 기관으로, 동화산물의 생산을 통해 벼의 수량 결정에 영향을 준다. 따라서, 상위엽의 형태적 특징은 다수성 벼 품종의 육성을 위한 필수적인 고려요소이다. 본 연구에서는, 연차간 안정적으로 발현하는 3개의 엽폭 조절 QTL인 qLW4.1, qLW4.2, qLW7을 탐지하였다. 이들은 분석집단에서 나타난 엽폭 표현형 변이의 5.2~44.9% 를 설명할 수 있었다. qLW4.2 영역에 대한 후보유전자 분석 결과, 해당 QTL 영역에서 엽폭 조절 유전자인 NAL1을 발견하였다. 상위엽은 수량에 대해 정의 간접효과 나타냈으며, 그 효과의 크기는 수당립수에 대한 상위엽의 정의 직접효과와 수수에 대한 상위엽의 부의 직접효과에 의해 결정되었다. 한국 벼 유전자원에서 엽폭은 상대적으로 좁은 범위에서 표현형 변이를 나타내었으며, 이는 특정 상위엽폭이 한국 자원에서 선호 되었음을 시사한다. NAL1의 하플로타입 분석결과는 대다수의 한국 자원들이 자포니카형 하플로타입을 지닌 반면에, 모든 통일형 품종들은 인디카형을 지니고 있음을 밝혀냈다. 이러한 결과는 유용 대립유전자형인 자포니카형 NAL1의 도입을 통해 통일형 품종의 다수성 형질을 더욱 향상시킬 수 있음을 의미 한다.

Eighteen years have passed since Korea introduced plant variety protection (PVP) system. Korea is being considered as one of the countries which introduced PVP system successfully. However, there have been lots of changes in circumstances surrounding PVP system during this period. Regarding future direction of PVP system in Korea, firstly the function and role of three organizations which now independently operate PVP system need to be reorganized to improve efficiency in PVP operation dealing with global issues. Secondly, authorities need to devise more user-oriented application form and process. This is because breeders feel some difficulties in preparing application documents. Thirdly, Korea has to create sound environments which guarantee effective enforcement of breeders’ rights and secure reliability of the system against infringement. Regarding decision of infringement, a reasonable threshold should be set up to decide whether certain varieties are different from protected varieties or not using both growing test and DNA test. For essentially derived varieties (EDV), authorities need to establish a reasonable threshold to decide whether there is an essential derivation or not. In addition, to prevent dispute between PVP holders and farmers regarding the use of farm saved seeds in the future, clarification of farm saved seed article in legislation is necessary. Lastly, there might be some contradiction between PVP and Nagoya protocol in disclosure of origin, prior informed consent, benefit sharing, etc. In advance of enactment of domestic ABS law, authority needs to study impact of Nagoya protocol on PVP system to minimize confusion and damage on breeders.

‘유럽연합 품종보호에 관한 규정’(기본규정)에 근거하여 운영되는 유럽연합 품종보호제도는 1995년 도입되었으며, 유럽연합 품종보호사무소에 한 번의 출원으로 유럽연합(EU) 28개 회원국에서 품종보호 등록품종에 대한 배타적인 권리를 누릴 수 있는 효율적인 제도이다. 출원료는 650유로이고 연간 심사료는 작물 그룹별로 1,430∼3,210유로 범위이며연간 품종보호료는 작물에 상관없이 250유로이다. 2013년도 출원건수는 3,297건으로 제도 도입 후 최대 출원건수를 기록하였고 품종보호사무소 설립이후 50개국 이상으로부터 출원이 이루어졌으며, 거의 매년 1/3이상은 네덜란드(2013년 1,226건)에서 출원되고 있다. 2013년도 품종보호 등록건수는 2,706건으로 역대 최고 출원건수를 기록하였고 2013년말 현재 유지되고 있는 품종보호권은 21,576건이다. 기본규정은 UPOV의 1991협약을 반영하여 권리범위가 1978협약에 비해 확대되었으나 수확물에 대한 권리범위가 구체적으로 기술되지 않아 육종가 권리의 사각지대가 발생할 수 있다. 육종가 권리 예외 조항에 따라 농업인은 일부 농작물류에 대해 일반적인 로열티보다 적은 금액의 로열티로 자가채종 종자를 사용할 수 있다. 그러나 육종가는 자가채종 종자 사용에 대한 정보 획득의 어려움 등으로 로열티 징수에 어려움을 겪고 있다. 기본유래품종 조항은 육종가 예외조항에 의해 발생할 수 있는 유사·복제 품종 문제를 예방할 수 있지만 기본유래품종 여부를 판단하는 표준 프로토콜이나 임계치가 없는 실정이다. 유럽연합 역내에서 조화된 품종보호제도가 운영되고 있지만 육종가의 권리행사 여건은 유럽연합 회원국별로 차이가 큰 편이며 일부의 경우 권리침해 문제를 해결하기 위한 시스템이 제대로 작동하고 있지 않은 상황이다. 유럽연합 역내에서 범국가적으로 운영되고 있는 유럽연합 품종보호제도가 한층 더 발전하기 위해서는 이러한 문제들을 해결해야 할 것으로 보인다.

