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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Journal of Plant Biotechnology
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Journal DOI :
The Korean Society of Plant Biotechnology
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Volume & Issues
Volume 37, Issue 4 - Dec 2010
Volume 37, Issue 3 - Sep 2010
Volume 37, Issue 2 - Jun 2010
Volume 37, Issue 1 - Mar 2010
Selecting the target year
Current status on plant functional genomics
Cho, Yong-Gu ; Woo, Hee-Jong ; Yoon, Ung-Han ; Kim, Hong-Sig ; Woo, Sun-Hee ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 115~124
DOI : 10.5010/JPB.2010.37.2.115
As the completion of genome sequencing, large collection of expression data and the great efforts in annotating plant genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. Functional genome analysis of plants has entered the high-throughput stage. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. However, to identify the exact function of unknown genes it is necessary to understand each gene's role in the complex orchestration of all gene activities in the plant cell. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns. The most conclusive information about changes in gene expression levels can be gained from analysis of the varying qualitative and quantitative changes of messenger RNAs, proteins and metabolites. New technologies have been developed to allow fast and highly parallel measurements of these constituents of the cell that make up gene activity. We have reviewed currently employed technologies to identify unknown functions of predicted genes including map-based cloning, insertional mutagenesis, reverse genetics, chemical mutagenesis, microarray analysis, FOX-hunting system, gene silencing mutagenesis, proteomics and chemical genomics. Recent improvements in technologies for functional genomics enable whole-genome functional analysis, and thus open new avenues for studies of the regulations and functions of unknown genes in plants.
Current status of Ac/Ds mediated gene tagging systems for study of rice functional genomics in Korea
Lee, Gang-Seob ; Park, Sung-Han ; Yun, Do-Won ; Ahn, Byoung-Ohg ; Kim, Chang-Kug ; Han, Chang-Deok ; Yi, Gi-Hwan ; Park, Dong-Soo ; Eun, Moo-Young ; Yoon, Ung-Han ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 125~132
DOI : 10.5010/JPB.2010.37.2.125
Rice is the staple food of more than 50% of the worlds population. Cultivated rice has the AA genome (diploid, 2n=24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos (Hirochika. 1997) have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems has been utilized as main insertional mutagens in rice. A main drawback of a T-DNA scheme is that Agrobacteria-mediated transformation in rice requires extensive facilities, time, and labor. In contrast, the Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. Revertants can be utilized to correlate phenotype with genotype. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertionally mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been launched by collaborative works from 2001 in Korea.
Rice functional genomics using T-DNA mutants
Ryu, Hak-Seung ; Ryoo, Na-Yeon ; Jung, Ki-Hong ; An, Gynheung ; Jeon, Jong-Seong ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 133~143
DOI : 10.5010/JPB.2010.37.2.133
Rice (Oryza sativa) is a major cereal crop that has been developed as a monocot model species. In past decades rice researchers have established valuable resources for functional genomics in rice, such as complete genome sequencing, high-density genetic maps, a full length cDNA database, genome-wide transcriptome data, and a large number of mutants. Of these, rice mutant lines are very important to definitively determine functions of genes associated with valuable agronomic traits. In this review we summarize the progress of functional genomics approaches in rice using T-DNA mutants.
Current status on expression profiling using rice microarray
Yoon, Ung-Han ; Kim, Yeon-Ki ; Kim, Chang-Kug ; Hahn, Jang-Ho ; Kim, Dong-Hern ; Lee, Tae-Ho ; Lee, Gang-Seob ; Park, Soo-Chul ; Nahm, Baek-Hie ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 144~152
DOI : 10.5010/JPB.2010.37.3.144
As the International Rice Genome Sequencing Project (IRGSP) was completed in 2005 and opened to the public, many countries are making a lot of investments in researches on the utilization of sequence information along with system development. Also, the necessity of the functional genomics researches using microarray is increased currently to secure unique genes related with major agricultural traits and analyze metabolic pathways. Microrarray enables efficient analysis of large scale gene expression and related transcription regulation. This review aims to introduce available microarrays made based on rice genome information and current status of gene expression analysis using these microarrays integrated with the databases available to the public. Also, we introduce the researches on the large scale functional analysis of genes related with useful traits and genetic networks. Understanding of the mechanism related with mutual interaction between proteins with co-expression among rice genes can be utilized in the researches for improving major agricultural traits. The direct and indirect interactions of various genes would provide new functionality of rice. The recent results of the various expression profiling analysis in rice will promote functional genomic researches in plants including rice and provide the scientists involved in applications researches with wide variety of expression informations.
