Rice stripe disease, caused by rice stripe virus (RSV), is one of the major virus diseases in east Asia. The objective of this study was conducted to identify new resistance genetic source to rice stripe virus (RSV) disease. Genetic diversity of 155 rice cultivars was evaluated using 9 co-dominant InDel markers and STS marker ST10. These cultivars were classified into two groups by cluster analysis based on Nei`s genetic distances. The marker showed different band pattern among RSV resistance or susceptible cultivar. In comparison with bioassay for RSV resistance and genotyping using SSR markers showed that Stv-bi and InDel 7 marker observed recombination value within 3.8% and RSV resistance gene was closely related to InDel 7. Also InDel 7 divided as resistance type alleles and susceptible type alleles except for some varieties. Interestingly, 02428, Daw dam, Erguailai, Padi Adongdumarat, PERVOMAJSZKIJ, and Tung Ting Wan Hien 1 showed Japonica type in InDel 7 marker. However, these cultivars revealed resistant to RSV bioassay. These results indicate that those cultivar can be able to get the different gene resistance with Stv-bi gene. Newly identified resistance gene is considered useful for improving RSV resistance in japonica rice. Therefore, we will progress the allelism test and genetic analysis for identification of new gene source.

MYB-like domain (MLD) gene is a transcription factor that plays a diverse role in plant development and in response to abiotic stresses. In this study, we isolated and developed CaMV35S::OsMLD rice lines and determined its expression pattern under abiotic stresses. It has Myb_CC_LHEQLE superfamily similar to most transcription factor genes but with a very unique binding domain of SHLQKYR in the C-terminal region. Overexpressing rice lines showed enhanced tolerance to salinity with elevated mRNA transcript. Additionally, mRNA transcripts were up-regulated by ABA, H2O2 and dehydration stresses. Further investigation in the enhanced tolerance to salinity showed an increased accumulation of proline and a decreased in malondialdehyde contents indicating that OsMLD gene may be involved in the regulation of proline and osmolytes during abiotic stresses. These results showed that OsMLD gene could be used in the development of rice intended for soil with salinity-related problem.

Cold stress at the seedling stage is a major threat to rice production. Cold tolerance is controlled by complex genetic factors. We used an F7 recombinant inbred line (RIL) population of 123 individuals derived from the cross of a cold-tolerant japonica and a cold-sensitive indica cultivars, for QTL mapping. Phenotypic evaluation of the parents and RILs in an 18/8oC (day/night) cold-stress regime showed continuous variations for cold tolerance or sensitivity. Six QTLs for seedling cold tolerance were identified on chromosomes 1, 2, 4, 10, and 11 with percent phenotypic variation (R2) ranging from 6.1% to 16.5%. Three main-effect QTLs (qSCT1, qSCT4, and qSCT11) were detected in all cold-tolerant RILs which explained high sum of phenotypic variation (SPV) ranging from 27.1% to 50.6%. Two QTLs (qSCT1 and qSCT11) on chromosomes 1 and 11 were fine mapped. The marker In1-c3 from ORF LOC_Os01g69910 of the BAC clone B1455F06 encoding calmodulin-binding transcription activator (CAMTA) and another marker, In11-d1 from ORF LOC_Os11g37720 (Duf6 gene) of the BAC clone OSJNBa0029K08, co-segregated with seedling cold tolerance. These two InDel markers amplified 241-bp and 158-bp alleles, respectively, in cold-tolerant RILs, and in the cold-tolerant donor Jinbu, which were absent in cold-sensitive parent BR29 and cold-sensitive RILs.

Microsatellite marker is one of the most suitable markers for variety identification as it has great discrimination power for varieties with limited genetic variation. The suitability of simple sequence repeat (SSR) markers for varietal identification and genetic diversity were evaluated for 325 rice varieties. Four hundred thirty six pairs of SSR primers were screened against 11 rice varieties. Twenty six primer pairs were highly polymorphic and reproducible. These primer sets were used to construct a DNA profile database containing 325 rice varieties grown in Korea through automatic detection system (ABI 3130XL). Microsatellite polymorphism was showed to be high. A total of 331 polymorphic amplified fragments were obtained by using 26 microsatellite markers. The number of alleles per locus ranged from 9 to 18 with an average of 12.73 alleles per locus. The average polymorphism information content (PIC) was 0.734 ranging from 0.555 to 0.880. Three hundred thirty one SSR loci were used to calculate Jaccard’s distance coefficients for UPGMA cluster analysis. These varieties were separated into several distinctive groups corresponding to varietal types. Almost all of the varieties were discriminated by SSR marker genotypes. This information may be useful to select comparative variety through comparison of genetic relationship analysis between existing variety and candidate varieties in distinctive tests.

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R2 = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R2 = 11.25%) and trough viscosity (p < 0.01, R2 = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.

