• Genes and Genomics
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• v.40 no.12
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• pp.1351-1361
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• 2018

A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some of these QTLs being successfully cloned. However, no QTLs conferring to the OSR trait have been located in the perennial O. sativa L. To identify QTLs associated with OSR and to evaluate cold tolerance. 286 $F_{12}$ recombinant inbred lines (RILs) derived from a cross between the cold tolerant variety Gr89-1 and cold sensitive variety Shuhui527 (SH527) were used. A total of 198 polymorphic simple sequence repeat (SSR) markers that were distributed uniformly on 12 chromosomes were used to construct the linkage map. The gene ontology (GO) annotation of the major QTL was performed through the rice genome annotation project system. Three main-effect QTLs (qOSR2, qOSR3, and qOSR8) were detected and mapped on chromosomes 2, 3, and 8, respectively. These QTLs were located in the interval of RM14208 (35,160,202 base pairs (bp))-RM208 (35,520,147 bp), RM218 (8,375,236 bp)-RM232 (9,755,778 bp), and RM5891 (24,626,930 bp)-RM23608 (25,355,519 bp), and explained 19.6%, 9.3%, and 11.8% of the phenotypic variations, respectively. The qOSR2 QTL displayed the largest effect, with a logarithm of odds score (LOD) of 5.5. A total of 47 candidate genes on the qOSR2 locus were associated with 219 GO terms. Among these candidate genes, 11 were related to cell membrane, 7 were associated with cold stress, and 3 were involved in response to stress and biotic stimulus. OsPIP1;3 was the only one candidate gene related to stress, biotic stimulus, cold stress, and encoding a cell membrane protein. After QTL mapping, a total of three main-effect QTLs-qOSR2, qOSR3, and qOSR8-were detected on chromosomes 2, 3, and 8, respectively. Among these, qOSR2 explained the highest phenotypic variance. All the QTLs elite traits come from the cold resistance parent Gr89-1. OsPIP1;3 might be a candidate gene of qOSR2.

• Journal of the Korean Society of International Agriculture
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• v.23 no.5
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• pp.560-569
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• 2011

In Japan, plant genomics research is mainly leaded by the national research institutes. The various structural studies such as rice genome has allowed researchers to analyze useful traits, and to focus their commercialization. With aims to facilitate structural and functional study in plant genome, NIAS (National Institute of Agrobiological Sciences) constructed Poaceae genome DB and RIKEN (Rikagaku Kenkyusho) built DB for Arabidopsis genome and plant full-length cDNA. NIG (National Institute of Genetics) constructed a national biological resources DB (National Bio Resource Project). This compiling DB provides a variety of genome-related research materials for researchers in the field. Recently, as an effort to resolve global issues of food supply and environmental problems, New Agri-genome Project has been performed aiming to develop an innovative agricultural technologies for the quantity, disease resistance and identifying useful genes related to environmental problems. In addition, in order to improve agricultural productivity in developing countries, JIRCAS assisted technical supports for the plant genome research and developed NERICA rice, which is suitable for African area. Such these approaches are expected to contribute to solving the global issues about food, energy and environment in the world.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.6
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• pp.533-538
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• 2004

An introgression line, WH79006 was produced from a single plant from $BC_5F_3$ families from a cross between Hwaseongbyeo used as a recurrent parent and O. minuta (BBCC, Ace. No. 101154) as a donor parent, which was subsequently self-pollinated for three generations. WH79006 resembled the O. sativa parent, Hwaseongbyeo. However it differed from Hwaseongbyeo in several traits including days to heading, culm length, grain size, spikelets per panicle and fertility. These differences in the traits between WH79006 and Hwaseongbyeo can be attributed to the O. minuta introgressions. To detect the introgressions, 294 SSR markers of known chromosomal position have been used. At least, 28 introgressed chromosomal segments have been identified using SSR markers and they map to all chromosomes except chromosome 2. The size of the introgressed segments ranged from 4 to 35cM. A QTL related to culm length was detected using 75 $F_2$ plants from the Hwaseongbyeo/WH79006 cross. This QTL, cl6 located on chromosome 6 explained $9.6\%$ of the total phenotypic variation in the population. This QTL has not been detected in the previous QTL studies between Oryza sativa cultivars, indicating potentially novel alleles from O. minutan.

