A field study was conducted to understand nitrogen use efficiency of high yielding Japonica rice varieties under three levels of nitrogen fertilizer (90, 150 and 210 kg N ha -1 ) in Iksan, Korea. Two high yielding rice varieties, Boramchan and Deuraechan, and an control variety, Dongjin2, were grown in fine silty paddy. Nitrogen use efficiencies (NUE) were 83.3, 56.3, and 41.2 in 90, 150, and 210 kg N ha -1 fertilizer level, respectively. Total nitrogen uptake varied significantly among nitrogen levels and varieties. Variety Dongjin2 showed the highest nitrogen uptake efficiency (NUpE), while Boramchan and Deuraechan showed higher nitrogen utilization efficiency (NUtE). However, Nitrogen harvest index (NHI) was higher in Boramchan (0.58) than Deuraechan (0.57) and Dongjin2 (0.53). Rough rice yield showed linear relationship with total nitrogen uptake (R 2 =0.72) within the range of nitrogen treatments. Boramchan produced significantly higher rough rice yield (8546 kg ha -1 ) which mainly due to higher number of panicles per m 2 compared to Deuraechan (7714 kg ha -1 ). Deuraechan showed higher number of spikelets per panicle, but showed lower yield due to lower number of panicle per m 2 . Rice varieties showed different nitrogen uptake ability and NUE at different nitrogen level. Plant breeders and agronomist should take advantage of the significant variations and relationships among grain yield, NUpE, and NUE.

The required for Mla12 resistance (RAR1) protein is essential for the plant immune response. In rice, a model monocot species, the function of Oryza sativa RAR1 (OsRAR1) has been little explored. In our current study, we characterized the response of a rice osrar1 T-DNA insertion mutant to infection by Magnaporthe oryzae, the causal agent of rice blast disease. osrar1 mutants displayed reduced resistance compared with wild type rice when inoculated with the normally virulent M. oryzae isolate PO6-6, indicating that OsRAR1 is required for an immune response to this pathogen. We also investigated the function of OsRAR1 in the resistance mechanism mediated by the immune receptor genes Pib and Pi5 that encode nucleotide binding-leucine rich repeat (NB-LRR) proteins. We inoculated progeny from Pib/osrar1 and Pi5/osrar1 heterozygous plants with the avirulent M. oryzae isolates, race 007 and PO6-6, respectively. We found that only Pib-mediated resistance was compromised by the osrar1 mutation and that the introduction of the OsRAR1 cDNA into Pib/osrar1 rescued Pib-mediated resistance. These results indicate that OsRAR1 is required for Pib-mediated resistance but not Pi5-mediated resistance to M. oryzae.

This study investigated the nutrients and anti-nutrients of produced resveratrol GM rice (Iksan-515, Iksan-526, Dongjin) that were cultivated Iksan and Suwon regions. Among the rice samples, Iksan-515 and Iksan-526 are produced resveratrol GM rice. Reveratrol is health-beneficial compound with strong antioxidant and antitumor activities. Red wine is believed to the main source of resveratrol in the human diet. Recent studies have associated resveratrol with the cardio-protective effect observed among people with moderate resveratrol consumption. Moreover, resveratrol has been possess chemoprotective activity. In present study, we determined the substantial equivalence between GM rice and seedling sort. We investigated the nutrients and anti-nutrients of produced resveratrol GM rice and analyzed nutrients including moisture, crude fat, ash, crude protein, fatty acids, amino acids and minerals. The results of this analysis showed equivalence between GM rice and non-GM rice. We determined phenolic compounds including naringenin, vallin and investigated 4 tocopherols (α-, β-, γ-, δ-tocopherol) and 4 tocotrienols (α-, β-, γ-, δ-tocotrienol). Among the all rice cultivars, they showed substancial equivalence between resveratrol GM rices and non-GM rice.

We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress and selected two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), that are highly expressed under heat stress in rice. OsSHSP1 and OsSHSP2 gene transcripts were highly induced in response to salt and drought. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under ABA and SA. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress. The network of both genes harboring 9 sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

Amylopectin composition is determined by the relative activity of soluble starch synthase (SSS) and granule-bound starch synthase (GBSS). Soluble starch synthase and starch branching enzymes are major determinants for the synthesis of amylopectin while GBSS1 is responsible for amylose synthesis in vivo. The formers are made of linear and branched molecules and the latter is composed of highly branched molecules. To increase the palatability of rice, down-regulation of amylose synthesis by antisense and RNA interference (RNAi) could be excellent and powerful tools for controlling the starch composition which is responsible for grain eating quality. The goal of this study is to generate breeding lines with lower amylose content relative to its wild type. This study also reports the results of the two down-regulating technology in lowering the amylose content of rice grain. Furthermore, this study elucidates the effect of using antisense and RNAi for SSS1 and GBSS1.

