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Tseng BS, Huang CC, King YC, Wu MT, Hsieh CH, Hsieh KT, Hsing YI, Jeng ST. Hydrogen peroxide regulates the Osa-miR156-OsSPL2/OsTIFY11b module in rice. Plant Cell Environ 2023. [PMID: 37212208 DOI: 10.1111/pce.14605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/23/2023]
Abstract
Field-grown rice (Oryza sativa L.), when exposed to various environmental stresses, produces high amounts of reactive oxygen species, such as H2 O2 . MicroRNAs (miRNAs) play crucial roles in plant stress responses. This study characterized the functions of H2 O2 -regulated miRNAs in rice. Small RNA deep sequencing revealed that miR156 levels decreased following H2 O2 treatment. Searches of the rice transcriptome and degradome databases indicated that OsSPL2 and OsTIFY11b are miR156-target genes. Interactions between miR156 and OsSPL2 and OsTIFY11b were confirmed using transient expression assays through agroinfiltration. In addition, the levels of OsSPL2 and OsTIFY11b transcripts were lower in transgenic rice plants overexpressing miR156 than in wild-type plants. The OsSPL2-GFP and OsTIFY11b-GFP proteins were localized to the nucleus. Yeast two-hybrid and bimolecular fluorescence complementation assays indicated interactions between OsSPL2 and OsTIFY11b. Furthermore, OsTIFY11b interacted with OsMYC2 to regulate the expression of OsRBBI3-3, which encodes a proteinase inhibitor. The results suggested that H2 O2 accumulation in rice suppresses the expression of miR156, and induces the expression of its target genes, OsSPL2 and OsTIFY11b, whose proteins interact in the nucleus to regulate the expression of OsRBBI3-3, which is involved in plant defense.
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Affiliation(s)
- Bo-Shun Tseng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Cheng-Chung Huang
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ming-Tsung Wu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Civil and Environmental Engineering, South Kensington Campus, Imperial College London, London, UK
| | - Chih-Hung Hsieh
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Kun-Ting Hsieh
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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2
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Lo SF, Chatterjee J, Biswal AK, Liu IL, Chang YP, Chen PJ, Wanchana S, Elmido-Mabilangan A, Nepomuceno RA, Bandyopadhyay A, Hsing YI, Quick WP. Closer vein spacing by ectopic expression of nucleotide-binding and leucine-rich repeat proteins in rice leaves. Plant Cell Rep 2022; 41:319-335. [PMID: 34837515 PMCID: PMC8850240 DOI: 10.1007/s00299-021-02810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Elevated expression of nucleotide-binding and leucine-rich repeat proteins led to closer vein spacing and higher vein density in rice leaves. To feed the growing global population and mitigate the negative effects of climate change, there is a need to improve the photosynthetic capacity and efficiency of major crops such as rice to enhance grain yield potential. Alterations in internal leaf morphology and cellular architecture are needed to underpin some of these improvements. One of the targets is to generate a "Kranz-like" anatomy in leaves that includes decreased interveinal spacing close to that in C4 plant species. As C4 photosynthesis has evolved from C3 photosynthesis independently in multiple lineages, the genes required to facilitate C4 may already be present in the rice genome. The Taiwan Rice Insertional Mutants (TRIM) population offers the advantage of gain-of-function phenotype trapping, which accelerates the identification of rice gene function. In the present study, we screened the TRIM population to determine the extent to which genetic plasticity can alter vein density (VD) in rice. Close vein spacing mutant 1 (CVS1), identified from a VD screening of approximately 17,000 TRIM lines, conferred heritable high leaf VD. Increased vein number in CVS1 was confirmed to be associated with activated expression of two nucleotide-binding and leucine-rich repeat (NB-LRR) proteins. Overexpression of the two NB-LRR genes individually in rice recapitulates the high VD phenotype, due mainly to reduced interveinal mesophyll cell (M cell) number, length, bulliform cell size and thus interveinal distance. Our studies demonstrate that the trait of high VD in rice can be achieved by elevated expression of NB-LRR proteins limited to no yield penalty.
