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.

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 (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.

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.

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.

식물생명공학 분야에 있어 기능유전체 연구는 식물체가 지니고 있는 유용한 유전자의 생물학적 기능을 밝히고, 농업적 유용성을 확보하여 가치를 부여하는 것을 목적으로 한다. 배추는 우리나라 대표 음식 중의 하나인 김치의 주원료이며 식품영양학적으로도 우수성이 인정되었고 약 5만 ha에서 연간 약 250만 톤이 생산되어 1조원의 국내 시장 및 1억 달러의 수출액을 기록하는 경제작물이다. 그리고 우리나라가 주요 종자수출국의 위치를 차지하고 있어 재배에 있어서나 경제적, 상업적으로 그 중요성이 매우 높은 작물이다. Multinational Brassica Genome Project (MBGP)가 시작되고 배추와 같은 속에 속하는 애기장대의 전 염기서열 분석이 완료됨으로써 배추의 기능유전체 연구가 더욱 활발해 질 수 있는 환경이 마련되었다. 또한 유전자 기능 분석 연구에 필요한 새로운 기술들이 계속 개발되고 있으며 우리나라를 선두로 하여 국제적으로도 연구가 이루어져 해마다 많은 성과들이 보고되고 있다. 본 총설에서는 기능유전체 연구의 첫 단계인 배추 돌연변이체 유기 방법을 시작으로 다양한 표현형의 돌연변이체를 소개하고 이 돌연변이 배추의 게놈내 flanking DNA 분석 및 유전자 동정, microarray를 이용한 유전자 분석, 대표적인 기능유전체 연구 사례를 제시하고자 하였다.

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 $\lambda$-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.

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.

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.

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.

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.

식물 종자오일의 지방산은 인간에 필수 지방산을 공급하는 식용 및 생필품 생산에 필요한 다양한 산업원료로 사용된다. 식물 오일의 식용 및 산업용 적합성과 경제성을 극대화하기 위해 유전공학에 의한 종자오일의 양과 지방산 조성 변형을 위한 대사조절연구가 계속 진행되고 있다. 하지만 식물에 일반적으로 존재하지 않는, 산업적으로 유용한 특이지방산의 합성과 종자오일로의 축적은 한계가 있음이 알려져 있다. 그 이유는 재배가 용이하며 생산성이 높은 오일식물의 acyltransferase가 특이지방산에 대한 기질특이성이 떨어지며 또한 특이지방산에 대한 세포막지질에서 종자오일로 전환시키는 편집기작 (editing mechanism)이 없기 때문으로 사료된다. 최근에 모델식물의 종자오일의 축적에 관여하는 acyltransferase에 관한 유전자들이 클로닝되었고, 특이지방산이 합성되는 인지질에서의 편집기작에 관여하는 acyltransferase 유전자들이 밝혀져 이들 유전자들의 정보를 이용하여 특이지방산을 효과적으로 생산.증진할 수 있는 기술이 개발될 수 있을 것으로 기대한다. 피마자오일의 주성분인 산업용 특이지방산인 리시놀레인 지방산을 오일식물에서 생산하기 위해 이에 관여할 것으로 추정되는 11개의 acyltransferase 유전자를 피마자 유전체 데이터베이스에서 존재함을 확인하였다. 이들 유전자들의 도입에 의해 형질전환 식물이 갖고 있지 않은 리시놀레인산에 대한 기질 특이성을 부여하여 종자오일 내의 특이지방산의 생산을 증가시킬 것으로 기대된다.

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, $2.0\;mg\;l^{-1}$ 2,4-dichlorophenoxyacetic acid (2,4-D), and $5.0\;mg\;l^{-1}$ L-glutamic acid with $30.0\;g\;l^{-1}$ sucrose and $4.0\;g\;l^{-1}$ 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, $0.2\;mg\;l^{-1}$ $\alpha$-naphthalene acetic acid (NAA), $2.0\;mg\;l^{-1}$ kinetin (Kn), and $2.0\;g\;l^{-1}$ 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.