57 results on '"Jeung JU"'
Search Results
2. Weed Control Efficacy of Sorghum Shoot Extract Extracted with Various Solvents
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LE, Thi Hien, JIA, Wei Qiang, WON, Ok Jae, OH, Taek–Keun, SHINOGI, Yoshiyuki, PARK, Kee Woong, and LEE, Jeung Ju
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Phenolic compound ,fungi ,Sorghum shoot ,food and beverages ,Weed control ,Natural herbicide - Published
- 2018
3. Weed Control Efficacy of Sorghum Shoot Extract Extracted with Various Solvents
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Wei Qiang Jia, Jeung Ju Lee, Ok Jae Won, Yoshiyuki Shinogi, Taek Keun Oh, Kee Woong Park, and Thi Hien Le
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Horticulture ,biology ,Shoot ,Sorghum ,biology.organism_classification ,Weed control ,Agronomy and Crop Science ,Biotechnology - Published
- 2018
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4. Allelopathic Suppression of Sorghum bicolor (L.) Moench Shoot Extracts on Weed Germination and on Weeds Treated by Foliar Application
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Ok Jae Won, Jung Sung Chung, Taek Keun Oh, Yoshiyuki Shinogi, Kee Woong Park, Jeung Ju Lee, and Thi Fflen Le
- Subjects
Horticulture ,Germination ,Shoot ,Sorghum bicolor ,Biology ,Weed ,Agronomy and Crop Science ,Allelopathy ,Biotechnology - Published
- 2018
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5. Allelopathic Suppression of Sorghum bicolor (L.) Moench Shoot Extracts on Weed Germination and on Weeds Treated by Foliar Application
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LE, Thi Hien, OH, Taek–Keun, WON, Ok Jae, SHINOGI, Yoshiyuki, Lee, Jeung Ju, PARK, Kee Woong, and CHUNG, Jung–Sung
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weed control ,food and beverages ,phenolic compounds ,natural herbicide ,Sorghum - Published
- 2018
6. Herbicidal Selectivity and Mode of Action of EK–2612 in Rice and Barnyardgrass
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Oh, Taek–Keun, Uddin, Md. Romij, Lee, Jeung Ju, Shinogi, Yoshiyuki, and Park, Kee Woong
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Herbicide selectivity ,mode of action ,ACCase - Published
- 2015
7. Herbicidal Selectivity and Mode of Action of EK–2612 in Rice and Barnyardgrass
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Taek Keun Oh, Md. Romij Uddin, Yoshiyuki Shinogi, Kee Woong Park, and Jeung Ju Lee
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Chlorosis ,biology ,food and beverages ,Echinochloa ,Meristem ,biology.organism_classification ,Pyruvate carboxylase ,Chloroplast ,chemistry.chemical_compound ,Biosynthesis ,chemistry ,Botany ,PEST analysis ,Mode of action ,Agronomy and Crop Science ,Biotechnology - Abstract
Weeds have always been recognized as one of the major constraints on yield and quality of rice and have been proved a significant pest problem in temperate rice culture (Ioannis and Kico, 2005). The barnyardgrass (Echinochloa crus–galli L.) is a highly prolific annual grass weed that is widely distributed in the tropics as well in most of the rice growing regions in the world believed to control it for maximizing rice production. EK–2612, a new synthesized herbicide commonly known as grass killers has been developed for the selective post emergence control of a wide range of grass weeds including barnyardgrass. This compound belongs to cyclohexanediones (CHDs) family, which was developed in the late 1970’s and has been used to control grass species in dicotyledonous crops (Iwataki and Hirono 1978; Swisher and Corbin 1982). Two classes of grass killer herbicide i.e., the aryloxyphenoxy propionates (AOPPs) and the CHDs have been reported as acetyl–CoA carboxylase (ACCase) inhibitors. In plants, two forms of ACCase have been identified those are located in the chloroplast, the primary site of plant fatty acid biosynthesis, and in the cytosol (Sasaki et al., 1995; Konishi et al., 1996). Chloroplastic ACCase is a vital point of plant metabolism (Ohlrogge and Jaworski 1997). The CHD herbicides act on the plastidic enzyme ACCase. ACCase is a key enzyme involved in the biosynthesis of fatty acids, particularly is active in meristematic tissues, and its inhibition results in cessation of growth followed by the chlorosis of the young leaves and the eventual necrosis of the whole plant (Harwood 1989; Gronwald 1991). This enzyme acts by catalyzing the formation of malonyl–CoA from the ATP–dependent carboxylation of acetyl–CoA (Powles & Yu, 2010). The objective of this study was to determine the herbicidal activity of the compound EK–2612 and to determine the mechanism of selectivity between rice and barnyardgrass.
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- 2015
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8. Distribution and Control of Aquatic Weeds in Waterways and Riparian Wetlands
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Jong Yeong Pyon, Sang Woo Kim, Kee Woong Park, and Jeung Ju Lee
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geography ,geography.geographical_feature_category ,biology ,Najas ,Hydrilla ,Salvinia natans ,Wetland ,Ceratophyllum demersum ,biology.organism_classification ,Phragmites ,Agronomy ,Myriophyllum verticillatum ,Botany ,Ambrosia artemisiifolia - Abstract
Many irrigated and drainage canals, reservoirs, lakes, and rivers are choked by the explosive growth of aquatic weeds, resulting in enormous direct loss in Korea. Distribution of aquatic weeds and exotic invasive plant species in irrigation and drainage waterways, and riparian wetlands was reviewed to provide basic information for management of aquatic weeds and invasive plant species in wetlands. Dominant emergent weeds in canals, reservoirs and lakes were Phragmites communis, Leersia japonica, Zizania latifolia, Conyza canadensis, C. annuus, Rumex crispus, Panicum dichotomiflorum, Bidens frondosa, and Oenothera odorata. Dominant emergent weeds in wetlands of rivers include Digitaria sanguinalis, P. communis, R. crispus, Artemisia princeps, Humulus japonicus, Echinochloa crusgalli, B. frondosa, and Persicaria thunbergii. In irrigation and drainage canals and lakes, dominant submersed weeds were Hydrilla verticillata, Najas minor, Potamogeton malaianus, P. crispus, Ceratophyllum demersum, Myriophyllum verticillatum, Salvinia natans, and Trapa natans. Dominant exotic weeds in wetlands include Trifolium repens, O. odorata, C. annuus, B. frondosa, Avena fatua, Ambrosia artemisiifolia, X. strumarium, and P. dichotomiflorum. Approaches to aquatic weed control were mechanical, chemical and biological control techniques. Periodic monitoring of aquatic weeds and exotic weeds, and their integrated management studies are needed in waterways and riparian wetlands in Korea.
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- 2015
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9. Weed Control and Safety of Transgenic Rice Event, CPPO06 in Direct-Seeding Flooded Rice Field
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Bumkyu Lee, Hong-Gyu Kang, Ok Jae Won, Chang-Gi Kim, Jeung Ju Lee, Kee Woong Park, Min Yong Eom, and Su Hyuk Park
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Juglans mandshurica ,Echinochloa oryzoides ,Agronomy ,Sowing ,Protoporphyrinogen oxidase ,Phytotoxicity ,Annual Weeds ,Biology ,Weed control ,biology.organism_classification ,Genetically modified rice - Abstract
This study was conducted to evaluate the efficacy of weed control and phytotoxicity of oxyfluorfen using a transgenic rice line (CPPO06 event) resistant to protoporphyrinogen oxidase (Protox) inhibiting herbicides in the direct-seeding flooded rice. Five annual weeds including Echinochloa oryzoides and two perennial weeds were occurred in the test field. Oxyfluorfen at 120 g a.i. ha -1 in the application timing of two days before sowing and 0 and five days after sowing showed more than 90% weed control value except for Juglans mandshurica. Total weed control value was more than 95% in any application timing indicating a highly effective herbicide in the direct-seeding flooded rice. When compared with untreated control, no visual injuries were detected at single and double dosage of oxyfluorfen. The agronomic characteristics and yield components of CPPO06 event was reasonable in any time of application in this study. Based on these data, oxyfluorfen application before and after sowing can be applied to provide effective weed management in the direct-seeding flooded field.