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Affiliation(s)
- Shuen-Fang Lo
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC.
| | - Jolly Chatterjee
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Akshaya K Biswal
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz km. 45, El Batán, Texcoco, CP 56237, México
| | - I-Lun Liu
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Yu-Pei Chang
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Pei-Jing Chen
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Samart Wanchana
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | | | - Robert A Nepomuceno
- National Institute of Molecular Biology and Biotechnology, University of the Philippines (BIOTECH-UPLB), Los Baños, 4031, Philippines
| | | | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - William Paul Quick
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines.
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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3
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Jang S, Cho JY, Do GR, Kang Y, Li HY, Song J, Kim HY, Kim BG, Hsing YI. Modulation of Rice Leaf Angle and Grain Size by Expressing OsBCL1 and OsBCL2 under the Control of OsBUL1 Promoter. Int J Mol Sci 2021; 22:7792. [PMID: 34360554 PMCID: PMC8346013 DOI: 10.3390/ijms22157792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
Leaf angle and grain size are important agronomic traits affecting rice productivity directly and/or indirectly through modulating crop architecture. OsBC1, as a typical bHLH transcription factor, is one of the components comprising a complex formed with LO9-177 and OsBUL1 contributing to modulation of rice leaf inclination and grain size. In the current study, two homologues of OsBC1, OsBCL1 and OsBCL2 were functionally characterized by expressing them under the control of OsBUL1 promoter, which is preferentially expressed in the lamina joint and the spikelet of rice. Increased leaf angle and grain length with elongated cells in the lamina joint and the grain hull were observed in transgenic rice containing much greater gibberellin A3 (GA3) levels than WT, demonstrating that both OsBCL1 and OsBCL2 are positive regulators of cell elongation at least partially through increased GA biosynthesis. Moreover, the cell elongation was likely due to cell expansion rather than cell division based on the related gene expression and, the cell elongation-promoting activities of OsBCL1 and OsBCL2 were functional in a dicot species, Arabidopsis.
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Affiliation(s)
- Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jeollabuk-do 55365, Korea;
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan;
| | - Jwa-Yeong Cho
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon 25451, Korea; (J.-Y.C.); (H.-Y.K.)
| | - Gyung-Ran Do
- Planning and Coordination Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do 55365, Korea;
| | - Yeeun Kang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jeollabuk-do 55365, Korea;
| | - Hsing-Yi Li
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan;
| | - Jaeeun Song
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (J.S.); (B.-G.K.)
| | - Ho-Youn Kim
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon 25451, Korea; (J.-Y.C.); (H.-Y.K.)
| | - Beom-Gi Kim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (J.S.); (B.-G.K.)
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
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4
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Alam O, Gutaker RM, Wu CC, Hicks KA, Bocinsky K, Castillo CC, Acabado S, Fuller D, d'Alpoim Guedes JA, Hsing YI, Purugganan MD. Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia. Mol Biol Evol 2021; 38:4832-4846. [PMID: 34240169 PMCID: PMC8557449 DOI: 10.1093/molbev/msab209] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast Asia. The history of dispersal across islands of Southeast Asia, and the role of Taiwan and the Austronesian expansion in this process remain largely unresolved. Here, we reconstructed the routes of dispersal of O. sativa ssp. japonica rice through Taiwan and the northern Philippines using whole-genome re-sequencing of indigenous rice landraces coupled with archaeological and paleoclimate data. Our results indicate that japonica rice found in the northern Philippines diverged from Indonesian landraces as early as 3500 BP. In contrast, rice cultivated by the indigenous peoples of the Taiwanese mountains has complex origins. It comprises two distinct populations, each best explained as a result of admixture between temperate japonica that presumably came from northeast Asia, and tropical japonica from the northern Philippines and mainland Southeast Asia respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2600 BP, while gene flow from the northern Philippines occurred before ∼1300 years BP. This coincides with a period of intensified trade established across the South China Sea. Finally, we find evidence for positive selection acting on distinct genomic regions in different rice subpopulations, indicating local adaptation associated with the spread of japonica rice.