The goals of this research project are to identify the genes controlling plant architecture through the establishment of foundation for molecular breeding and to develop new rice varieties with useful characters associated with high yield leading to its commercialization. The research subjects of this project are as follows: improvement of plant architecture including tiller angle and number associated to harvest-index, construction of genetic and QTL map related to plant architecture and isolation of target genes, development of molecular markers with high efficiency, and further study for the mechanisms of recombination event and reproductive barrier occurring from cross between subspecies, development of new elite rice varieties with high yield and its commercialization. The isolated genes and products of this research project will be patented and molecular markers for those genes will be applied to breeding procedure. The breeding materials produced as outcomes will be provided to other breeders for further breeding programs. The developed varieties will be patented and registered to the national list of varieties, and will be distributed to our agricultural industries for the increase of its competitiveness and farmer’s income. The patents for genes, molecular markers, and varieties will be licensed out to uphold the agricultural biotechnology industries.

To understand the molecular mechanism of leaf morphogenesis in rice, ethylmethane sulfonate (EMS) treated Ilpoom mutant line with semi-narrow and adaxially rolled leaf phenotype was identified. The leaf rolling character is said to be more advantageous under high temperature and heat stress, and play as one of the defensive mechanisms. The F1 plants, generated from a cross of Ilpoom and mutant, showed normal phenotype. Genetic analysis of its F2 population suggested that the mutation was controlled by a single recessive gene with segregation ratio of 3:1. Using F2 mapping population derived from a cross of Ilpoom mutant and Milyang23, each chromosomes were screened with STS markers by the bulked segregant analysis (BSA) method. The candidate region was detected to a long arm of chromosome 1 near the centromeric region. Fine mapping of the locus is currently conducted. Moreover, other morphological characterizations of the mutant plants were identified. Cytological analysis of the leaf suggested that deformation of the bulliform cells led to the smaller size and less number of the bulliform cells, and caused leaf rolling trait.

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.

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.

Leaves are the organ for photosynthesis, respiration and transpiration, and have a major effect on crop yield. Therefore, leaf shape and structure are important agronomic traits in breeding for ideal type plant. We obtained a new abaxially rolled leaf mutant from Ilpum(Oryza sativa ssp. japonica) by the treatment of ethyl methane sulfonate(EMS). The abaxially rolled leaf mutant showed reduced plant height and panicle length, increased tiller number and panicle number than Ilpum. LRI(Leaf rolling index) analysis showed that the mutant have high value compared to the wild-type. In cross section analysis, the mutant was observed to have increased of bulliform cell number and size, and led to the outcurved leaf rolling. The phenotypes of the F1 plants derived from the cross between the mutant and Ilpum were normal. In F2 population, segregation ratio between the wild type and the mutant was 3:1. This genetic analysis indicated that leaf rolling is controlled by single recessive gene. Bulked segregant analysis(BSA) and genetic mapping were conducted using F2 population derived from the cross between mutant and Milyang23(Oryza sativa ssp. indica). According to the results, the gene was located on the long arm of chromosome2. Fine mapping is in progress.