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- 2015
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10. A Survey of Weeds Occurrence on Paddy Fields in Chungnam Province in Korea
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Ok Jae Won, In Yong Lee, Ki Seon Hwang, Su Hyuk Park, Jeung Ju Lee, Kee Woong Park, Su Jeoung Suh, Min Yong Eom, and Sung Min Han
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education.field_of_study ,biology ,Agronomy ,Monochoria vaginalis ,Aneilema ,Population ,Dominance (ecology) ,Paddy field ,Echinochloa ,biology.organism_classification ,education ,Weed control ,Weed - Abstract
The survey of weed occurrence was conducted to identify problematic weed species on the paddy field. Total 524 sites of the 17 regions in Chungnam Province in Korea were investigated from June to August, 2013. In the whole region, 23 weed species were identified including 19 annuals and 4 perennials. The most dominant weed species in Chungnam paddy fields were Echinochloa crus-galli (25.3%), followed by Monochoria vaginalis (11.9%), Eleocharis kuroguwai (10.3%), Bidens tripartite (9.3%) and Aneilema japonicum (8.5%). The 95.2% of the investigation sites was determined under dominance value 1 (range of cover <10: numerous individuals) by Braun-Branquet indicating proper weed control in the paddy fields. This information could be useful for estimation of future weed occurrence, weed population dynamics and establishment of weed control methods in Chungnam Province in Korea.
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- 2013
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11. Efficacy of glufosinate-ammonium to control annual and perennial weeds on the ridges of paddy fields
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Kee Woong Park, Ok Jae Won, WeiQiang Jia, and Jeung Ju Lee
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Agronomy ,Perennial plant ,biology ,Equisetum arvense ,Soil Science ,Elymus ,Poa annua ,Phytotoxicity ,Echinochloa ,biology.organism_classification ,Weed control ,Weed ,Agronomy and Crop Science - Abstract
This study was conducted to evaluate the efficacy and phytotoxicity of glufosinate-ammonium in controlling annual and perennial weeds on paddy ridges. Glufosinate-ammonium SL (900 g a. i./ha) and glufosinate-ammonium ME (600 g a. i./ha) mixed with fluthiacet-methyl (10 g a. i./ha) were tested in the field experiments. Five annual weed species, Glycine soja, Erigeron canadensis, Disitaria ciliaris, Poa annua and Echinochloa utilis, and four perennial weed species Elymus tsukushensis, Taraxacum platycarpum, Equisetum arvense and Artemisia princeps were identified on the paddy ridges. The results of this experiment indicated that these annual and perennial weeds could be effectively controlled by both the herbicides. Application of these herbicides did not negatively affect the number of tillers and plant height of rice grown near the treated paddy ridges. Therefore, it can be concluded that the non-selective glufosinate-ammonium can provide an effective control of weeds on the paddy ridges if application is properly made.
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- 2017
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12. Distribution and Control of Aquatic Weeds in Waterways and Riparian Wetlands
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Pyon, Jong Yeong, primary, Kim, Sang Woo, additional, Lee, Jeung Ju, additional, and Park, Kee Woong, additional
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- 2015
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13. Weed Control and Safety of Transgenic Rice Event, CPPO06 in Direct-Seeding Flooded Rice Field
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Won, Ok Jae, primary, Park, Su Hyuk, additional, Eom, Min Yong, additional, Kim, Chang-Gi, additional, Lee, Bum Kyu, additional, Kang, Hong-Gyu, additional, Lee, Jeung Ju, additional, and Park, Kee Woong, additional
- Published
- 2015
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14. Efficacy of glufosinate-ammonium to control annual and perennial weeds on the ridges of paddy fields.
- Author
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WEIQIANG JIA, OK JAE WON, KEE WOONG PARK, and JEUNG JU LEE
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GLUFOSINATE ,PADDY fields ,PHYTOTOXICITY - Abstract
This study was conducted to evaluate the efficacy and phytotoxicity of glufosinateammonium in controlling annual and perennial weeds on paddy ridges. Glufosinateammonium SL (900 g a. i./ha) and glufosinate-ammonium ME (600 g a. i./ha) mixed with fluthiacet-methyl (10 g a. i./ha) were tested in the field experiments. Five annual weed species, Glycine soja, Erigeron canadensis, Disitaria ciliaris, Poa annua and Echinochloa utilis, and four perennial weed species Elymus tsukushensis, Taraxacum platycarpum, Equisetum arvense and Artemisia princeps were identified on the paddy ridges. The results of this experiment indicated that these annual and perennial weeds could be effectively controlled by both the herbicides. Application of these herbicides did not negatively affect the number of tillers and plant height of rice grown near the treated paddy ridges. Therefore, it can be concluded that the non-selective glufosinate-ammonium can provide an effective control of weeds on the paddy ridges if application is properly made. [ABSTRACT FROM AUTHOR]
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- 2017
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15. A Survey of Weeds Occurrence on Paddy Fields in Chungnam Province in Korea
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Hwang, Ki Seon, primary, Won, Ok Jae, additional, Park, Su Hyuk, additional, Eom, Min Yong, additional, Han, Sung Min, additional, Suh, Su Jeoung, additional, Lee, In Yong, additional, Lee, Jeung Ju, additional, and Park, Kee Woong, additional
- Published
- 2013
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16. Application of the Ilizarow technique to the complications of tibial open fracture report of two cases
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Song, Eun Kyoo, primary, Jeung, Ju Chull, additional, Rowe, Sung Man, additional, and Kim, Hyung Soon, additional
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- 1991
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17. Clinical Study on Monteggia Lesion
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Rowe, Sung Man, primary, Moon, Eun Sun, additional, Lee, Chun Tek, additional, and Jeung, Ju Chull, additional
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- 1991
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18. Pyogenic Atlanto-Axial Instability Complicated after Tonsillectomy: Report of A Case
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Chung, Jae Yoon, primary, Chung, Go Hun, additional, and Jeung, Ju Chull, additional
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- 1991
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19. GWAS analysis reveals the genetic basis of blast resistance associated with heading date in rice.
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Lee SY, Lee G, Han J, Ha SK, Lee CM, Kang K, Jin M, Suh JP, Jeung JU, Mo Y, and Lee HS
- Abstract
Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its Heading date 1 ( Hd1 ) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes ( Os06g0286500 , Os06g0286700 , and Os06g0287500 ) located at Piz locus on chromosome 6, and one at the Pi-ta locus ( Os12g0281300 ) on chromosome 12. Haplotype analysis revealed blast resistance associated with Piz locus was exclusively specific to Type 14 hd1 among japonica rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lee, Lee, Han, Ha, Lee, Kang, Jin, Suh, Jeung, Mo and Lee.)
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- 2024
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20. Allelic combinations of Hd1, Hd16, and Ghd7 exhibit pleiotropic effects on agronomic traits in rice.
- Author
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Lee SY, Jeung JU, and Mo Y
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- Plant Breeding, Phenotype, Quantitative Trait Loci, Alleles, Oryza genetics
- Abstract
Heading date is a critical agronomic trait that significantly affects grain yield and quality in rice. As early heading is typically associated with reduced yield due to shorter growth duration, it is essential to harness optimum heading date genes and their allelic combinations to promote heading while minimizing yield penalties. In this study, we identified quantitative trait loci (QTLs) for heading date and other major agronomic traits in a recombinant inbred line (RIL) population derived from a cross between Koshihikari and Baegilmi. Analyses on 3 major QTLs for heading date and their underlying genes (Hd1, Hd16, and Ghd7) revealed their pleiotropic effects on culm length, panicle length, and head rice percentage. Additionally, Ghd7 exhibited pleiotropic effects on panicle number and grain size. Among 8 different types of allelic combinations of the 3 heading date genes, RILs carrying a single nonfunctional hd16 or ghd7 under the functional background of the other 2 genes (Hd1hd16Ghd7 and Hd1Hd16ghd7) showed potential for maintaining yield and quality-related traits while accelerating heading. These results provide valuable insights for fine-tuning heading dates in rice breeding programs., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
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- 2024
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21. RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.