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Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Rafal M Gutaker
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA.,Royal Botanic Garden, Kew, Richmond, London, TW9 3AE UK
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.,Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Karen A Hicks
- Department of Biology, Kenyon College, Gambier, Ohio 43022 USA
| | | | | | - Stephen Acabado
- Department of Anthropology, University of California, Los Angeles, CA USA
| | - Dorian Fuller
- Institute of Archaeology, University College London, London, United Kingdom.,School of Cultural Heritage, North-West University, Xi'an, China
| | - Jade A d'Alpoim Guedes
- Department of Anthropology and Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA.,Institute for the Study of the Ancient World, New York University, New York, NY 10028 USA
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5
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Sánchez-Sanuy F, Peris-Peris C, Tomiyama S, Okada K, Hsing YI, San Segundo B, Campo S. Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus. BMC Plant Biol 2019; 19:563. [PMID: 31852430 PMCID: PMC6921540 DOI: 10.1186/s12870-019-2156-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/21/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in eukaryotes. In rice, MIR7695 expression is regulated by infection with the rice blast fungus Magnaporthe oryzae with subsequent down-regulation of an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6). NRAMP6 functions as an iron transporter in rice. RESULTS Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance. During pathogen infection, iron accumulated in the vicinity of M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced iron accumulation and resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCPS4, were also highly upregulated in wild-type rice plants grown under high iron supply. CONCLUSIONS Our data support a positive role of miR7695 in regulating rice immunity that further underpin links between defense and iron signaling in rice. These findings provides a basis to better understand regulatory mechanisms involved in rice immunity in which miR7695 participates which has a great potential for the development of strategies to improve blast resistance in rice.
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Affiliation(s)
- Ferran Sánchez-Sanuy
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Cristina Peris-Peris
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Shiho Tomiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yue-Ie Hsing
- Institute of Plant and Microrbial Biology, Academia Sinica, Taipei, Taiwan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
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6
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Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nat Commun 2019; 10:24. [PMID: 30604755 PMCID: PMC6318337 DOI: 10.1038/s41467-018-07974-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
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Affiliation(s)
- Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Ernandes Manfroi
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, 305-8687, Ibaraki, Japan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Emilie Debladis
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France.
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France.
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Salvador-Guirao R, Baldrich P, Tomiyama S, Hsing YI, Okada K, San Segundo B. OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice. Ann Bot 2019; 123:79-93. [PMID: 30032201 PMCID: PMC6344094 DOI: 10.1093/aob/mcy141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 06/30/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNAs. Although a plethora of miRNAs have been found to be regulated by pathogen infection in plants, the biological function of most miRNAs remains largely unknown. Here, the contribution of OsDCL1 to rice immunity was investigated. METHODS Activation-tagged Osdcl1a (Osdcl1a-Ac) rice mutants were examined for resistance to pathogen infection. mRNA and small RNA deep sequencing, quantitative real-time PCR (RT-qPCR) and stem-loop reverse tanscripion-PCR (RT-PCR) were used to examine DCL1a-mediated alterations in the rice transcriptome. Rice diterpene phytoalexins were quantified by liquid chromatography-tandem mass spectrometry (LC-MSMS). Accumulation of O2·- was determined by nitroblue tetrazolium (NBT) staining. KEY RESULTS dcl1a-Ac mutants exhibit enhanced susceptibility to infection by fungal pathogens which was associated with a weaker induction of defence gene expression. Comparison of the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants revealed misregulation of genes involved in detoxification of reactive oxygen species. Consequently, dcl1a-Ac plants accumulated O2·- in their leaves and were more sensitive to methyl viologen-induced oxidative stress. Furthermore, dcl1a-Ac plants showed downregulation of diterpenoid phytoalexin biosynthetic genes, these genes also being weakly induced during pathogen infection. Upon pathogen challenge, dcl1a-Ac plants failed to accumulate major diterpenoid phytoalexins. OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs. CONCLUSIONS OsDCL1a activation enhances susceptibility to infection by fungal pathogens in rice. Activation of OsDCL1a represses the pathogen-inducible host defence response and negatively regulates diterpenoid phytoalexin production. These findings provide a basis to understand the molecular mechanisms through which OsDCL1a mediates rice immunity.