High temperature impediment in developing stages of crops has been occurred due to the impact of global warming. Rice production is notable to be sensitive to increasing environmental temperature and grain filling temperatures are already approaching threatening levels in many countries with rice cultivation. Recent proteomic analyses exposed impulsive changes of metabolisms during rice grain development. Interestingly, proteins involved in glycolysis, citric acid cycle, lipid metabolism, and proteolysis were accumulated at higher levels in mature grain than those of developing stages. High temperature (HT) stress in rice ripening period enhances damaged (chalky) grains which have loosely compacted shape starch granules. We carried out two-dimensional gel electrophoresis to analyze protein profiles during grain filling and different developmental stages of rice seed maturation. Proteins were separated from the fertilized seeds (seeds from 7 days and 21 days after fertilization) and seed maturation stage using IEF in the first-dimension and SDS-PAGE in the second dimension along with MALDI-TOF mass spectrometry. More than 1,000 protein spots were detected on a two-dimensional gel electrophoresis. A total of 120 different protein spots out of 140 protein spots were identified by MALDI-TOF and nano LCQ-TOF mass spectrometer. The identified proteins were categorized into six (6) different groups according to their expression patterns during grain filling and seed maturation. Some proteins were confirmed during seed development stages such as cytoplasmic malate dehydrogenase, whereas others were appeared at a specific stage like putative subtilisin-like protease, germin-like, seed allergenic proteins. Furthermore, the chalking mechanism of rice grain under the HT stress could be discussed in terms of grain starch glycome, transcriptome, and proteome.

Plant transformation systems have been developed using several different approaches, and the development of reliable and efficient transformation systems is still one of the most important breakthroughs in molecular biology and biotechnology of rice. However, there are many cultivars in rice and transformation efficiency is dependent on the cultivar. The conventional Agrobacterium-mediated rice transformation system using secondary calli requires 14-16 weeks for establishing transgenic plantlets, and it is thought that somaclonal variation through the Tos17 retrotransposon occurs during the tissue culture stage. Here, we modified an Agrobacterium-mediated transformation system in rice cultivar Dongjin, adding an endosperm removal step that is critical to transformation frequency and changing the Agrobacterium strain and media composition. This method increased transformation efficiency and stability. These results will provide valuable information for scientists to use a reliable and efficient rice transformation system.

The HWC-line of rice showed wide compatibility with both indica and japonica cultivars, tall culm length, long and slender grain shape. For QTL analysis, two F2 populations were derived from the crosses between the HWC-line and each of two Korean variety, Dasanbyeo (Korean Tongil-type cultivar) and Hwacheongbyeo (temperate japonica cultivar), respectively. A total of 190 F2 plants were evaluated in each of two F2 populations. Eight agronomic characters were measured for QTL analysis in F2 populations and parents. Two molecular linkage maps were constructed. In the F2 population from cross between HWC-line / Dasanbyeo (HD) cross, 93 STS markers and 13 SSR markers were mapped on 12 chromosomes, covering a total length of 1942.6 cM, with an average distance of 18.33cM between adjacent markers. In the F2 population from HWC-line / Hwacheongbyeo (HH) cross, 28 STS markers, 29 SSR markers and 1 FNP marker were mapped on 11 chromosomes, spanning a total length of 925.53cM, with an average distance of 15.96cM between adjacent markers. In the F2 population from HD cross, 16 M-QTLs and 1 E-QTL were detected for culm length, spikelets per panicle, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 7 QTLs of spikelet fertility, grain length, grain width and grain shape were newly identified in this study. In the F2 population from HH cross, 15 M-QTLs were detected for culm length, panicle length, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 6 QTLs of culm length, grain length, grain width and grain shape were newly identified in this study. The QTLs identified in this study would provide basic information on putative functional genes related agronomic characters and facilitate breed new rice cultivar.

Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and affects gene expression within the plant genome. To monitor the genome-wide transcriptome changes by ionizing radiation, we used rice Affimetrix GeneChip microarray to identify genes that are up- or down regulated by gamma-ray (200 Gy, 60Co source), cosmic-ray and ion beam (40 Gy, 220 MeV carbon ion). The overall expression patterns between gamma-ray and ion beam were similar but cosmic-ray was regulated differently. Combined results from all 3 radiations identified 27 up-regulated genes and 188 down regulated genes. These results mean the induction of similar mechanism changes in treatments of gamma ray and ion beam. However the different expression in treatment of cosmic-ray might be due to the other environmental conditions. Among the commonly up- or down- regulated genes, we chose highly up- or down- regulated several genes and confirmed its regulation in response to ionizing radiation exposure by RT-PCR analysis. Moreover, we showed that specific co-expression networks of candidate radio marker genes by ARACNE algorithm. Our results present profiles of gene expression related to different ionizing radiation and marker gene to predict sensitivity to ionizing radiation, such as GS (glutelin subunit) and FBX322.