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Shrestha AMS, Gonzales MEM, Ong PCL, Larmande P, Lee HS, Jeung JU, Kohli A, Chebotarov D, Mauleon RP, Lee JS, and McNally KL
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- Software, Epigenomics methods, Computational Biology methods, Polymorphism, Single Nucleotide, Genomics methods, Genome, Plant, Chromosome Mapping, Databases, Genetic, Oryza genetics, Quantitative Trait Loci, Genome-Wide Association Study, Data Mining
- Abstract
Background: As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources., Results: We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs., Conclusions: RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf., (© The Author(s) 2024. Published by Oxford University Press on behalf of GigaScience.)
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- 2024
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22. Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars.
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Mo Y, Lee CM, Park HM, Ha SK, Kim MJ, Kwak J, Lee HS, Lee JH, and Jeung JU
- Abstract
Optimizing flowering time in crop plants is critical for maximizing yield and quality under target environments. While there is a wide range of heading date variation in Korean rice cultivars, the underlying gene mechanisms are unclear. Here, we sequenced the protein coding regions of Hd1 , the major rice heading date gene, from 293 Korean rice cultivars and investigated the associations between Hd1 allele types and major agronomic traits under four different environments. There were four functional Hd1 and five nonfunctional hd1 alleles distributed among the 293 Korean rice cultivars. The effects of the Hd1 allele types were highly significant for days to heading in all four environments, explaining 51.4-65.8% of the phenotypic variation. On average, cultivars carrying nonfunctional hd1 headed 13.7 days earlier than those carrying functional Hd1 . While the Hd1 allele types exhibited highly significant effects on culm length and protein content under all four environments, the differences between cultivars carrying Hd1 and hd1 were minimal. The effects of the Hd1 allele types on amylose content were significant in only one of the four environments. Our results provide useful information for fine-tuning rice heading dates by utilizing different Hd1 alleles in rice breeding programs.
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- 2021
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23. Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement.
- Author
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Lee JS, Chebotarov D, McNally KL, Pede V, Setiyono TD, Raquid R, Hyun WJ, Jeung JU, Kohli A, and Mo Y
- Abstract
Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8-10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.
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- 2021
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24. Characterization of QTLs and Candidate Genes for Days to Heading in Rice Recombinant Inbred Lines.
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Mo Y, Jeong JM, Ha SK, Kim J, Lee C, Lee GP, and Jeung JU
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- Adaptation, Physiological, Flowers growth & development, Genotype, Oryza growth & development, Plants, Genetically Modified growth & development, Flowers genetics, Gene Expression Regulation, Plant, Genes, Plant, Oryza genetics, Plant Breeding methods, Plants, Genetically Modified genetics, Quantitative Trait Loci
- Abstract
Understanding the gene mechanisms controlling days to heading (DH) is important in rice breeding for adaption in the target environment. Using a recombinant inbred line population derived from the cross between two japonica rice cultivars, Koshihikari and Baegilmi, we identified three consistent quantitative trait loci (QTLs) for DH for two years, qDH3 , qDH6 , and qDH7 on chromosomes 3, 6, and 7, respectively. While Baegilmi contributed the allele for early heading at qDH6 and qDH7 with the additive effect of five days each, Koshihikari contributed the allele for early heading at qDH3 with the additive effect of three days. Notably, pyramiding two or more alleles for early heading at these QTLs accelerated heading effectively. Sequencing of Hd16 , Hd1 , and Ghd7 , the previously known heading date genes underlying qDH3 , qDH6 , and qDH7 , respectively, revealed that Baegilmi and Koshihikari carry different alleles at the three genes. Molecular markers were developed to screen the allelic compositions of the three genes among 295 Korean commercial rice cultivars. The results showed that few cultivars carry alleles for early heading at the three genes, highlighting that DH can be further accelerated and fine-tuned in breeding programs by combining the desirable alleles of Hd16 , Hd1 , and Ghd7 .
- Published
- 2020
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25. A New SNP in Rice Gene Encoding Pyruvate Phosphate Dikinase (PPDK) Associated with Floury Endosperm.
- Author
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Wang H, Ham TH, Im DE, Lar SM, Jang SG, Lee J, Mo Y, Jeung JU, Kim ST, and Kwon SW
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- Endosperm growth & development, Gene Expression Regulation, Enzymologic, Oryza growth & development, Phenotype, Endosperm genetics, Flour analysis, Gene Expression Regulation, Plant, Oryza genetics, Plant Proteins genetics, Polymorphism, Single Nucleotide, Pyruvate, Orthophosphate Dikinase genetics
- Abstract
Rice varieties with suitable flour-making qualities are required to promote the rice processed-food industry and to boost rice consumption. A rice mutation, Namil(SA)-flo1, produces grains with floury endosperm. Overall, grains with low grain hardness, low starch damage, and fine particle size are more suitable for use in flour processing grains with waxy, dull endosperm with normal grain hardness and a high amylose content. In this study, fine mapping found a C to T single nucleotide polymorphism (SNP) in exon 2 of the gene encoding cytosolic pyruvate phosphate dikinase (cy OsPPDK ). The SNP resulted in a change of serine to phenylalanine acid at amino acid position 101. The gene was named FLOURY ENDOSPERM 4-5 ( FLO4-5 ). Co-segregation analysis with the developed cleaved amplified polymorphic sequence (CAPS) markers revealed co-segregation between the floury phenotype and the flo4-5 . This CAPS marker could be applied directly for marker-assisted selection. Real-time RT-PCR experiments revealed that PPDK was expressed at considerably higher levels in the flo4-5 mutant than in the wild type during the grain filling stage. Plastid ADP-glucose pyrophosphorylase small subunit (AGPS2a and AGPS2b) and soluble starch synthase ( SSIIb and SSIIc) also exhibited enhanced expression in the flo4-5 mutant.
- Published
- 2020
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26. A new SNP in cyOsPPDK gene is associated with floury endosperm in Suweon 542.
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Wang H, Mo YJ, Im DE, Jang SG, Ham TH, Lee J, Jeung JU, and Kwon SW
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- Edible Grain growth & development, Flour, Gene Expression Regulation, Plant, Mutagenesis, Insertional, Mutation, Oryza growth & development, Seeds genetics, Seeds growth & development, Starch genetics, Edible Grain genetics, Endosperm genetics, Oryza genetics, Pyruvate, Orthophosphate Dikinase genetics
- Abstract
Pyruvate orthophosphate dikinase (PPDK) is a component of glycolysis to mediate endosperm energy charge by adjusting the ratio of ATP to ADP and AMP that proposed to balance the flow of carbon into starch, protein, fatty acid and amino acid biosynthesis. However, these were inconsistent with the first report of a T-DNA insertional knockout mutant of the rice PPDK gene (flo4) showed that rice with inactivated PPDK gene failed to produce a opaque seeds. Therefore, the PPDK might have multifaceted functions in grain filling stage, which in some ways might depend on the direction of the reversible catalysis. Suweon 542 is a rice (Oryza sativa L.) mutant developed from Oryza sativa ssp. japonica cv. Namil. Suweon 542 has a milky-white floury endosperm suitable for dry filling, with low starch damage, low grain hardness, and fine flour particle size. The mutant locus on chromosome 5 controls the floury endosperm phenotype of Suweon 542. Fine mapping of this locus is required for efficient breeding of rice germplasm suitable for dry milling. In this study, whole genome of Suweon 542 and Milyang 23 were re-sequenced using Illumina HiSeq 2500. Co-segregation analysis of F
3:4 family populations derived from Suweon 542/Milyang 23 was performed using eight CAPS markers and phenotypic evaluation of the endosperm. The target region was mapped to a 33 kb region and identified to encode cytosolic pyruvate orthophosphate dikinase protein (cyOsPPDK). A G→A SNP in exon 8 of cyOsPPDK resulting in a missense mutation from Gly to Asp at amino acid position 404 was responsible for the floury endosperm of Suweon 542. qRT-PCR experiments revealed that FLO4-4 was expressed to a considerably higher level in Suweon 542 than in Namil during the grain filling stage. Overall, fine mapping of FLO4-4 and candidate gene analysis provided further insight into the floury endosperm of rice, and reveal a novel SNP in cyOsPPDK gene can affect the floury endosperm phenotype through active PPDK gene during grain filling stage.- Published
- 2018
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27. OsMPK3 is a TEY-type rice MAPK in Group C and phosphorylates OsbHLH65, a transcription factor binding to the E-box element.