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Affiliation(s)
- Raquel Salvador-Guirao
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Shiho Tomiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
- For correspondence. E-mail
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8
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Lo SF, Fan MJ, Hsing YI, Chen LJ, Chen S, Wen IC, Liu YL, Chen KT, Jiang MJ, Lin MK, Rao MY, Yu LC, Ho THD, Yu SM. Genetic resources offer efficient tools for rice functional genomics research. Plant Cell Environ 2016; 39:998-1013. [PMID: 26301381 DOI: 10.1111/pce.12632] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/13/2015] [Accepted: 08/16/2015] [Indexed: 05/07/2023]
Abstract
Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.
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Affiliation(s)
- Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ming-Jen Fan
- Department of Biotechnology, Asia University, Lioufeng Road, Wufeng, Taichung, 413, Taiwan, ROC
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Liang-Jwu Chen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Shu Chen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Wufeng, Taichung, 413, Taiwan, ROC
| | - Ien-Chie Wen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Wufeng, Taichung, 413, Taiwan, ROC
| | - Yi-Lun Liu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ku-Ting Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Mirng-Jier Jiang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ming-Kuang Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Meng-Yen Rao
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Lin-Chih Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Tuan-Hua David Ho
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, ROC
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Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 2015; 16:538. [PMID: 26194356 PMCID: PMC4508813 DOI: 10.1186/s12864-015-1762-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS Here we present the Rice TE database (RiTE-db)--a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.
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Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
| | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Moaine El Baidouri
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Elena Barghini
- Department of Agriculture, Food, and Environment, University of Pisa, 56124, Pisa, Italy.
| | - Rosa M Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Angelina Angelova
- School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland.
| | - Carlos E Maldonado L
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Stefan Roffler
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Hajime Ohyanagi
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101, China.
| | | | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
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Hou CY, Wu MT, Lu SH, Hsing YI, Chen HM. Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data. BMC Genomics 2014; 15:15. [PMID: 24405808 PMCID: PMC3898255 DOI: 10.1186/1471-2164-15-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 01/06/2014] [Indexed: 11/26/2022] Open
Abstract
Background Degradation is essential for RNA maturation, turnover, and quality control. RNA degradome sequencing that integrates a modified 5′-rapid amplification of cDNA ends protocol with next-generation sequencing technologies is a high-throughput approach for profiling the 5′-end of uncapped RNA fragments on a genome-wide scale. The primary application of degradome sequencing has been to identify the truncated transcripts that result from endonucleolytic cleavage guided by microRNAs or small interfering RNAs. As many pathways are involved in RNA degradation, degradome data should contain other RNA species besides the cleavage remnants of small RNA targets. Nevertheless, no systematic approaches have been established to explore the hidden complexity of plant degradome. Results Through analyzing Arabidopsis and rice RNA degradome data, we recovered 11 short motifs adjacent to predominant and abundant uncapped 5′-ends. Uncapped ends associated with several of these short motifs were more prevalent than those targeted by most miRNA families especially in the 3′ untranslated region of transcripts. Through genome-wide analysis, five motifs showed preferential accumulation of uncapped 5′-ends at the same position in Arabidopsis and rice. Moreover, the association of uncapped 5′-ends with a CA-repeat motif and a motif recognized by Pumilio/Fem-3 mRNA binding factor (PUF) proteins was also found in non-plant species, suggesting that common mechanisms are present across species. Based on these motifs, potential sources of RNA ends that constitute degradome data were proposed and further examined. The 5′-end of small nucleolar RNAs could be precisely captured by degradome sequencing. Position-specific enrichment of uncapped 5′-ends was seen upstream of motifs recognized by several RNA binding proteins especially for the binding site of PUF proteins. False uncapped 5′-ends produced from capped transcripts through non-specific PCR amplification were common artifacts among degradome datasets. Conclusions The complexity of plant RNA degradome data revealed in this study may contribute to the alternative applications of degradome in RNA research.