The strategy and current status of Brassica rapa genome project
Mun, Jeong-Hwan ; Kwon, Soo-Jin ; Park, Beom-Seok ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 153~165
DOI : 10.5010/JPB.2010.37.2.153
Brassica rapa is considered an ideal candidate to act as a reference species for Brassica genomic studies. Among the three basic Brassica species, B. rapa (AA genome) has the smallest genome (529 Mbp), compared to B. nigra (BB genome, 632 Mbp) and B. oleracea (CC genome, 696 Mbp). There is also a large collection of available cultivars of B. rapa, as well as a broad array of B. rapa genomic resources available. Under international consensus, various genomic studies on B. rapa have been conducted, including the construction of a physical map based on 22.5X genome coverage, end sequencing of 146,000 BACs, sequencing of >150,000 expressed sequence tags, and successful phase 2 shotgun sequencing of 589 euchromatic region-tiling BACs based on comparative positioning with the Arabidopsis genome. These sequenced BACs mapped onto the B. rapa genome provide beginning points for genome sequencing of each chromosome. Applying this strategy, all of the 10 chromosomes of B. rapa have been assigned to the sequencing centers in seven countries, Korea, UK, China, India, Canada, Australia, and Japan. The two longest chromosomes, A3 and A9, have been sequenced except for several gaps, by NAAS in Korea. Meanwhile a China group, including IVF and BGI, performed whole genome sequencing with Illumina system. These Sanger and NGS sequence data will be integrated to assemble a draft sequence of B. rapa. The imminent B. rapa genome sequence offers novel insights into the organization and evolution of the Brassica genome. In parallel, the transfer of knowledge from B. rapa to other Brassica crops would be expected.
Current status of Brassica rapa functional genome research in Korea
Yu, Jae-Gyeong ; Park, Ji-Hyun ; Park, Young-Doo ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 166~173
DOI : 10.5010/JPB.2010.37.2.166
The purpose of functional genome research is to identify biological function of useful gene and to give an agricultural value in plant biotechnology. Brassica rapa is an economic crop which recorded 1,000 billion won of domestic market and 100 million dollar of exports and it produces 2.5 million ton in 50,000 ha as a major ingredient of representative Korean food, Kimchi. Furthermore, it is very important crop economically and commercially because Korea is major seed exporter. The fact that Multinational Brassica Genome Project (MBGP) was launched and Arabidopsis thaliana, affiliated to same genus with B. rapa, has been fully sequenced activated functional genome research of B. rapa. Besides new technologies related to gene function analysis keep developing, many results are reporting every year by international research including Korea. This review paper introduces development of Chinese cabbage mutants which is a first step in functional genome research, variant phenotypes of mutants, flanking DNA analysis in B. rapa genome, gene identification, gene analysis using microarray, and representative researches.
Systematic approaches to identify functional genes using the FOX-hunting system in Chinese cabbage
Lee, In-Hoo ; Jung, Yu-Jin ; Park, Jong-In ; Nou, Ill-Sup ; Kang, Kwon-Kyoo ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 174~185
DOI : 10.5010/JPB.2010.37.2.174
Full-length cDNAs are essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products. To elucidate the functions of a large population of Chinese cabbage (Brassica rapa) genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the full-length cDNA Over-eXpresser (FOX) gene hunting system. With oligo dT column it purify the each mRNA from the flower organs, leaf and stem tissue. And about 120,000 cDNAs from the library were transformed into
-pFLCIII-F vector. Of which 115,000 cDNAs from the library were transformed into T-DNA binary vector, pBigs for transformation study. We used normalized full-length cDNA and introduced each cDNA into Arabidopsis by in planta transformation. Full-length Chinese cabbage cDNAs were expressed independently under the CaMV 35S promoter in Arabidopsis. Selfed seeds were harvested from transgenic Arabidopsis. We had selected 2,500 transgenic plants by hygromycin antibiotic tolerant test, and obtained a number of transgenic mutants. Each transgenic Arabidopsis was investigated in morphological changes, fertility and leaf colour. As a result, 285 possible morphological mutants were identified. Introduced cDNA was isolated by PCR amplification of the genomic DNA from the transgenic mutants. Sequencing result and BLAST analysis showed that most of the introduced cDNA were complete cDNAs and functional genes. Also, we examined the effect of Bromelain on enhancing resistance to soft rot in transgenic Chinese cabbage 'Osome'. The bromelain gene identified from FOX hunting system was transformed into Chinese cabbage using Agrobacterium methods. Transformants were screened by PCR, then RT-PCR and real time PCR were performed to analyze gene expression of cysteine protease in the T1 and T2 generations. The anti-bacterial activity of bromelain was tested in Chinese cabbages infected with soft rot bacteria. The results showed that the over-expressed bromelain gene from pineapple conferred enhanced resistance to soft rot in Chinese cabbage.
