Genome-wide identification and extensive analysis of rice-endosperm preferred genes using reference expression database

홍우종,유요한,박선아,문선옥,김성렬,안진흥,정기홍 한국식물학회 2017 Journal of Plant Biology Vol.60 No.3

Studying endosperm development in crop species enables us to understand the molecular mechanisms for producing and metabolizing carbohydrates as a main energy source. A significant accumulation of genome-wide transcriptome data can enhance the performance of metaexpression data for diverse applications. Using a gene search tool in Genevestigator (https://genevestigator.com/) for anatomical samples, we first conducted a meta-anatomical expression analysis based on 2566 Affymetrix array data in rice (Oryza sativa) and intended to identify 400 endospermpreferred probes. Tissue-preferred expression patterns were confirmed by performing an additional meta-analysis of anatomical expression data comprising 219 spatial or temporal Agilent 44K array data. We then identified 299 genes that showed strong endosperm-preferred expression. The functional significance of 24 previously characterized genes was evaluated, and tissue-specific expression patterns of two genes were validated using a GUS reporter system. This second approach demonstrated that new tools are available for delivering agronomic traits in the endosperm. MapMan (mapman.gabipd.org/) analysis revealed the Metabolism and Regulation overviews associated with the process of endosperm development. In particular, the starch metabolism pathway is very closely related to that process in rice. We then constructed a regulatory network using both KEGG (www. genome.jp/ kegg/) pathway information for our candidate genes and a predicted protein–protein interaction network tool. Examination of an osbzip58-1 mutant with defects in endosperm development was combined with global transcriptome data in the network. Our results indicated that osbzip58-1 regulates the starch and sucrose metabolism pathways as well as the production of seed storage protein precursors. This new fundamental information adds to our understanding about the molecular mechanism for endosperm development in rice, and the resulting data will contribute to future studies that work to enhance the agronomic trait(s) associated with the endosperm.

Construction and Application of Functional Gene Modules to Regulatory Pathways in Rice

홍우종,Anil Kumar Nalini Chandran,전종성,정기홍 한국식물학회 2017 Journal of Plant Biology Vol.60 No.4

Signal transduction and transcriptional regulationpathways are key elements in the control of diverse physiologicalresponses and agronomic traits in plants. The regulatory rolesof more than 1,000 known genes have been functionallycharacterized in rice, a model crop plant, and many of themare associated with transcriptional regulation and signaltransduction pathways. In this study, we collected andanalyzed 417 known genes associated with regulatorypathways, about 40% of the known genes, using the regulationoverview installed in the MapMan toolkit. Connecting novelgenes to current knowledge about regulatory pathways canelucidate their molecular functions and inspire ideas forfurther applications. We have summarized the functions ofknown regulatory genes in the areas of transcriptional regulation,epigenetic regulation, protein modification, protein degradation,signaling and hormone metabolism, also we have emphasizedthe unique features of several gene families in these classes,including MADS box families, which are strongly associatedwith the regulation of floral organ identity and floweringtime. In addition, our construction of functional modules infour agronomic categories, morphological, physiological,biotic stress and abiotic stress, suggests a basic frameworkfor expanding current knowledge about regulatory pathwaysto enhance agronomic traits in rice. We also provide a quickillustration of the positive and negative regulatory relationshipsof the target gene to manipulate agronomic trait by usinggenome-wide transcriptome data of knockout or overexpressionmutations of genes of interest in each functional module.

Comparative Analysis of Flanking Sequence Tags of T-DNA/Transposon Insertional Mutants and Genetic Variations of Fast-neutron Treated Mutants in Rice

정기홍,홍우종 한국식물학회 2018 Journal of Plant Biology Vol.61 No.2

Whole genome sequencing analyses of 1,504fast-neutron (FN)-induced mutants of ‘Kitaake’ rice varietyhave revealed a new mutant population covering 58.6% oftransposable element (TE) genes and 47.6% of non-TEgenes throughout the rice genome. Mutation rate for TE geneis much higher in FN-induced mutants (58.6%) than inflanking sequence tag (FST) population (25.7%), implyingthat the former are more randomly generated than the latter. By adding this resource to FST population, we found that themutation rate for the rice genome increases from 53.1% to78.1% and more importantly, the rate with multiple allelesincreases from 35.2% to 56.1%. To test the functionalsignificance of mutants produced by both FN-induction andT-DNA/transposon insertions, we analyzed the coverage offunctionally characterized genes by using the Overview offunctionally characterized Genes in Rice Online database(OGRO, http://qtaro.abr.affrc.go.jp/ogro/table). These combinedgenetic resources cover the mutations for 90.9% of functionallycharacterized genes for morphological traits, 91.0% forphysiological traits, and 92.6% for resistance or tolerancetraits, indicating that a gene-indexed mutant population thatincludes FN-induced mutants is valuable to future researchfor improving most of the important agronomic traits.