- Author
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Shin HY, You MK, Jeung JU, and Shin JS
- Subjects
- Amino Acid Sequence, Animals, Basic Helix-Loop-Helix Transcription Factors genetics, Cyclopentanes pharmacology, E-Box Elements, Hemiptera physiology, Magnaporthe physiology, Mitogen-Activated Protein Kinases genetics, Molecular Sequence Data, Oryza cytology, Oryza genetics, Oryza immunology, Oxylipins pharmacology, Phosphorylation, Phylogeny, Plant Growth Regulators pharmacology, Plant Proteins genetics, Plant Proteins metabolism, Protein Binding, Salicylic Acid pharmacology, Seedlings cytology, Seedlings enzymology, Seedlings genetics, Seedlings immunology, Sequence Alignment, Stress, Physiological, Basic Helix-Loop-Helix Transcription Factors metabolism, Gene Expression Regulation, Plant, Mitogen-Activated Protein Kinases metabolism, Oryza enzymology, Plant Diseases immunology, Signal Transduction
- Abstract
Key Message: OsMPK3 is a TEY-type rice MAPK belonging to Group C and directly phosphorylates OsbHLH65 in the nucleus. OsMPK3 and OsbHLH65 are induced by biotic stress and defense-related hormones. Mitogen-activated protein kinases (MAPKs) are involved in the majority of signaling pathways that regulate plant development and stress tolerance via the phosphorylation of target molecules. Plant MAPKs are classified into two subtypes, TEY and TDY, according to the TxY (x = E or D) motif in their activation loop, and the TDY motif is unique to plant MAPKs. In rice, 17 MAPKs have been classified into six groups. To date, the functions of many TDY-type rice MAPKs have been characterized, but little is known of the TEY-type MAPKs in Group C and their possible target substrates. In the study reported here, we determined that a TEY-type rice MAPK belonging to subgroup C, named OsMPK3, phosphorylates its substrate OsbHLH65 in the nucleus. Our electrophoresis mobility shift assay results revealed that OsbHLH65 specifically binds to the E-box cis-element, but not to the G-box. Both OsMPK3 and OsbHLH65 were induced by treatments with rice blast (Magnaporthe grisea), brown planthopper (Nilaparvata lugens), and defense-related hormones, such as methyl jasmonic acid and salicylic acid. Our results suggest the possibility that OsMPK3 contributes to the defense signal transduction by phosphorylating the basic helix-loop-helix transcription factor.
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- 2014
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28. Effects of allelic variations in starch synthesis-related genes on grain quality traits of Korean nonglutinous rice varieties under different temperature conditions.
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Mo YJ, Jeung JU, Shin WC, Kim KY, Ye C, Redoña ED, and Kim BK
- Abstract
Influences of allelic variations in starch synthesis-related genes (SSRGs) on rice grain quality were examined. A total of 187 nonglutinous Korean rice varieties, consisting of 170 Japonica and 17 Tongil-type varieties, were grown in the field and in two greenhouse conditions. The percentages of head rice and chalky grains, amylose content, alkali digestion value, and rapid visco-analysis characteristics were evaluated in the three different environments. Among the 10 previously reported SSRG markers used in this study, seven were polymorphic, and four of those showed subspecies-specific allele distributions. Six out of the seven polymorphic SSRG markers were significantly associated with at least one grain quality trait (R (2) > 0.1) across the three different environments. However, the association level and significance were markedly lower when the analysis was repeated using only the 170 Japonica varieties. Similarly, the significant associations between SSRG allelic variations and changes in grain quality traits under increased temperature were largely attributable to the biased allele frequency between the two subpopulations. Our results suggest that within Korean Japonica varieties, these 10 major SSRG loci have been highly fixed during breeding history and variations in grain quality traits might be influenced by other genetic factors.
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- 2014
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29. Agronomic and genetic analysis of Suweon 542, a rice floury mutant line suitable for dry milling.
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Mo YJ, Jeung JU, Shin YS, Park CS, Kang KH, and Kim BK
- Abstract
Background: Producing rice flour of good quality by dry milling is necessary to reduce milling costs and promote the processed rice food industry. This study was conducted to evaluate the dry milling properties of Suweon 542, a floury endosperm mutant, and identify the chromosomal region responsible for the floury endosperm characteristics., Results: Compared with the wild type, after dry milling process, the grain hardness of Suweon 542 was significantly lower because of its round and loosely packed starch granules. Also, the flour of Suweon 542 had significantly smaller particles and less damaged starch than Namil and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Considering that the yield loss of Suweon 542 due to its floury endosperm was largely compensated for by an increased number of spikelets per panicle, Suweon 542 has potential value as a raw material for rice flour production. Association analysis using 70 genome-wide SSR markers and 94 F2 plants derived from Suweon 542/Milyang 23 showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of Suweon 542 was directed by a major recessive locus, flo7(t), located in the 19.33-19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F2 population., Conclusions: The floury endosperm of Suweon 542 is suitable for dry milling, with a small flour particle size and low damaged starch content. Further physical mapping of flo7(t), the floury endosperm locus of Suweon 542, would facilitate efficient breeding of rice cultivars with proper dry milling adaptability that can be used in the processed rice food industry.
- Published
- 2013
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30. Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice.
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Suh JP, Jeung JU, Noh TH, Cho YC, Park SH, Park HS, Shin MS, Kim CK, and Jena KK
- Abstract
Background: The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (Xa4 + xa5 + Xa21) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality., Results: Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of Xoo prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of Xoo, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes Xa4, xa5 and Xa21 provided a higher resistance to Xoo than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL., Conclusions: The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will have a high impact on the yield stability and sustainability of rice productivity.
- Published
- 2013
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31. A cystathionine-β-synthase domain-containing protein, CBSX2, regulates endothecial secondary cell wall thickening in anther development.
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Jung KW, Kim YY, Yoo KS, Ok SH, Cui MH, Jeong BC, Yoo SD, Jeung JU, and Shin JS
- Subjects
- Arabidopsis enzymology, Arabidopsis genetics, Arabidopsis growth & development, Arabidopsis Proteins genetics, Cell Wall drug effects, Cell Wall genetics, Chloroplasts drug effects, Chloroplasts enzymology, Chloroplasts genetics, Cyclopentanes pharmacology, Cystathionine beta-Synthase genetics, DNA, Bacterial genetics, DNA, Bacterial metabolism, Flowers enzymology, Flowers genetics, Flowers ultrastructure, Hydrogen Peroxide metabolism, Lignin metabolism, Microscopy, Electron, Scanning, Oxylipins pharmacology, Phloroglucinol metabolism, Plant Infertility, Plants, Genetically Modified enzymology, Plants, Genetically Modified genetics, Plants, Genetically Modified growth & development, Protein Structure, Tertiary, Signal Transduction, Thioredoxins genetics, Thioredoxins metabolism, Two-Hybrid System Techniques, Arabidopsis Proteins metabolism, Cell Wall enzymology, Cystathionine beta-Synthase metabolism, Flowers growth & development, Gene Expression Regulation, Developmental
- Abstract
Anther formation and dehiscence are complex pivotal processes in reproductive development. The secondary wall thickening in endothecial cells of the anther is a known prerequisite for successful anther dehiscence. However, many gaps remain in our understanding of the regulatory mechanisms underlying anther dehiscence in planta, including a possible role for jasmonic acid (JA) and H(2)O(2) in secondary wall thickening of endothecial cells. Here, we report that the cystathionine β-synthase domain-containing protein CBSX2 located in the chloroplast plays a critical role in thickening of the secondary cell walls of the endothecium during anther dehiscence in Arabidopsis. A T-DNA insertion mutant of CBSX2 (cbsx2) showed increased secondary wall thickening of endothecial cells and early anther dehiscence. Consistently, overexpression of CBSX2 resulted in anther indehiscence. Exogenous JA application induced secondary wall thickening and caused flower infertility in the cbsx2 mutant, whereas it partially restored fertility in the CBSX2-overexpressing lines lacking the wall thickening. CBSX2 directly modulated thioredoxin (Trx) in chloroplasts, which affected the level of H(2)O(2) and, consequently, expression of the genes involved in secondary cell wall thickening. Our findings have revealed that CBSX2 modulates the H(2)O(2) status, which is linked to the JA response and in turn controls secondary wall thickening of the endothecial cells in anthers for dehiscence to occur.