Expression and regulation of self-incompatible genes in Brassica
Park, Jong-In ; Lee, In-Ho ; Watanabe, Masao ; Nou, Ill-Sup ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 186~195
DOI : 10.5010/JPB.2010.37.2.186
In most self-incompatible plant species, recognition of self-pollen is controlled by a single locus, termed the S-locus. The self-incompatibility (SI) system in Brassica is controlled sporophytically by multiple alleles at a single locus, designated as S, and involves cell-cell communication between male and female. Two highly polymorphic S locus genes, SLG (S locus glycoprotein) and SRK (S receptor kinase), have been identified, both of which are expressed predominantly in the stigmatic papillar cell. Gain-of-function experiments have demonstrated that SRK solely determines S haplotype-specificity of the stigma, while SLG enhances the recognition reaction of SI. The sequence analysis of the S locus genomic region of B. campestris (syn. rapa) has led to the identification of an anther-specific gene, designated as SP11/SCR, which is the male S determinant. Molecular analysis has demonstrated that the dominance relationships between S alleles in the stigma were determined by SRK itself, but not by the relative expression level. In contrast, the expression of SP11/SCR from the recessive S allele was specifically suppressed in the S heterozygote, suggesting that the dominance relationships in pollen were determined by the expression level of SP11/SCR. Furthermore, recent studies on recessive allele-specific DNA methylation of Brassica self-incompatibility alleles demonstrate that DNA methylation patterns in plants can vary temporally and spatially in each generation. In this review, we firstly present overview of self incompatibility system in Brassica and then describe dominance relationships in Brassica self- incompatibility regulated by allele-specific DNA methylation.
Comprehensive proteome analysis using quantitative proteomic technologies
Kamal, Abu Hena Mostafa ; Choi, Jong-Soon ; Cho, Yong-Gu ; Kim, Hong-Sig ; Song, Beom-Heon ; Lee, Chul-Won ; Woo, Sun-Hee ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 196~204
DOI : 10.5010/JPB.2010.37.2.196
With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.
Current status on carbon metabolic engineering in plants
Kim, Dong-Hern ; Lee, Si-Myung ; Park, Jong-Suk ; Kim, Soo-Jin ; Kim, Beom-Ki ; Yun, In-Sun ; Kim, Dul-I ; Byun, Myung-Ok ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 205~211
DOI : 10.5010/JPB.2010.37.2.205
Yield productivity of staple crops must be increased at least 50% by 2050, in order to feed the world population which is expected to reach 90 billions. Photosynthetic carbon assimilation and carbohydrate metabolism leading to the production of starch would be the final frontier to quest for new sources of technology enabling such a drastic increase of crop productivity. In this review, attempts to genetically engineer plant photosynthetic carbon reduction cycle and metabolic pathways to increase starch production are introduced.
Principal methods to produce marker-free GM plants
Woo, Hee-Jong ; Shin, Kong-Sik ; Lee, Ki-Jong ; Kweon, Soon-Jong ; Cho, Yong-Gu ; Suh, Seok-Cheol ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 212~219
DOI : 10.5010/JPB.2010.37.1.212
Selectable marker gene systems are vital for the development of transgenic plants, but the presence of selectable marker genes encoding antibiotic or herbicide resistance in genetically modified plants poses a number of problems. A lot of research results and various techniques have been developed to produce marker-free GM plants. The aim of this review is to describe the principal methods used for eliminating selectable marker genes to generate marker-free GM plants, concentrating on the three significant methods(co-transformation, site-specific recombinase-mediated excision, non-selected transformation) in several marker-free techniques.