Genome-wide Analysis of Root Hair Preferred RBOH Genes Suggests that Three RBOH Genes are Associated with Auxin-mediated Root Hair Development in Rice

김의정,김유진,홍우종,이찬희,전종성,정기홍 한국식물학회 2019 Journal of Plant Biology Vol.62 No.3

Plant homologs of mammalian NADPH oxidase,respiratory burst oxidase homologs (RBOH), mainly oxidizeNADPH to NADP+ and transfer electrons to water. Themembrane residing RBOHs thus produce reactive oxygenspecies (ROS), which allows plants to withstand abiotic andbiotic environmental stresses. To understand the spatial andtemporal function of rice (Oryza sativa) RBOH genes, weperformed expression analysis of nine RBOH genes using qRTPCRand microarray data. The expression profiling data suggestthat RBOH genes have diverse roles in various tissues andorgans as well as responses to hormonal treatments. Amongthem, OsRBOH2, OsRBOH3, and OsRBOH5 are preferentiallyexpressed in root hairs. Exogenous auxin upregulates theexpression of OsRBOH1, OsRBOH2, OsRBOH3, OsRBOH4,and OsRBOH8 in root hairs, while the expression of OsRBOH7and OsRBOH9 is downregulated. In roots, treatment with anRBOH inhibitor, diphenyleneiodonium (DPI), suppressed theaccumulation of ROS in trichoblast cells which initiate roothairs, suggesting that RBOH-mediated ROS could play animportant role in root hair initiation in the trichoblast cells of riceroots. Promoter analysis revealed that OsRBOH3 and OsRBOH5contain many known cis-acting regulatory elements (CREs)associated with root hair development such as the root hair cisactingelement, RHE. OsRBOH2 and OsRBOH3, which areupregulated after treatment with indole-3-acetic acid (IAA) withsignificant expression in root hairs, might be key players in roothair elongation via an auxin-dependent pathway in rice.

Rice RHC Encoding a Putative Cellulase is Essential for Normal Root Hair Elongation

문선옥,Anil Kumar Nalini Chandran,김유진,고윤실,홍우종,안균흥,이찬희,정기홍 한국식물학회 2019 Journal of Plant Biology Vol.62 No.1

Root hairs are tubular shaped protuberances ofroot epidermal cells and are found in nearly all vascularplants. Co-ordinate expression of a number of root hairmorphogenesis genes involved in cytoskeleton reorganization,changes in homeostasis and distribution of ion gradients, andcell wall reassembly are required during root hair cellelongation. In this report, we have characterized a root hairspecificputative cellulase gene in rice, OsRHC. OsRHC isspecifically expressed in elongating root hairs and OsRHC istargeted to the plasma membrane. The mutation of the OsRHCgene by a T-DNA knock-out and CRISPR-Cas9 systemcauses a severe reduction in root hair length. Bimolecularfluorescence complementation analysis demonstrated that theOsRHC protein interacts with a root hair-specific cellulosesynthase protein (OsCSLD1) in the plasma membrane. Furthermore, we observed a moderate reduction of cellulosecontent in the osrhc mutant. Our results suggest that theplasma membrane-localized OsRHC plays a critical role incell wall remodeling during root hair extension.

Overexpression of the ginseng GH18 gene confers salinity tolerance in Arabidopsis

노가영,김지현,조성원,김영훈,정주영,홍우종,정기홍,박규림,손홍주,Jo Ick-Hyun,송영훈,김선태,김유진 한국식물생명공학회 2022 Plant biotechnology reports Vol.16 No.6

Glycoside hydrolase family 18 (GH18) genes are known as chitinase, which catalyzes the ß-1,4-glycosidic bond in amino polysaccharides. GH18 genes have been found in diverse organisms with multiple physiological roles. Despite their vital role in plant defense, the role of the GH18 family in ginseng (Panax ginseng) has not been investigated to date. In this study, we identifed 26 members of the GH18 family from the ginseng genome and cloned a Class III member, PgGH18. Expression of PgGH18 was highly up-regulated in response to salt stress in ginseng. In subcellular localization analysis, PgGH18 protein was predominantly identifed in the cytoplasm, and signals in the plasma membrane were connected with apoplast by plasmolysis. Overexpression of PgGH18 in Arabidopsis exhibited a higher germination ratio and maintained longer root growth than the wild type (WT) under salt stress. When treated with salt stress, it was observed that reactive oxygen species (ROS) accumulated more in transformants than it did in the WT. Our study suggests that a Class III member of the GH18 gene family, PgGH18, plays a role in abiotic stress defense in ginseng rather than fungal response. PgGH18 functions as a positive regulator of salinity tolerance, representing an important target for developing salt-tolerant ginseng cultivars via genetic engineering or breeding marker

Defense Response to Pathogens Through Epigenetic Regulation in Rice

전종성,정기홍,Trung Viet Hoang,VO THI XUAN KIEU,홍우종 한국식물학회 2018 Journal of Plant Biology Vol.61 No.1

Epigenetic factors have recently emerged as key regulators of the defense response to pathogens in plants. The epigenetic mechanisms underlying defense regulation have been investigated mostly in Arabidopsis, while our understanding of the epigenetic regulation of defense in rice is limited. In this review, we summarize recent findings surrounding epigenetic mechanisms for defense in rice, primarily focusing on DNA methylation, histone modification, and small RNA regulation. In particular, we focused on RNA-directed DNA methylation (RdDM) and other epigenetic regulatory mechanisms that are involved in disease resistance. Finally, we explored potential epigenetic factors that might regulate the defense response in rice by analyzing available microarray data that can be used to uncover details of epigenetics regulation.