The number of spikelets per panicle in rice is determined by characters of the panicle such as the number of primary branches (PB) and secondary branches (SB) and panicle length (PL). It is a quantitative traits controlled by several genes. In this study, the nucleotide polymorphism and haplotype diversity of coding region of genes related to number of spikelets per panicle (SPP), including APO1, APO2, FON1, DEP1, GN1a, GHD8, HD1, and SP1, were analyzed using 45 varieties which showed significant phenotypic variations for PL, PB, SB and SPP. Significant correlations were observed among all the panicle traits. A total of 151 polymorphisms, including 114 SNPs and 26 indels were detected in coding region of 8 genes which constructed 52 haplotypes. Neutrality tests revealed that population subdivision event or balancing selection occurred in locus of APO2, FON1, and HD1 whereas no significant deviation from neutrality was detected in the other genes, suggesting a neutral evolution. Based on the results of GLM association analysis, 34 polymorphic sites in 6 genes were significantly related with the 4 panicle related-traits.

Plastochron and phyllotaxy are important traits to determine plant architecture. A plastochron 1-6 mutant was derived from japonica rice cultivar Koshihikari treated with ethylmethane sulfonate (EMS). The plastochron 1-6 mutant showed reduced plant height, shorter internode length, smaller and more leaves than Koshihikari, its wild type. In addition, the mutant has abnormal panicle, abnormal seed and upper node tillers. The F1 plants between mutant and Koshihikari were normal. In F2 population, segregation ratio between the wild type and mutant was fitted to 3:1. This genetic analysis indicated that plastochron 1-6 is controlled by a single recessive gene. Bulked segregant analysis revealed that the gene was located on chromosome 10. Through sequencing analysis, we found that plastochron 1-6 mutant had a single nucleotide transition occurred in the first exon of LOC_Os10g26340 (encoding P450 CYP78A11). 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.

Single nucleotide polymorphisms (SNPs) are the most abundant variation in plant genomes. As DNA markers, SNPs are rapidly replacing simple sequence repeats (SSRs) and sequence tagged sites (STSs) markers, because SNPs are more abundant, stable, easy to automation, efficient, and increasingly cost-effective. We developed a 96-plex indica/japonica SNP genotyping set for genetic analysis and molecular breeding in rice using Fluidigm platform. Informative SNPs for indica/japonica populations were selected from 1536 Illumina SNPs and 44K Affymetrix SNP chip data of Rice Diversity and our resequencing data sets. Selected SNPs were evenly distributed across 12 chromosomes and average physical distance between adjacent SNP markers was 4.38Mb. We conducted genetic diversity analysis of 49 Bangladesh germplasm and check varieties to test a 96-plex indica/japonica SNP genotyping set we developed. High-throughput Fluidigm SNP genotyping system will serve a more efficient and valuable tool for genetic diversity analysis, DNA fingerprinting, quantitative trait locus (QTL) mapping and background selection for crosses between indica and japonica in rice. 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.

Rice embryo contains valuable materials which are related to human health and industrial material, thus controlling embryo size is more and more important in the field of rice breeding. Especially, main health-aid components such as γ -aminobutyric acid (GABA), tocopherol and vitamins showed positive-correlation with embryo size. We obtained three enlarged embryo character mutants derived from Hwacheongbyeo (Korean japonica cultivar) by treatment of chemical mutagen, N-methyl-N-nitrosourea(MNU). These three mutants were named according to their embryo size as ge-m, ge, ge-s. The result of allelism test between Hwacheongbyeo, ge-m, ge and ge-s represented that the embryo size of ge and ge-s was controlled by the same gene(Giant embryo, GE). Through GE locus sequencing of three mutants, we found that each of ge and ge-s mutant has a point mutation, causing non synonymous amino acid substitution. On the other hand, ge-m mutant, the embryo of which featured intermediate size in between those of Hwacheongbyeo and ge, turned out to be non-allelic to the GE locus, suggesting it is likely a novel gene, which influences rice embryo development through a different mechanism than GE gene. Fine mapping of ge-m is currently in progress. 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 spikelet number per panicle (SPP) in rice is a quantitative trait controlled by numerous genes. To identify the alleles of these genes, we conducted sequencing of coding region or UTR of 13 genes which are known for controlling SPP trait, subjected to 48 rice cultivars covering 27 Indica, 17Japonica, and 4 Tongil types. The genes were EP3(ERECT PANICLE 3), RCN1(REDUCED CULM NUMBER 1), RCN2(REDUCED CULM NUMBER 2), FZP(FRIZZY PANICLE), LAX1(LAX PANICLE 1), MOC1(MONOCULM 1) APO1(ABERRANT PANICLE ORGANIZATION 1), APO2(ABERRANT PANICLE ORGANIZATION 2), DEP1(DENSE AND ERECT PANICLE 1), FON1(FLORAL ORGAN NUMBER 1), GHD8(GRAIN NUMBER, PLANT HEIGHT, AND HEADING DATE 8), GN1A(GRAIN NUMBER 1A), and HD1(HEADING DATE1). As a result, 1 synonymous SNP was found in EP3, RCN1 and RCN2. In LAX1 and MOC1, 1 non-synonymous SNP was identified. But none of SNP was found from the coding region of FZP. Moreover, 3, 6, 7, 8, 9 and 10 alleles were detected in APO1 and APO2, FON1, GHD8, GN1A, DEP1, and HD1 respectively. The multiple regression analysis revealed that GHD8, DEP1 and HD1 had strong effects on spikelet number of primary branch. In addition, HD1 had strong effects on spikelet number of secondary branch, and for total spikelet number per panicle as well. 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.