- Published
- 2013
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32. A novel F-box protein represses endothecial secondary wall thickening for anther dehiscence in Arabidopsis thaliana.
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Kim YY, Jung KW, Jeung JU, and Shin JS
- Subjects
- Arabidopsis growth & development, Arabidopsis ultrastructure, Arabidopsis Proteins metabolism, Cell Growth Processes physiology, Cell Wall metabolism, Flowers cytology, Flowers growth & development, Flowers metabolism, Flowers ultrastructure, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Plants, Genetically Modified, Arabidopsis cytology, Arabidopsis metabolism, F-Box Proteins metabolism
- Abstract
In plants, the regulation of protein turnover by the ubiquitin proteasome system (UPS) is a key posttranslational mechanism underlying diverse cellular processes. However, the participation of the UPS in cellular processes involved in anther dehiscence, especially endothecial secondary wall (ESW) thickening, has not been characterized. Here, we report that a novel F-box protein in arabidopsis, designated SAF1 (Secondary wall thickening-Associated F-box 1), negatively regulates ESW thickening in the anther. SAF1 is predominantly expressed in flower tissues and interacts with Arabidopsis-Skp1-like 19 (ASK19). SAF1-overexpressed (Ox) lines showed reduced fertility due to a lack or loss of ESW thickening in the anther and inhibition of the expression of relevant genes, such as IRREGURAR XYLEMs (IRXs) in flowers. These findings suggest that the novel Skp/Cul/F-box (SCF) complex consisting of SAF1 as an F-box protein and ASK19 as a Skp functions in secondary wall thickening of the anther endothecium., (Copyright © 2011 Elsevier GmbH. All rights reserved.)
- Published
- 2012
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33. A stress-responsive caleosin-like protein, AtCLO4, acts as a negative regulator of ABA responses in Arabidopsis.
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Kim YY, Jung KW, Yoo KS, Jeung JU, and Shin JS
- Subjects
- Adaptation, Physiological drug effects, Arabidopsis cytology, Arabidopsis Proteins genetics, DNA, Bacterial genetics, Droughts, Gene Expression Regulation, Plant drug effects, Gene Knockdown Techniques, Genes, Plant genetics, Germination drug effects, Mannitol pharmacology, Mutagenesis, Insertional drug effects, Mutagenesis, Insertional genetics, Mutation genetics, Organ Specificity drug effects, Plant Stomata cytology, Plant Stomata drug effects, Plant Stomata physiology, Plant Vascular Bundle cytology, Plant Vascular Bundle drug effects, Plant Vascular Bundle metabolism, Plants, Genetically Modified, Promoter Regions, Genetic genetics, Protein Binding drug effects, Seeds drug effects, Seeds growth & development, Signal Transduction genetics, Sodium Chloride pharmacology, Subcellular Fractions drug effects, Subcellular Fractions metabolism, Abscisic Acid pharmacology, Arabidopsis drug effects, Arabidopsis physiology, Arabidopsis Proteins metabolism, Calcium-Binding Proteins metabolism, Plant Proteins metabolism, Stress, Physiological drug effects
- Abstract
Caleosins or related sequences have been found in a wide range of higher plants. In Arabidopsis, seed-specific caleosins are viewed as oil-body (OB)-associated proteins that possess Ca(2+)-dependent peroxygenase activity and are involved in processes of lipid degradation. Recent experimental evidence suggests that one of the Arabidopsis non-seed caleosins, AtCLO3, is involved in controlling stomatal aperture during the drought response; the roles of the other caleosin-like proteins in Arabidopsis remain largely uncharacterized. We have demonstrated that a novel stress-responsive and OB-associated Ca(2+)-binding caleosin-like protein, AtCLO4, is expressed in non-seed tissues of Arabidopsis, including guard cells, and down-regulated following exposure to exogenous ABA and salt stress. At the seed germination stage, a loss-of-function mutant (atclo4) was hypersensitive to ABA, salt and mannitol stresses, whereas AtCLO4-overexpressing (Ox) lines were more hyposensitive to those stresses than the wild type. In adult stage, atclo4 mutant and AtCLO4-Ox plants showed enhanced and decreased drought tolerance, respectively. Following exposure to exogenous ABA, the expression of key ABA-dependent regulatory genes, such as ABF3 and ABF4, was up-regulated in the atclo4 mutant, while it was down-regulated in AtCLO4-Ox lines. Based on these results, we propose that the OB-associated Ca(2+)-binding AtCLO4 protein acts as a negative regulator of ABA responses in Arabidopsis.
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- 2011
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34. Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.).
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Suh JP, Jeung JU, Lee JI, Choi YH, Yea JD, Virk PS, Mackill DJ, and Jena KK
- Subjects
- Chromosome Mapping, Crops, Agricultural genetics, Crops, Agricultural growth & development, Crops, Agricultural physiology, Crosses, Genetic, Genes, Plant, Genetic Markers, Genome, Plant, Genotype, Haplotypes, Oryza growth & development, Phenotype, Reproduction genetics, Stress, Physiological genetics, Adaptation, Physiological genetics, Cold Temperature, Oryza genetics, Oryza physiology, Quantitative Trait Loci
- Abstract
Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. Even though low temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo, to produce 153 F(8) recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance with respect to percent seed set using cold-water (18-19 degrees C) irrigation in the field and controlled air temperature (17 degrees C) in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366. Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production.
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- 2010
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35. Novel bifunctional nucleases, OmBBD and AtBBD1, are involved in abscisic acid-mediated callose deposition in Arabidopsis.
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You MK, Shin HY, Kim YJ, Ok SH, Cho SK, Jeung JU, Yoo SD, Kim JK, and Shin JS
- Subjects
- Amino Acid Sequence, Arabidopsis enzymology, Arabidopsis genetics, Botrytis, Cloning, Molecular, DNA, Plant genetics, Deoxyribonucleases genetics, Gene Expression Profiling, Gene Expression Regulation, Plant, Magnaporthe, Molecular Sequence Data, Oryza enzymology, Plants, Genetically Modified enzymology, Plants, Genetically Modified genetics, Plants, Genetically Modified growth & development, Ribonucleases genetics, Sequence Alignment, Abscisic Acid metabolism, Arabidopsis growth & development, Deoxyribonucleases metabolism, Glucans metabolism, Oryza genetics, Ribonucleases metabolism
- Abstract
Screening of the expressed sequence tag library of the wild rice species Oryza minuta revealed an unknown gene that was rapidly and strongly induced in response to attack by a rice fungal pathogen (Magnaporthe oryzae) and an insect (Nilaparvata lugens) and by wounding, abscisic acid (ABA), and methyl jasmonate treatments. Its recombinant protein was identified as a bifunctional nuclease with both RNase and DNase activities in vitro. This gene was designated OmBBD (for O. minuta bifunctional nuclease in basal defense response). Overexpression of OmBBD in an Arabidopsis (Arabidopsis thaliana) model system caused the constitutive expression of the PDF1.2, ABA1, and AtSAC1 genes, which are involved in priming ABA-mediated callose deposition. This activation of defense responses led to an increased resistance against Botrytis cinerea. atbbd1, the knockout mutant of the Arabidopsis ortholog AtBBD1, was susceptible to attack by B. cinerea and had deficient callose deposition. Overexpression of either OmBBD or AtBBD1 in atbbd1 plants complemented the susceptible phenotype of atbbd1 against B. cinerea as well as the deficiency of callose deposition. We suggest that OmBBD and AtBBD1 have a novel regulatory role in ABA-mediated callose deposition.
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- 2010
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36. Construction of genomic DNA library of Korean ginseng (Panax ginseng C. A. MEYER) and development of sequence-tagged sites.