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Affiliation(s)
| | | | | | | | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
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11
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Hsu YC, Tseng MC, Wu YP, Lin MY, Wei FJ, Hwu KK, Hsing YI, Lin YR. Genetic factors responsible for eating and cooking qualities of rice grains in a recombinant inbred population of an inter-subspecific cross. Mol Breed 2014; 34:655-673. [PMID: 25076839 PMCID: PMC4092229 DOI: 10.1007/s11032-014-0065-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 03/04/2014] [Indexed: 05/07/2023]
Abstract
The eating and cooking qualities of rice grains are the major determinants of consumer preference and, consequently, the economic value of a specific rice variety. These two qualities are largely determined by the physicochemical properties of the starch, i.e. the starch composition, of the rice grain. In our study, we determined the genetic factors responsible for the physicochemical properties of starch in recombinant inbred lines (RILs) of japonica cv. Tainung 78 × indica cv. Taichung Sen 17 (TCS 17) cultivated over two crop seasons by examining palatability characteristics and several Rapid Viscosity Analyzer (RVA) parameters. Thirty-four quantitative trait loci (QTLs), each explaining between 1.2 and 78.1 % phenotypic variation, were mapped in clusters on eight chromosomes in 190 RILs genotyped with 139 markers. Ten pairs of QTLs were detected in the two environments, of which seven were in agreement with previous findings, suggesting that these QTLs may express stable experimental populations across various environments. Waxy (Wx), which controls amylose synthesis, was determined to be a primary gene regulating the physicochemical properties of cooked rice grains, as indicated by the presence of a major QTL cluster on chromosome 6 and by marker regression analysis. Six starch synthesis-related genes (SSRGs) which were located in the QTL intervals significantly differed in terms of gene expression between the two parents during grain-filling and were important genetic factors affecting physicochemical properties. The expression of four genes, PUL, ISA2, GBSSI, and SSII-3, was significantly upregulated in TCS 17, and this expression was positively correlated with six traits. The effects of the six SSRGs and gene interaction depended on genetic background and environment; grain quality may be fine tuned by selecting for SBE4 for japonica and PUL for indica. We provide valuable information for application in the breeding of new rice varieties as daily staple food and for use in industrial manufacturing by marker-assisted selection.
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Affiliation(s)
- Yu-Chia Hsu
- Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Meng-Chun Tseng
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Yong-Pei Wu
- Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Meng-Ying Lin
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Fu-Jin Wei
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Kae-Kang Hwu
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Yue-Ie Hsing
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
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Wu YP, Ko PY, Lee WC, Wei FJ, Kuo SC, Ho SW, Hour AL, Hsing YI, Lin YR. Comparative analyses of linkage maps and segregation distortion of two F₂ populations derived from japonica crossed with indica rice. Hereditas 2010; 147:225-36. [PMID: 21039459 DOI: 10.1111/j.1601-5223.2010.02120.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To facilitate genetic research, we constructed two linkage maps by employing two F₂ populations derived from rice inter-subspecific crosses, japonica Tainung 67 (TNG67)/indica Taichung Sen 10 (TCS10) and japonica TNG67/indica Taichung Sen 17 (TCS17). We established linkage map lengths of 1481.6 cM and 1267.4 cM with average intervals of 13.8 cM and 14.4 cM by using 107 and 88 PCR markers for coverage of 88% of the rice genome in TNG67/TCS10 and TNG67/TCS17, respectively. The discrepancy in genetic maps in the two populations could be due to different cross combinations, crossing-over events, progeny numbers and/or markers. The most plausible explanation was segregation distortion; 18 markers (16.8%) distributed at nine regions of seven chromosomes and 10 markers (11.4%) at four regions of four chromosomes displayed severe segregation distortion (p < 0.01)in TNG67/TCS10 and TNG67/TCS17, respectively. All segregation-distorted markers in these two populations corresponded to reported reproductive barriers, either gametophytic or zygotic genes but not to hybrid breakdown genes. The observed recombination frequency, which was higher or lower than the intrinsic frequency, revealed the association of segregation distortion skewed to the same or different genotypes at the consecutive markers. The segregation distortion, possibly caused by reproductive barriers, affects the evaluation recombination frequencies and consequently the linkage analysis of QTLs and positional cloning.