The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is one of the most serious insect pests affecting cultivated rice (Oryza sativa L.) in temperate regions of East Asia. To understand the genetic basis of the GRH resistance, a F2 population derived from across between a highly resistant variety,Cheongnam and a susceptible variety, Junambyeo was analyzed by genetic analysis and association mapping. GRH resistance was evaluated using the F2 populations. The results showed that a single dominant gene in Cheongnam. DNA from 22 F2 individuals being either resistant or susceptible were pooled to produce bulk resistant and bulk susceptible DNA samples. Parents and bulks were screened with 192 SSR markers and twolinked SSRmarker, RM6082 and RM20145 were identified.Subsequent mapping in the original mapping population showed that thelocusis flanked by the SSR markers, RM20130 and RM20152 on chromosome 6. To physically map this locus, the-linked markers were landed on the artificial chromosome clones of the reference cv., Nipponbare, released by the International Rice Genome Sequencing Project. The DNA markers found to be closely linked to Grh3 would be useful for marker-assisted selection for the improvement of resistance to GRH in rice.

This study investigated the functional substances, including phenolics, tocopherol compounds in rice (Onnuri, Nampyeong, Dongjin, Deuraechan, Hopum, Iksan-515, Iksan-526) that were cultivated in Iksan region. Specially, Iksan-515 and Iksan-526 were produced resveratrol rice. Resveratrol is health-beneficial compound with strong antioxidant activity. Iksan-515 and Iksan-526 were contained resveratrol compound while, other rice varieties did not showed resveratrol. The total phenolic compounds showed similar concentrations in 7 rice varieties. Especially, Iksan-526 revealed 273.3 ㎍ g-1 and Iksan-515 was 264.8 ㎍ g-1. In this study, we analyzed vitamin E contents of 7 varieties of rice. The total tocopherols revealed 418.3 ㎍ g-1 in Iksan-526, 401.2 ㎍ g-1 in Iksan-515 and 413.3 ㎍ g-1 in Hopum. We determined 4 tocopherols (α-, β-, γ-, δ-) and 4 tocotrienols (α-, β-, γ-, δ-). Among the all samples, β-tocotrienol showed higher average concentrations (101.3 ㎍ g-1) than other compounds and, γ-tocotrienol revealed second higher concentration (94.5 ㎍ g-1). On the other hand, δ-tocopherol was not detected in all rice samples.

This study was carried out to determine the contents of antioxidant activity of colored rice lines which derived from a mutant of MGI079 induced by MGI079 tissue culture in rice (Oryza sativa L.). The antioxidant activities were evaluated by assaying polyphenol, flavonoid, DPPH free radical and color values of colored rice lines, respectively. Among 8 lines including Heugnam of colored rice, the 70% ethanol extracts decreased in the order of MGI079-2-1>MGI079-2-6>MGI079-2-R,Heugnam>MGI079-1-R>MGI079-2-1>MGI079, MGI079-1-1, MGI079-1-6. The rice lines of highest polyphenolic compound was MGI079-2-6 and the next were Heugnam, MGI079-2-R, MGI079-2-1, MGI079-1-R, MGI079-1-6, MGI079-1-1, MGI079, MGI079-OP-R with the order of higher content. The flavonoid was higher in order of MGI079-2-1, MGI079-2-6, Heugnam, MGI079-2-R, MGI079-1-R, MGI079-1-6, MGI079-OP-R, MGI079, MGI079-1-1. The DPPH free radical was higher in order of MGI079-2-1, MGI079-2-6, Heugnam, MGI079-1-6, MGI079-1-1, MGI079-2-R, MGI079-1-R, MGI079-OP-R, MGI079. For chromaticity, a negative correlation was exhibited between the color value and the 70% ethanol extracts, polyphenolic compound, flavonoid, DPPH free radical. The grain characters in brown rice of a mutant of MGI079 showed similar to that of a donor plant, MGI079. Whereas, chemical characteristics of brown rice in two colored rice lines(MGI079-2-1, MGI079-2-6) were lower in amylose and lipid contents and were higher four times in zinc that of a donor plant, MGI079. Two colored rice lines(MGI079-2-1, MGI079-2-6) showed relatively high antioxidative activity in every results of antioxidant activity tests.

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%.