• Journal of Plant Biotechnology
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• v.30 no.1
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• pp.19-25
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• 2003

Radiation technique in agriculture was initiated to develop mutant rice. Seeds of Daechungbyeo rice were irradiated with 250 Gy gamma ray for the purpose of inducing and selecting rice variants. Some quantitative traits of the variants in M$_{8}$ generation were evaluated and RAPD analysis was carried out. Variants showed a wider range of agronomic characteristics in both a positive and a negative direction compared with their original variety. The new mutants were characterized by an increased or decreased in plant height, lodging resistance and shorter panicle. RAPD analysis showed that polymorphic bands were presented in most of the primers. In comparison with the original variety, variants were classified into four groups through UPGMA analysis. Among mutants no. 91, 139, 140 and 141 was ranked as salt tolerance and the proline content of these mutants was more increased than that of original variety. The lines of 139, 140 and 141 had the highest genetic distance as compared to original variety in the dendrogram. It is expected that such variants will be useful not only for studying molecular genetics but also for breeding research and genetic analysis.s.

• Microbiology and Biotechnology Letters
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• v.17 no.4
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• pp.307-312
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• 1989

Strain No.77-AG-567 showed antifungal activity against Pyricularia oryzas and Sphaerotheca fuliginea. In the process of purification of active component this strain was found to produce blasticidin S together with another antibiotic. This compound was identified as being acetoxycyc-heximide, also referred to as E-73, by UV and $^1$H NMR spectral data. Identification of this strain led us to conclude that strain No.77-AG-567 is most probably be Streptomyces atratus. It showed different characteristics from S. atbutus, so far known to produce both blasticidin S and acetoxycycloheximide. Particularly worthy of note was the difference in spore surface. In addition, acetoxycycloheximide has been known to have activity only against yeast and tumor cells but we found that it also has activity against Pyricularia oryzae and Sphasrotheca fuliginea.

• Mycobiology
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• v.44 no.3
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• pp.171-179
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• 2016

In the screening of marine mangrove derived fungi for lovastatin productivity, endophytic Aspergillus luchuensis MERV10 exhibited the highest lovastatin productivity (9.5 mg/gds) in solid state fermentation (SSF) using rice bran. Aspergillus luchuensis MERV10 was used as the parental strain in which to induce genetic variabilities after application of different mixtures as well as doses of mutagens followed by three successive rounds of genome shuffling. Four potent mutants, UN6, UN28, NE11, and NE23, with lovastatin productivity equal to 2.0-, 2.11-, 1.95-, and 2.11-fold higher than the parental strain, respectively, were applied for three rounds of genome shuffling as the initial mutants. Four hereditarily stable recombinants (F3/3, F3/7, F3/9, and F3/13) were obtained with lovastatin productivity equal to 50.8, 57.0, 49.7, and 51.0 mg/gds, respectively. Recombinant strain F3/7 yielded 57.0 mg/gds of lovastatin, which is 6-fold and 2.85-fold higher, respectively, than the initial parental strain and the highest mutants UN28 and NE23. It was therefore selected for the optimization of lovastatin production through improvement of SSF parameters. Lovastatin productivity was increased 32-fold through strain improvement methods, including mutations and three successive rounds of genome shuffling followed by optimizing SSF factors.

• Plant Resources
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• v.5 no.2
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• pp.141-154
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• 2002

In this experiment, three kinds of mutations(ge, re, and eml )relating to the size of embryos were used to study their generation, genetic mechanism and developmental characteristics, and the interactions between embryo and endosperm were also examined. Giant embryo mutation comprises 7 kinds including the already isolated ge, and ge-2, which share an identical gene site. The SAM and the size of radicule for the ge showed little difference compared to a normal type. The number of embryo cells did not increased as much as it would affect the size of embryo. Therefore, the enlargement of embryo was due to the enlargement of scutellum that originated from the corpulence of each cell. Both F$_1$' s of re ]and odm 49 formed reduce embryos, and other combinations of hybridization showed all wild type of embryo sizes. Accordingly, the odm 49 must have an identical gene site of re 1, while odm 48 and odm 62 have different gene sites. Their shoots and radicules also shrank by the same ratio, however no sign of physical change was noticed. The size of embryo cell showed no change, while the number of cells was the half of that of wild types. The three gene sites of re represent all of them control the size of the entire embryo forming organs. The eml 1 was defined to have temperature sensibilities that the generation of endosperms was active at a high temperature while that was hampered at a low temperature.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.37 no.2
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• pp.185-197
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• 1992