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Affiliation(s)
- Yong-Pei Wu
- Department of Agronomy, Chiayi Agricultrual Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
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13
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Lo SF, Yang SY, Chen KT, Hsing YI, Zeevaart JAD, Chen LJ, Yu SM. A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice. Plant Cell 2008; 20:2603-18. [PMID: 18952778 PMCID: PMC2590730 DOI: 10.1105/tpc.108.060913] [Citation(s) in RCA: 280] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 09/19/2008] [Accepted: 09/30/2008] [Indexed: 05/18/2023]
Abstract
Gibberellin 2-oxidases (GA2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (GAs). Two classes of GA2oxs inactivate GAs through 2beta-hydroxylation: a larger class of C(19) GA2oxs and a smaller class of C(20) GA2oxs. In this study, we show that members of the rice (Oryza sativa) GA2ox family are differentially regulated and act in concert or individually to control GA levels during flowering, tillering, and seed germination. Using mutant and transgenic analysis, C(20) GA2oxs were shown to play pleiotropic roles regulating rice growth and architecture. In particular, rice overexpressing these GA2oxs exhibited early and increased tillering and adventitious root growth. GA negatively regulated expression of two transcription factors, O. sativa homeobox 1 and TEOSINTE BRANCHED1, which control meristem initiation and axillary bud outgrowth, respectively, and that in turn inhibited tillering. One of three conserved motifs unique to the C(20) GA2oxs (motif III) was found to be important for activity of these GA2oxs. Moreover, C(20) GA2oxs were found to cause less severe GA-defective phenotypes than C(19) GA2oxs. Our studies demonstrate that improvements in plant architecture, such as semidwarfism, increased root systems and higher tiller numbers, could be induced by overexpression of wild-type or modified C(20) GA2oxs.
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Affiliation(s)
- Shuen-Fang Lo
- Institute of Molecular Biology, National Chung-Hsing University, Taichung 402, Taiwan, Republic of China
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14
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Yu SM, Ko SS, Hong CY, Sun HJ, Hsing YI, Tong CG, Ho THD. Global functional analyses of rice promoters by genomics approaches. Plant Mol Biol 2007; 65:417-425. [PMID: 17922261 DOI: 10.1007/s11103-007-9232-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 08/22/2007] [Indexed: 05/25/2023]
Abstract
Promoters play key roles in conferring temporal, spatial, chemical, developmental, or environmental regulation of gene expression. Promoters that are subject to specific regulations are useful for manipulating foreign gene expression in plant cells, tissues, or organs with desirable patterns and under controlled conditions, and have been important for both basic research and applications in agriculture biotechnology. Recent advances in genomics technologies have greatly facilitated identification and study of promoters in a genome scale with high efficiency. Previously we have generated a large T-DNA tagged rice mutant library (TRIM), in which the T-DNA was designed with a gene/promoter trap system, by placing a promoter-less GUS gene next to the right border of T-DNA. GUS activity screens of this library offer in situ and in planta identifications and analyses of promoter activities in their native configurations in the rice genome. In the present study, we systematically performed GUS activity screens of the rice mutant library for genes/promoters constitutively, differentially, or specifically active in vegetative and reproductive tissues. More than 8,200 lines have been screened, and 11% and 22% of them displayed GUS staining in vegetative tissues and in flowers, respectively. Among the vegetative tissue active promoters, the ratio of leaf active versus root active is about 1.6. Interestingly, all the flower active promoters are anther active, but with varied activities in different flower tissues. To identify tissue specific ABA/stress up-regulated promoters, we compared microarray data of ABA/stress induced genes with those of tissue-specific expression determined by promoter trap GUS staining. Following this approach, we showed that the peroxidase 1 gene promoter was ABA up-regulated by 4 fold within 1 day of exposure to ABA and its expression is lateral root specific. We suggest that this be an easy bioinformatics approach in identifying tissue/cell type specific promoters that are up-regulated by hormones or other factors.