Increasing demand on cereal grains to meet the population growth requires more production of rice as well as other cereals, which is supposed to rise up to 40% until 2030. Grain size and shape are critical factors determining grain yield. Several genes on grain shape and size have been reported, and of them, seven cloned genes were chosen for haplotype analysis, such as GS3, GW2, qSW5, GS6, GW8, GS5, and TGW6. We genotyped 218 rice varieties which had diverse grain size and shape originating from 25 countries. As for GS3 and qSW5, PCR markers were developed for point mutation and deletion, respectively. For the other five genes in which functional SNPs were reported, we designed primer sets to distinguish a fuctional allele for each gene. GW2 and TGW6 had two alleles, while the other five genes displayed three alleles which were evenly distributed throughout the population. Analysis on the relationship between haplotype of the genes and grain phenotype is in progress. We expect that desirable allelic combination of genes would assure the optimal grain size and shape for higher grain yield and market quality. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No.PJ009076), Rural Development Administration, Republic of Korea.

To obtain a better insight into a possible common regulatory mechanism shared in response to heat and cold stresses in model monocot plant, expression profiling for several selected transcripts of rice (O. sativa L.) was examined from meiotic stage panicle samples of a number of different cultivars including both heat/cold tolerant and susceptible varieties. Induction of several of these genes in response to heat stress treatment was observed across all different rice varieties tested, but no differential induction kinetics between the heat-tolerant and susceptible varieties was discernable for these genes. On the other hand, a few genes that are known to be involved in ROS signaling showed different induction kinetics between the tolerant and susceptible varieties, suggesting that these genes might be playing a key role in conferring the heat/cold stress tolerance at reproductive stage of tolerant rice varieties. This approach was also augmented by comparative gene expression data analyses, utilizing expression data of other monocots and dicots model plants available in the database. Based upon these results, a preliminary gene pyramiding effort to estimate contributing factor of several selected alleles after putting these genes together is underway. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No.PJ009076), Rural Development Administration, Republic of Korea.

New QTLs were identified for high grain yield with long panicle in rice. A total of 137 F15 recombinant inbred lines (RILs) derived from a cross between Dasanbyeo (Tongil) and TR22183 (japonica), together with the parents were evaluated for 16 agronomic traits at IRRI in dry and wet seasons under different phosphorus (P) and irrigation conditions. A linkage map was constructed using 236 polymorphic markers in 384-plex Bead Xpress indica-japonica single nucleotide polymorphism (SNP) platform. P and water effects were significant in both wet and dry seasons. Both parents and RILs showed varying degree of sensitivities to scarcities in water and phosphorus in terms of panicle length. Collocating with 20 yield-related QTLs, the panicle QTLs on chromosomes 1 (pl01) ,2 (pl02), 9 (pl09), and 11 (pl11) under low P and rainfed conditions were identified. RILs with TR22183 allele at pl11 showed longer panicle length under low P input rainfed condition in dry and wet seasons. The whole-genome sequences of the two varieties are being compared to design the molecular markers for fine-mapping and candidate gene identification. Based on Nipponbare MSU 7.0 annotation, a total of 1464 genes with predicted function were identified within the four QTL regions. Candidate genes identified in other studies for QTLs under low P and water conditions, such as calmodulin and dehydrin genes, were targeted for designing molecular markers for fine-mapping and expression analysis. Pyramiding the panicle length QTLs correlating with yield QTLs will provide an opportunity of improving yield traits.

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.

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.