Differences in the amount and chemical characteristics of the epicuticular waxes on rice leaves were studied for the active tillering and heading stages of rice varieties differing widely in gross leaf-surface property and genetics. The amount of waxes on surfaces of rice leaf-blades was determined by extraction with chloroform and chemical composition of the waxes was characterized by thin layer chromatography, gas liquid chromatography and infrared spectrophotometry. The amount of waxes varied by variety and significantly with growth stage. The amount at the heading stage was 1.7 to 3.6 mg/g fresh weight of leaves, which was two to three times as much as that at the tillering stage of 0.8 to 1.8 mg/g fresh weight. The waxes consisted of seven chemical classes, namely diols, fatty acids, fatty alcohols, fatty aldehydes, fatty esters, saturated and unsaturated hydrocarbons. Diols and unsaturated hydrocarbons were identified as new chemical classes of the rice epicuticular waxes. The polar constituents such as dials, fatty acids and fatty alcohols and the non-polars such as fatty aldehydes, fatty esters, and saturated and unsaturated hydrocarbons were identified at the heading stage, but at the tillering stage only the non-polar compounds were identified. In the carbon numbers (C) of the chemical classes, diols were composed entirely of C30 and acids were mainly of C30 and C31. In alcohols, primary alcohols were composed of C13 and C32, and the secondary alcohols were of C14, C16 and / or C30 regardless of the rice varieties. The acid portion of fatty esters, mainly composed of C22 and C23, showed low cabon numbers compared with the aldehydes. The alcohol portion of them showed a wide distribution in carbon numbers from C13 to C26 depending on the rice varieties. Hydrocarbons had odd carbon numbers, consisting mainly of C29 and C31.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.53 no.2
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• pp.217-223
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• 2008

Amylose and protein contents are important traits determining the edible quality of rice, especially in East Asian countries. Near-Infrared Reflectance Spectroscopy (NIRS) has become a powerful tool for rapid and nondestructive quantification of natural compounds in agricultural products. To test the practically of using NIRS for estimation of brown rice amylose and protein contents, the spectral reflectances ($400{\sim}2500\;nm$) of total 9,483 accessions of rice germplasm in Rural development Administration (RDA) Genebank ere obtained and compared to chemically determined amylose and protein content. The protein content of tested 119 accessions ranged from 6.5 to 8.0% and 25 accessions exhibited protein contents between 8.5 to 9.5%. In case of amylose content, all tested accessions ranged from 18.1 to 21.7% and the grade from 18.1 to 19.9% includes most number of accessions as 152 and 4 accessions exhibited amylose content between 20.5 to 21.7%. The optimal performance calibration model could be obtained from original spectra of brown rice using MPLS (Modified Partial Least Squares) with the correlation coefficients ($r_2$) for amylose and protein content were 0.865 and 0.786, respectively. The standard errors of calibration (SEC) exhibited good statistic values: 2.078 and 0.442 for amylose and protein contents, respectively. All these results suggest that NIR spectroscopy may serve as reputable and rapid method for quantification of brown rice protein and amylose contents in large numbers of rice germplasm.

• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.13-13
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• 2014

Species belonging to the genus Fusarium are widely distributed and cause diseases in many plants. Isolation of fungal strains from air or cereals is necessary for disease forecasting, disease diagnosis, and population genetics [1]. Previously we showed that Fusarium species are resistant to toxoflavin produced by the bacterial rice pathogen Burkholderia glumae while other fungal genera are sensitive to the toxin, resulting in the development of a selective medium for Fusarium species using toxoflavin [2]. In this study, we have tried to elucidate the resistant mechanism of F. graminearum against toxoflavin and interaction between the two pathogens in nature. To test whether B. glumae affects the development of F. graminearum, the wild-type F. graminearum strains were incubated with either the bacterial strain or supernatant of the bacterial culture. Both conditions increased the conidial production five times more than when the fungus was incubated alone. While co-incubation resulted in dramatic increase of conidial production, conidia germination delayed by either the bacterial strain or supernatant. These results suggest that certain factors produced by B. glumae induce conidial production and delay conidial germination in F. graminearum. To identify genes related to toxoflavin resistance in F. graminearum, we screened the transcriptional factor mutant library previously generated in F. graminearum [3] and identified one mutant that is sensitive to toxoflavin. We analyzed transcriptomes of the wild-type strain and the mutant strain under either absence or presence of toxoflavin through RNAseq. Expression level of total genes of 13,820 was measured by reads per kilobase per million mapped reads (RPKM). Under the criteria with more than two-fold changes, 1,440 genes were upregulated and 1,267 genes were down-regulated in wild-type strain than mutant strain in response to toxoflavin treatment. A comparison of gene expression profiling between the wild type and mutant through gene ontology analysis showed that genes related to metabolic process and oxidation-reduction process were highly enriched in the mutant strain. The data analyses will focus on elucidating the resistance mechanism of F. graminearum against toxoflavin and the interaction between the two pathogens in rice. Further evolutionary history will be traced through figuring out the gene function in populations and in other filamentous fungi.