Acyltransferases for production of industrial oils in transgenic plants
Kim, Hyun-Uk ; Lee, Kyeong-Ryeol ; Park, Jong-Sug ; Roh, Kyung-Hee ; Kim, Sun-Hee ; Kim, Jong-Bum ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 220~227
DOI : 10.5010/JPB.2010.37.2.220
Fatty acids in seed oil from plants are essential for human nutrients and have been used for industrial purpose. The growing demands of seed oil as food resources and feedstocks for industrial uses have attempted to modify fatty acid composition and to increase oil content in transgenic plants. However, production of unusual fatty acids in transgenic plants are limited, which is not synthesized the level same as original plants. This bottleneck was common for production of several unusual fatty acids in transgenic plants and suggests that there is different for substrate preference in oil metabolic pathway enzymes between host oil plants and original wild plants. Review of acyltransferases involved in acyl-editing and seed oil accumulation of oil plant and wild-plant producing unusual fatty acids will design strategies to maximize the production of unusual fatty acids in transgenic plants. In here, we identified eleven acyltransferase genes in castor based on sequence homology, which will be useful to increase hydroxy unusual fatty acids in transgenic plants.
Establishment of a novel plant regeneration system from suspension-derived callus in the halophytic Leymus chinensis (Trin.)
Sun, Yan-Lin ; Hong, Soon-Kwan ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 228~235
DOI : 10.5010/JPB.2010.37.2.228
The establishment of cell suspension culture and plant regeneration of the halophytic Leymus chinensis (Trin.) are described in this study for the first time. Callus induction solid medium containing Murashige and Shoog (MS) basic salt,
2,4-dichlorophenoxyacetic acid (2,4-D), and
L-glutamic acid with
gelrite for solidification induced the highest rate of cell division in Type 1 callus among calli of various types. Liquid medium with the same hormone distribution was therefore, used for cell suspension culture from Type 1 callus. Over a 30 d suspension culture at 100 rpm, great amounts of biomass were accumulated, with 71.07% average daily increment and 22.32-fold total fresh weight increment. Comparison of before and after suspension culture, the distribution of different size callus pieces and the maintenance of callus type were basically unaltered, but a slight increase in relative water contents was observed. To induce the potential of plant regeneration, the directly transferring on plant regeneration solid medium containing MS basic salt,
-naphthalene acetic acid (NAA),
kinetin (Kn), and
casamino acid and indirectly transferring were simultaneously performed. Even now growth rates of suspension-derived callus on solid medium were approximately half of those of Type 1 callus, but faster somatic embryogenesis was observed. Rooting of all regenerated shoots was successfully performed on half-strength MS medium. All plants appeared phenotypically normal.
Chinese cabbage transformation of HSP101 gene using mannose selection system
Hur, Suel-Hye ; Min, Byung-Whan ;
Journal of Plant Biotechnology, volume 37, issue 2, 2010, Pages 236~241
DOI : 10.5010/JPB.2010.37.2.236
A new selectable marker system has been adapted for use in Agrobacterium mediated transformation of Chinese cabbage. This selection system utilizes the pmi gene encoding for phosphomannose-isomerase that converts mannose-6-phosphate to fructose-6-phosphate. Only transgenic plants were able to metabolize the selection agent, mannose, into a usable source of carbon, fructose. Cotyledon explants from 5-day-old seedlings with 2 days pre-culture were infected with Agrobacterium tumefaciens strain LBA4404 harboring a new constructed vector pNWBHSP101 containing the heat tolerance responsible heat shock protein 101 (HSP101) gene with full codon modification. After culture and selection on MS medium supplemented with 3 mg/L BAP, 1 mg/L NAA, 0.6% mannose, 2.0% sucrose. Polymerase chain reaction, Southern blot analysis and Northern blot analysis were used to identify and characterize the transgenic plants with the integrated HSP101 gene. Transgenic plants have been established in soil and flowered in the greenhouse.