During the last decade, considerable progress has been made to understand the molecular mechanisms of M. grisea infection in rice plants and 10 rice blast R genes have been identified and characterized via map-based cloning methods. In case of rice germplasm, the genetic backgrounds of each germplasm accessions are not uniform and the evaluation for pathogenicity is difficult. To solve these problems, we applied the single resistance gene markers to rice germplasm accessions. A molecular survey was conducted to identify the presence of major blast resistance (R) gene in 363 accessions of Korea landrace rice germplasm. The results revealed that the resistance gene Pik-p (100%), Pib (98%), Pi-d(t)2 (98%) and Piz (76%) were widely observed in tested rice germplasm, but Pita-2, Pik and Pi39 gene were identified in less than 10 accessions. Most of landrace contain the four or five different resistant genes, but these results was not consist of field nursery screening. 13 accessions were shown the blast resistance in field nursery screening and Pik-p, Pib, Pi-d(t)2 and Piz genes were observed in these accessions. The evaluation results of blast resistance genes in rice germplasm will help in breeding of multi disease resistant varieties.

Recently, proteome analysis is becoming a powerful tool for the functional characterization of plants. Due to the availability of vast nucleotide sequence information and based on the progress achieved in sensitive and rapid protein identification by mass spectrometry, proteome approaches open up now perspectives to analyze the complex functions of model crop species at different level. In this study, we have N-terminal sequencing data for the 100 embryo and 53 seed proteins of rice separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) were collected and systematically organized for a protein sequence data-file. An attempt was made to link the embryo proteins of rice to DNA sequences for understanding their functions. One hundred proteins of the 700 spots were detected in the embryo using 2-DE gels whereas we used micro sequenced. Of these, 28% of the embryo proteins were matched to DNA sequences with known functions, but 72% of the proteins were identified to be unknown functions as previously reported by Woo et al.,. In addition, twenty-four spots of protein with 100% of homology and nine with over 80% were matched to ESTs (expressed sequence tags) after expanding the amino acid sequences of the protein spots by Database searches using the available EST databases of rice at the NCBI (http://www/ncbi.nlm.nih.gov/) and DDBJ (http://www.ddbj.nig.ac.jp/). Also, a total of 53 proteins out of 700 protein spots separated on the 2-DE gels were analyzed by the peptide mass fingerprinting method (MALDI-TOF/MS). High-quality mass spectra suitable for peptide mass fingerprinting were obtained from 41 spots. Using the ESI-Q-TOF/MS, however, we were able to identify 53 seed proteins of rice, including 12 proteins not registered in database. The rapid expansion of DNA sequence databases to the utilization of EST now provides the whole or partial gene sequences of model organisms, and the recent advances in protein micro-characterization by mass spectrometry allow the possibility of linking these DNA sequences to the proteins in functional complexes. Proteome Database of rice is updated, and is available on the World Wide Web at http://gene64.rda.affrc.go. This work shows that the proteome analysis could be a useful strategy to link the sequence information to the functional genomics.

Mutation breeding is characterized by its merit, creation of new mutant characters and addition of very few traits without disturbing other characters of variety. Gamma ray is generally used to induce mutation in various crops. Heading dat is one of the key factors in the regional and seasonal adaptation of rice verity. This study was carried out to evaluate agronomic characteristics, genetic variation and grain quality of early heading rice (Oryza sativa L. cv. Dongjin 1) lines derived from gamma-ray (Co60, 300 Gy) irradiation. The average heading date of the early heading lines in M7 and M8 generation was faster than that of mother verity as 11 (line γ-2), 10 Aug (line γ-5), 6 Aug (γ-1 line), 5 Aug (γ-3 and X-1), 4 (line γ-4) days, respectively. The selected lines showed shorter culm length and ear length compared with the control. Total spikelets per panicle, percent ripened grain and thousand grain weight of the lines were also mostly shorter or lower than those of the control except total spikelets per panicle of γ-4 and γ-5 lines. When genetic variations of rps16-trnK region were evaluated by nucleotide analysis, nucleotide length of the rps16-trnK region was 664 bp in all the early-heading lines and control. Out of 5 sites of nucleotide transposition detected in the region, however, 2 sites were appeared only in the early-heading lines. Amylose content of the early heading lines ranged from 18.3% to 18.4% and the content was included in high eating quality. Protein content of the lines ranged from 6.6% to 7.0%. The content belonged to Top-rice showing under 7% of protein content. Toyo taste value of the lines ranged from 76.3% to 84.8%.

Geneally, rice seeds regardless indica or japonica are showing low germination ratio or completely lost germination ability together with lost of good eating quality under high temperature and humidity conditions. Thus, this study was designed to evaluate a longevity for conservation of good eating quality during long term storage in rice. For the longevity evaluation, germination ability was studied after 5 days of high temperature and humidity stress (50℃/RH 95%). Dharial, originated from Bangladesh and showing weedy type with red pericarp, was selected as a good donor for longevity genes. A mutant was developed from Dharial through EMS mutagenesis and two populations of Dharial/4*Ilmibyeo and Dharial/4*Gopumbyeo were also developed for genetic study. In the 2-DE analysis followed by MALDI-TOF MS with wild and mutant lines, several candidate genes were identified. In the longevity test of two populations, a few lines showing good germination ability after high temperature and humidity stress were selected and subjected to confirm the relationships between longevity and conservation of good eating quality under long term storage.