- Author
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Bang KH, Lee JW, Kim YC, Kim DH, Lee EH, and Jeung JU
- Subjects
- Korea, Plant Extracts isolation & purification, Plant Leaves genetics, Seeds genetics, Gene Library, Genome, Plant genetics, Panax genetics, Plant Extracts genetics, Sequence Tagged Sites
- Abstract
This study describes an efficient approach for developing sequence tagged sites (STS) for Panax ginseng C.A. MEYER, and their applications for line discrimination. By using the methylation filtering (MF) technique, a genomic library was constructed, in which clone inserts were derived from the hypomethylated regions of ginseng genome. A methylation unfiltered genomic library was also constructed and the clone inserts were compared to those from the MF library in terms of sequence characteristics. Sequence analysis revealed that MF efficiently enriched the protein coding region of P. ginseng, for which the repetitive DNA appeared to be as little as 2.5 fold lower than clones in the unfiltered library, and also indicated that the P. ginseng genome may contain a large fraction of methylated repetitive DNA elements. A total of 99 and 100 highly stringent STS primer sets were designed from the filtered and unfiltered library, respectively. Amplification products were tested for latent polymorphism across six cultivars of P. ginseng and other 2 Panax species using six endonucleases recognizing four-bases. STS primer sets described here will be useful for marker-assisted selection, genome mapping and line discrimination of P. ginseng or its cultivars from other Panax species.
- Published
- 2010
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37. High-resolution mapping of two rice brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta.
- Author
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Rahman ML, Jiang W, Chu SH, Qiao Y, Ham TH, Woo MO, Lee J, Khanam MS, Chin JH, Jeung JU, Brar DS, Jena KK, and Koh HJ
- Subjects
- Animals, Chromosomes, Plant, Crosses, Genetic, Epistasis, Genetic, Genetic Markers, Genes, Plant, Hemiptera genetics, Oryza genetics, Physical Chromosome Mapping, Quantitative Trait Loci
- Abstract
Brown planthopper (BPH) is one of the most destructive insect pests of rice. Wild species of rice are a valuable source of resistance genes for developing resistant cultivars. A molecular marker-based genetic analysis of BPH resistance was conducted using an F(2) population derived from a cross between an introgression line, 'IR71033-121-15', from Oryza minuta (Accession number 101141) and a susceptible Korean japonica variety, 'Junambyeo'. Resistance to BPH (biotype 1) was evaluated using 190 F(3) families. Two major quantitative trait loci (QTLs) and two significant digenic epistatic interactions between marker intervals were identified for BPH resistance. One QTL was mapped to 193.4-kb region located on the short arm of chromosome 4, and the other QTL was mapped to a 194.0-kb region on the long arm of chromosome 12. The two QTLs additively increased the resistance to BPH. Markers co-segregating with the two resistance QTLs were developed at each locus. Comparing the physical map positions of the two QTLs with previously reported BPH resistance genes, we conclude that these major QTLs are new BPH resistance loci and have designated them as Bph20(t) on chromosome 4 and Bph21(t) on chromosome 12. This is the first report of BPH resistance genes from the wild species O. minuta. These two new genes and markers reported here will be useful to rice breeding programs interested in new sources of BPH resistance.
- Published
- 2009
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38. Development of near-isogenic Japonica rice lines with enhanced resistance to Magnaporthe grisea.
- Author
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Kwon SW, Cho YC, Kim YG, Suh JP, Jeung JU, Roh JH, Lee SK, Jeon JS, Yang SJ, and Lee YT
- Subjects
- Crosses, Genetic, Genes, Plant, Genetic Markers, Immunity, Innate genetics, Phenotype, Magnaporthe isolation & purification, Oryza genetics, Oryza microbiology, Plant Diseases genetics, Plant Diseases microbiology
- Abstract
Thirteen near-isogenic lines (NILs) of japonica rice were developed via a backcross method using the recurrent parent Chucheong, which is of good eating quality but is susceptible to Magnaporthe grisea, and three blast resistant japonica donors, Seolak, Daeseong and Bongkwang. The agro-morphological traits of these NILs, such as heading date, culm length, and panicle length, were similar to those of Chucheong. In a genome-wide scan using 158 SSR markers, chromosome segments of Chucheong were identified in most polymorphic regions of the 13 NIL plants, and only a few chromosome segments were found to have been substituted by donor alleles. The genetic similarities of the 13 NILs to the recurrent parent Chucheong averaged 0.961, with a range of 0.932-0.984. Analysis of 13 major blast resistance (R) genes in these lines using specific DNA markers showed that each NIL appeared to contain some combination of the four R genes, Pib, Pii, Pik-m and Pita-2, with the first three genes being present in each line. Screening of nine M. grisea isolates revealed that one NIL M7 was resistant to all nine isolates; the remaining NILs were each resistant to between three and seven isolates, except for NIL M106, which was resistant to only two isolates. In a blast nursery experiment, all the NILs proved to be more resistant than Chucheong. These newly developed NILs have potential as commercial rice varieties because of their increased resistance to M. grisea combined with the desirable agronomic traits of Chucheong. They also provide material for studying the genetic basis of blast resistance.
- Published
- 2008
39. A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice.
- Author
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Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT, and Jena KK
- Subjects
- Chromosome Mapping, Chromosomes, Plant genetics, Genetic Markers, Magnaporthe, Amino Acid Motifs, Oryza genetics, Oryza microbiology, Plant Diseases genetics, Plant Diseases microbiology, Plant Proteins genetics
- Abstract
Rice blast disease caused by Magnaporthe grisea is a continuous threat to stable rice production worldwide. In a modernized agricultural system, the development of varieties with broad-spectrum and durable resistance to blast disease is essential for increased rice production and sustainability. In this study, a new gene is identified in the introgression line IR65482-4-136-2-2 that has inherited the resistance gene from an EE genome wild Oryza species, O. australiensis (Acc. 100882). Genetic and molecular analysis localized a major resistance gene, Pi40(t), on the short arm of chromosome 6, where four blast resistance genes (Piz, Piz-5, Piz-t, and Pi9) were also identified, flanked by the markers S2539 and RM3330. Through e-Landing, 14 BAC/PAC clones within the 1.81-Mb equivalent virtual contig were identified on Rice Pseudomolecule3. Highly stringent primer sets designed for 6 NBS-LRR motifs located within PAC clone P0649C11 facilitated high-resolution mapping of the new resistance gene, Pi40(t). Following association analysis and detailed haplotyping approaches, a DNA marker, 9871.T7E2b, was identified to be linked to the Pi40(t) gene at the 70 Kb chromosomal region, and differentiated the Pi40(t) gene from the LTH monogenic differential lines possessing genes Piz, Piz-5, Piz-t, and Pi-9. Pi40(t) was validated using the most virulent isolates of Korea as well as the Philippines, suggesting a broad spectrum for the resistance gene. Marker-assisted selection (MAS) and pathotyping of BC progenies having two japonica cultivar genetic backgrounds further supported the potential of the resistance gene in rice breeding. Our study based on new gene identification strategies provides insight into novel genetic resources for blast resistance as well as future studies on cloning and functional analysis of a blast resistance gene useful for rice improvement.
- Published
- 2007
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40. Identification of QTLs for some agronomic traits in rice using an introgression line from Oryza minuta.
- Author
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Rahman ML, Chu SH, Choi MS, Qiao YL, Jiang W, Piao R, Khanam S, Cho YI, Jeung JU, Jena K, and Koh HJ
- Subjects
- Crosses, Genetic, Epistasis, Genetic, Genetic Linkage, Oryza growth & development, Oryza genetics, Quantitative Trait Loci
- Abstract
Wild progenitor species provide potential gene sources for complex traits such as yield and multiple resistances to biotic and abiotic stresses, and thus are expected to contribute to sustainable food supplies. An introgression line 'IR71033-121-15' was derived from a wild species Oryza minuta (2n = 48, BBCC, Acc No. 101141) at IRRI. Introgression analysis using 530 SSR and STS markers revealed that at least 14 chromosomal segments distributed over 12 chromosomes had been introgressed from O. minuta. An F2:3 population from the cross between IR71033 and Junambyeo (a Korean japonica cultivar) consisting of 146 lines was used for quantitative trait loci (QTL) analysis of 16 agronomic traits. A total of 36 single-locus QTLs (S-QTLs) and 45 digenic epistasis (E-QTLs) were identified. In spite of it's inferiority of O. minuta for most of the traits studied, its alleles contributed positively to 57% of the QTLs. The other QTLs originated from either parent, IR71033 or Junambyeo. QTLs for phenotypically correlated traits were mostly detected on introgressed segments. Fourteen QTLs corresponded to QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. Twenty-two QTLs controlling yield and its components had not been detected in previous QTL studies. Of these, thirteen consisted of potentially novel alleles from O. minuta. QTLs from O. minuta introgression could be new sources of natural variation for the genetic improvement of rice.
- Published
- 2007
41. Identification of putative MAPK kinases in Oryza minuta and O. sativa responsive to biotic stresses.
- Author
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You MK, Oh SI, Ok SH, Cho SK, Shin HY, Jeung JU, and Shin JS
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Gene Expression Regulation, Plant, Molecular Sequence Data, Oryza genetics, Oryza microbiology, Oryza parasitology, Phylogeny, Plant Proteins chemistry, Plant Proteins genetics, Plant Proteins metabolism, Sequence Homology, Amino Acid, Insecta physiology, Magnaporthe physiology, Mitogen-Activated Protein Kinase Kinases metabolism, Oryza enzymology
- Abstract
The mitogen-activated protein kinase (MAPK) signaling cascade is critical for regulating plant defense systems against various kinds of pathogen and environmental stresses. One component of this cascade, the MAP kinase kinases (MAPKK), has not yet been shown to be induced in plants following biotic attacks, such as those by insects and fungi. We describe here a gene coding for a blast (Magnaporthe grisea)- and insect (Nilaparvata lugens)-responsive putative MAPK kinase, OmMKK1 (Oryza minuta MAPKK 1), which was identified in a library of O. minuta expressed sequence tags (ESTs). Two copies of OmMKK1 are present in the O. minuta genome. They encode a predicted protein with molecular mass 39 kDa and pI of 6.2. Transcript patterns following imbibition of plant hormones such as methyl jasmonic acid (MeJA), ethephone, salicylic acid (SA) and abscisic acid (ABA), as well as exposure to methyl viologen (MV), revealed that the expression of OmMKK1 is related to defense response signaling pathways. A comparative analysis of OmMKK1 and its O. sativa ortholog OsMKK1 showed that both were induced by stress-related hormones and biotic stresses, but that the kinetics of their responses differed despite their high amino acid sequence identity (96%).
- Published
- 2007
42. Dynamics of Xanthomonas oryzae pv. oryzae Populations in Korea and Their Relationship to Known Bacterial Blight Resistance Genes.
- Author
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Jeung JU, Heu SG, Shin MS, Vera Cruz CM, and Jena KK
- Abstract
ABSTRACT Developing resistant cultivars requires an understanding of the dynamics of the pathogen populations as well as the genetics of host resistance. Bacterial leaf blight (BB), caused by the vascular pathogen Xanthomonas oryzae pv. oryzae, has become one of the most devastating diseases of rice. We demonstrate here the quantitative analyses of responses of near-isogenic lines carrying various BB resistance (R) genes and R-gene combinations against 16 X. oryzae pv. oryzae isolates representing Korean BB pathotypes. The estimated main effects of each R gene against the 16 isolates identified prominent differences in BB pathotypes between Korea and other countries. Three major aspects of our quantitative observations and statistical analysis are (i) strong and broad resistance of xa5; (ii) independent and additive genetic actions of Xa4, xa5, and Xa21 under digenic or trigenic status; and (iii) a strong quantitative complementation effect contributed by the functional alleles of Xa4 and Xa21. We conclude that the pyramid line containing genes Xa4, xa5, and Xa21 would be the most promising and valuable genotype for improving Korean japonica cultivars for BB resistance.
- Published
- 2006
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43. High-resolution mapping of a new brown planthopper (BPH) resistance gene, Bph18(t), and marker-assisted selection for BPH resistance in rice (Oryza sativa L.).
- Author
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Jena KK, Jeung JU, Lee JH, Choi HC, and Brar DS
- Subjects
- Alleles, Analysis of Variance, Animals, Biological Assay, Chromosome Segregation, Chromosomes, Plant genetics, DNA, Plant genetics, Genetic Linkage, Genetic Markers genetics, Oryza parasitology, Plant Diseases genetics, Chromosome Mapping methods, Genes, Plant genetics, Hemiptera physiology, Immunity, Innate genetics, Oryza genetics, Plant Diseases parasitology, Selection, Genetic
- Abstract
Brown planthopper (BPH) is a destructive insect pest of rice in Asia. Identification and the incorporation of new BPH resistance genes into modern rice cultivars are important breeding strategies to control the damage caused by new biotypes of BPH. In this study, a major resistance gene, Bph18(t), has been identified in an introgression line (IR65482-7-216-1-2) that has inherited the gene from the wild species Oryza australiensis. Genetic analysis revealed the dominant nature of the Bph18(t) gene and identified it as non-allelic to another gene, Bph10 that was earlier introgressed from O. australiensis. After linkage analysis using MapMaker followed by single-locus ANOVA on quantitatively expressed resistance levels of the progenies from an F2 mapping population identified with marker allele types, the Bph18(t) gene was initially located on the subterminal region of the long arm of chromosome 12 flanked by the SSR marker RM463 and the STS marker S15552. The corresponding physical region was identified in the Nipponbare genome pseudomolecule 3 through electronic chromosome landing (e-landing), in which 15 BAC clones covered 1.612 Mb. Eleven DNA markers tagging the BAC clones were used to construct a high-resolution genetic map of the target region. The Bph18(t) locus was further localized within a 0.843-Mb physical interval that includes three BAC clones between the markers R10289S and RM6869 by means of single-locus ANOVA of resistance levels of mapping population and marker-gene association analysis on 86 susceptible F2 progenies based on six time-point phenotyping. Using gene annotation information of TIGR, a putative resistance gene was identified in the BAC clone OSJNBa0028L05 and the sequence information was used to generate STS marker 7312.T4A. The marker allele of 1,078 bp completely co-segregated with the BPH resistance phenotype. STS marker 7312.T4A was validated using BC2F2 progenies derived from two temperate japonica backgrounds. Some 97 resistant BC2F2 individuals out of 433 screened completely co-segregated with the resistance-specific marker allele (1,078 bp) in either homozygous or heterozygous state. This further confirmed a major gene-controlled resistance to the BPH biotype of Korea. Identification of Bph18(t) enlarges the BPH resistance gene pool to help develop improved rice cultivars, and the PCR marker (7312.T4A) for the Bph18(t) gene should be readily applicable for marker-assisted selection (MAS).
- Published
- 2006
- Full Text
- View/download PDF
44. A partial-complementary adapter for an improved and simplified ligation-mediated suppression PCR technique.
- Author
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Jeung JU, Cho SK, and Shin JS
- Subjects
- Arabidopsis genetics, Bacteriophage lambda genetics, Base Sequence, DNA chemistry, DNA Primers chemistry, Genetic Techniques, Molecular Sequence Data, Multigene Family, Oligonucleotides chemistry, Phosphorylation, Polymerase Chain Reaction instrumentation, Protein Isoforms, Polymerase Chain Reaction methods
- Abstract
Ligation-mediated suppression PCR (LMS-PCR) is a powerful tool for walking in unknown genomic DNA regions from known adjacent sequences. This approach has made it feasible to obtain promoter sequences and to enable researchers to identify full-length gene sequences or isoforms of multigene families. However, the advantages of LMS-PCR can be obviated by the presence of incomplete base modifications on the suppression adapters. We propose here that a 'partial-complementary adapter' is a more reliable suppression adapter, demanding only 5'-end phosphorylation. We also describe a simplified procedure for the easier preparation of PCR templates with very small quantities of DNA and a fast and direct characterization of the suppression-PCR products. A set of practical guidelines is proposed for pre-checking the efficiency of the adapter modification using two model systems: bacteriophage lambda (lambda) and Arabidopsis.