To characterize CBF/DREB1-homologue in rice, nine OsDREB1 genes have been identified and characterized in this lab. Among these, it was shown that OsDREB1D was induced by drought and slightly by cold stress. We found that OsDREB1A, -1D, and -1E could up-regulate OsDhn1:LUC construct in transactivation assay using rice protoplasts. Transgenic rice plants overexpressing OsDREB1D under the maize ubiquitin promoter (Ubi:OsDREB1D) revealed an enhanced stress tolerance to drought. We also generated transgenic rice of OsDREB1D under OsPOX1 promoter (OsPOX1:OsDREB1D), which is cold stress inducible preferentially in the reproductive organs of rice. We are currently examining the mechanism of the enhanced tolerance of the transgenic plants to drought stress using both molecular physiological and biochemical techniques.

Rice is the most important crop as the staple food and two priorities in rice production are high yield and good quality in Korea. Far more improvements in grain quality, especially eating quality are required to meet the demand of consumers in rice producing areas. In the study presented here, a recombinant inbred lines (RILs) population derived from a cross between a temperate japonica and a tropical japonica and its genetic linkage map were employed to locate the QTL locus underlying six parameters of RVA profiles. Out of six RVA profile parameters, two characteristics, breakdown viscosity (BDV) and setback viscosity (SBV) are more correlated to eating quality of cooled rice. A total of four QTLs for two RVA profile parameters were identified. Two QTLs, qBDV-6 and qBDV-9 for BDV were detected on chromosomes 6 and 9. These QTLs increased the BDV by 26.2 and 16.4 from Ilpumbyeo allele, respectively. A QTL, qBDV-6 in the interval RM540-RM587 of the wx gene on chromosome 6 was reacted as a major QTL which could explain 26.2% of the total phenotypic variation. A QTL, qBDV-9 in the interval RM5688-RM444 explained 7% of the total variation as a minor QTL. Two QTLs, qSBV-6 and qSBV-9 for SBV also identified at the same region with QTLs of BDV on chromosomes 6 and 9. A QTL, qSBV-6 in the interval of the wx gene on chromosome 6 could explain 24.4% of the total phenotypic variation. A QTL, qSBV-9 in the interval RM5688-RM444 explained 8.2% of the total variation. These QTL region on chromosomes 6 and 9 would be use as useful marker to select elite lines of good eating quality in early generations in japonica rice breeding.

For QTL analysis of agronomic traits based on cultivation of low and high altitude locations, BC1 F5 181 lines were developed from a cross of Tongil type Gayabyeo and japonica Chhomrong originated from Nepal. Plant materials were grown in both of low altitude area of Milyang, Korea and high altitude area of Khumaltar, Nepal. In QTLs analysis, a total of 42 QTLs were detected in days to flowering, culm length, panicle length, number of panicles/hill, panicle exertion, and spikelet ripening ratio. Although many of the QTLs were coincided between the two locations of Korea and Nepal, several QTLs were revealed as location specific in high altitude area of Khumaltar. Especially, the regions harboring marker RM489-RM14281 on chromo- some 3, RM5642-RM19049 on chromosome 5, and RM2854-RM6696 on chromosome 12 where QTLs were clustered and coincided between the two locations are considered as positive target regions for environmental independent traits. Furthermore, high rate of location specific QTLs such as panicle exertion and spikelet ripening ratio could be considered carefully for understanding the mechanism of cold tolerance based on cultivation of different altitude location.

MYB-like domain (MLD) gene is a transcription factor that plays a diverse role in plant development and in response to abiotic stresses. In this study, we isolated and developed CaMV35S::OsMLD rice lines and determined its expression pattern under abiotic stresses. The MLD has Myb_CC_LHEQLE superfamily similar to most transcription factor genes but with a very unique binding domain of SHLQKYR in the C-terminal region. Overexpressing rice lines showed enhanced tolerance to salinity with elevated mRNA transcript. Additionally, mRNA transcripts were up-regulated by ABA, H2O2 and dehydration stresses. Further investigation in the enhanced tolerance to salinity showed an increased accumulation of proline and a decreased in malondialdehyde contents indicating that OsMLD gene may be involved in the regulation of proline and osmolytes during abiotic stresses. These results showed that OsMLD gene could be used in the development of rice intended for soil with salinity-related problem.

벼 줄무늬잎마름병 저항성 유전자 및 연관 DNA 마커 탐색을 위하여 줄무늬잎마름병에 저항성인 통일형 품종인 신광 벼 이용 여교잡 집단을 육성하였다. 줄무늬잎마름병 저항성 유전자에 대한 QTL을 분석한 결과 11번 염색체에 위치하는 SSR 마커 RM6897이 탐색되었으며 전체 표현형 변이의 44.2%를 설명하였다. DNA 마커 RM6897은 여교잡 집단에서 생물검정과 유전자형이 일치하였다. 또한 자포니카 품종들에서 저항성 27품종과 감수성 23품종에 대해