- Published
- 2005
- Full Text
- View/download PDF
45. Characterization of Ty3-gypsy-like elements in Hibiscus syriacus.
- Author
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Jeung JU, Cho SK, Lee SJ, and Shin JS
- Subjects
- Amino Acid Sequence, Base Sequence, Genome, Plant, Hibiscus classification, Molecular Sequence Data, Nucleic Acid Hybridization, Polymorphism, Restriction Fragment Length, Sequence Alignment, Sequence Tagged Sites, Genes, Plant genetics, Hibiscus genetics, Retroelements genetics
- Abstract
Southern blot analysis revealed a ubiquitous distribu-tion and high copy number of Ty3-gypsy-like elements in the genome of Hibiscus syriacus. Comparative phylogenetic analysis of the large subunit of Rubisco and the integrase region of Ty3-gypsy elements in various plant species indicated that the retrotransposon-like sequences have different evolutionary histories and their own unique polymorphism in the H. syriacus population. Sequence-tagged site-restriction fragment length polymorphisms (STS-RFLP) analysis also indicated great variability in the numbers and sequences of Ty3-gypsy-like elements within H. syriacus varieties. Ty3-gypsy-like elements may still be active within H. syriacus, since Northern analysis of wounded leaves of H. syriacus variety Saehan with a probe for the integrase domain gave strong hybridization signals. The sequence heterogeneity and ubiquity of the Ty3-gypsy-like elements in H. syriacus genomes could provide reliable DNA markers for line identification as well for the analysis of genetic diversity in H. syriacus.
- Published
- 2005
46. Analysis of differentially expressed transcripts from planthopper-infested wild rice (Oryza minuta).
- Author
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Cho SK, Jung KW, Jeung JU, Kang KH, Shim KS, You MK, Yoo KS, Ok SH, and Shin JS
- Subjects
- Animals, DNA, Plant, Expressed Sequence Tags, Gene Library, Microarray Analysis, Oryza parasitology, Gene Expression Regulation, Plant physiology, Insecta physiology, Oryza genetics
- Abstract
A subtracted library was constructed from planthopper-infested wild rice (Oryza minuta) by suppression subtractive hybridization in combination with mirror orientation selection. To screen the differentially expressed transcripts in the library, we applied a cDNA microarray containing 960 random clones in a reverse Northern blot analysis using cDNA probes prepared from the mRNAs of control and planthopper-infested samples. On the basis of the signal intensities and expression ratios obtained from experiments performed in triplicate, we selected 383 clones. The elevated expression levels and overall profiles over time were verified by Northern blot analysis. Although Southern blot analysis showed similar copy numbers of the screened genes in O. minuta and O. sativa, it also revealed that the expression profiles had a different pattern. Functional categorization placed the identified transcripts in the categories of subcellular localization, metabolism, and protein fate. The presence of these expressed sequence tags implies that resistance of O. minuta to insect infestation can be achieved not only by an elevated expression of defense-related genes but also by enhanced metabolic activities.
- Published
- 2005
- Full Text
- View/download PDF
47. Comparative analysis of 5,211 leaf ESTs of wild rice (Oryza minuta).
- Author
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Cho SK, Ok SH, Jeung JU, Shim KS, Jung KW, You MK, Kang KH, Chung YS, Choi HC, Moon HP, and Shin JS
- Subjects
- Arabidopsis genetics, Base Sequence, Gene Expression Profiling, Gene Library, Molecular Sequence Data, Sequence Analysis, DNA, Expressed Sequence Tags, Oryza genetics, Plant Leaves genetics
- Abstract
The expressed sequence tags (ESTs) presented in this report are the first transcriptomes of wild rice. A cDNA library was constructed from 4-week-old leaf samples of greenhouse-grown Oryza minuta. The 5,211 cDNA clones of O. minuta represent 3,401 unique sequences, consisting of 2,787 singletons and 614 assembled sequences. Database comparisons of the cDNAs in GenBank's non-redundant databases using BLAST revealed that 4,957 of the 5,211 cDNAs (95.1%) showed a high degree of sequence homology to genes from other organisms. Most of the transcripts identified were genes related to metabolism, energy, protein biosynthesis and subcellular localization. The metabolism and energy categories of the O. minuta ESTs showed a considerably higher gene expression level than those of O. sativa ESTs. These data and genes can be utilized in rice breeding., (Copyright 2004 Springer-Verlag)
- Published
- 2004
- Full Text
- View/download PDF
48. Identification of genes induced in wound-treated wild rice (Oryza minuta).
- Author
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Cho SK, Jeung JU, Kang KH, Shim KS, Jung KW, You MK, Ok SH, Chung YS, Hwang HG, Choi HC, Moon HP, and Shin JS
- Subjects
- Databases, Nucleic Acid, Gene Expression Regulation, Plant, Gene Library, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Expressed Sequence Tags, Gene Expression Profiling, Oryza genetics, Oryza metabolism
- Abstract
A subtracted library was constructed from wound-treated wild rice (Oryza minuta) by suppression subtractive hybridization (SSH) in combination with mirror orientation selection (MOS). To distinguish between differentially expressed transcripts and false positive clones, DNA chips containing 960 random clones were applied as a form of reverse Northern screening. Based on the signal intensities and expression ratios obtained from experiments performed in triplicate, 371 clones were selected. ESTs produced from the subtracted library showed 63.2% redundancy, and 72% of all clones could be matched to the GenBank nonredundant database. Functional categorization placed the identified enriched genes in categories of subcellular localization, metabolism, cell rescue and defense, and transcription. These EST-related resistance mechanisms could be used in investigations into the defense mechanisms of wild species, and to provide new routes to improving the germplasm of cultivated rice.
- Published
- 2004
49. Identification of fungal ( Magnaporthe grisea) stress-induced genes in wild rice ( Oryza minuta).
- Author
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Shim KS, Cho SK, Jeung JU, Jung KW, You MK, Ok SH, Chung YS, Kang KH, Hwang HG, Choi HC, Moon HP, and Shin JS
- Subjects
- Blotting, Northern methods, DNA, Fungal genetics, DNA, Plant genetics, Expressed Sequence Tags, Gene Expression Profiling, Gene Library, Magnaporthe pathogenicity, Oligonucleotide Array Sequence Analysis, Sequence Alignment, Sequence Analysis, DNA, Genes, Plant physiology, Magnaporthe genetics, Oryza genetics, Oryza microbiology
- Abstract
To identify fungal stress-related genes in wild rice, Oryza minuta, we constructed a subtracted library using suppression subtractive hybridization in combination with mirror orientation selection. DNA chips containing 960 randomly selected cDNA clones were applied by reverse Northern analysis to eliminate false positive clones from the library and to prescreen differentially expressed genes. In total, 377 cDNA clones were selected on the basis of their signal intensities and expression ratios. Sequence analyses of these 377 cDNA fragments revealed that 180 of them (47.7%) represented unique genes. Of these 180 cDNAs, 89 clones (49.6%) showed significant homologies to previously known genes, while the remaining 91 did not match any known sequences. The putative functions of the 180 unique ESTs were categorized by aligning them with MIPS data. They were classified into seven different groups using microarray data-derived expression patterns and verified by Northern blotting.
- Published
- 2004
- Full Text
- View/download PDF
50. Expression of the bovine growth hormone alters the root morphology in transgenic tobacco plants.
- Author
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Oh K, Cheon BY, Cho SH, Truong HQ, Ok SH, Jeung JU, Choi JW, and Shin JS
- Subjects
- Animals, Cattle, Genetic Vectors, Growth Hormone genetics, Plant Roots cytology, Plant Roots genetics, RNA, Messenger analysis, RNA, Messenger biosynthesis, Nicotiana metabolism, Transformation, Genetic, Growth Hormone pharmacology, Plant Roots drug effects, Plants, Genetically Modified, Nicotiana genetics
- Abstract
The bovine growth hormone (bGH) is a natural peptide hormone that controls the differentiation, growth and metabolism, and is produced in the pituitary gland of cows. For the production of bGH from plants, two different bgh clones, of which the pGAbGH1 contaions only mature peptide sequences and the pGAbGH15 contains signal sequences and the first intron, as well as mature peptide sequences, were used. Those bghs under the control of the CaMV 35S promoter and NOS terminator were introduced to tobacco plants via Agrobacterium tumefaciens-mediated transformation. By PCR analyses using bgh and nptII specific primers, 17 and 21 putative transformants were respectively selected from pGAbGH1- and pGAbGH15-transformed tobacco plants. Northern blot analysis showed that the most of the transgenic lines expressed the bgh mRNA. Western blot analysis revealed that the pGAbGH1-transformed tobaccos produced recombinant bGH, but pGAbGH15-transformed ones did not produce the protein. Interestingly, some morphological changes were observed in the roots of transgenic tobacco plants. The transgenic tobacco plants had thick and short roots containing few root hairs in contrast to the non-transformed wild type plants.
- Published
- 2003
- Full Text
- View/download PDF
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