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Affiliation(s)
- Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
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15
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Lu CA, Lin CC, Lee KW, Chen JL, Huang LF, Ho SL, Liu HJ, Hsing YI, Yu SM. The SnRK1A protein kinase plays a key role in sugar signaling during germination and seedling growth of rice. Plant Cell 2007; 19:2484-99. [PMID: 17766403 PMCID: PMC2002608 DOI: 10.1105/tpc.105.037887] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Sugars repress alpha-amylase expression in germinating embryos and cell cultures of rice (Oryza sativa) through a sugar response complex (SRC) in alpha-amylase gene promoters and its interacting transcription factor MYBS1. The Snf1 protein kinase is required for the derepression of glucose-repressible genes in yeast. In this study, we explored the role of the yeast Snf1 ortholog in rice, SnRK1, in sugar signaling and plant growth. Rice embryo transient expression assays indicated that SnRK1A and SnRK1B act upstream and relieve glucose repression of MYBS1 and alphaAmy3 SRC promoters. Both SnRK1s contain N-terminal kinase domains serving as activators and C-terminal regulatory domains as dominant negative regulators of SRC. The accumulation and activity of SnRK1A was regulated by sugars posttranscriptionally, and SnRK1A relieved glucose repression specifically through the TA box in SRC. A transgenic RNA interference approach indicated that SnRK1A is also necessary for the activation of MYBS1 and alphaAmy3 expression under glucose starvation. Two mutants of SnRK1s, snrk1a and snrk1b, were obtained, and the functions of both SnRK1s were further studied. Our studies demonstrated that SnRK1A is an important intermediate in the sugar signaling cascade, functioning upstream from the interaction between MYBS1 and alphaAmy3 SRC and playing a key role in regulating seed germination and seedling growth in rice.
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Affiliation(s)
- Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China
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16
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Hsing YI, Chern CG, Fan MJ, Lu PC, Chen KT, Lo SF, Sun PK, Ho SL, Lee KW, Wang YC, Huang WL, Ko SS, Chen S, Chen JL, Chung CI, Lin YC, Hour AL, Wang YW, Chang YC, Tsai MW, Lin YS, Chen YC, Yen HM, Li CP, Wey CK, Tseng CS, Lai MH, Huang SC, Chen LJ, Yu SM. A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol Biol 2007; 63:351-64. [PMID: 17120135 DOI: 10.1007/s11103-006-9093-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Accepted: 09/12/2006] [Indexed: 05/12/2023]
Abstract
Using transfer DNA (T-DNA) with functions of gene trap and gene knockout and activation tagging, a mutant population containing 55,000 lines was generated. Approximately 81% of this population carries 1-2 T-DNA copies per line, and the retrotransposon Tos17 was mostly inactive in this population during tissue culture. A total of 11,992 flanking sequence tags (FSTs) have been obtained and assigned to the rice genome. T-DNA was preferentially ( approximately 80%) integrated into genic regions. A total of 19,000 FSTs pooled from this and another T-DNA tagged population were analyzed and compared with 18,000 FSTs from a Tos17 tagged population. There was difference in preference for integrations into genic, coding, and flanking regions, as well as repetitive sequences and centromeric regions, between T-DNA and Tos17; however, T-DNA integration was more evenly distributed in the rice genome than Tos17. Our T-DNA contains an enhancer octamer next to the left border, expression of genes within genetics distances of 12.5 kb was enhanced. For example, the normal height of a severe dwarf mutant, with its gibberellin 2-oxidase (GA2ox) gene being activated by T-DNA, was restored upon GA treatment, indicating GA2ox was one of the key enzymes regulating the endogenous level of GA. Our T-DNA also contains a promoterless GUS gene next to the right border. GUS activity screening facilitated identification of genes responsive to various stresses and those regulated temporally and spatially in large scale with high frequency. Our mutant population offers a highly valuable resource for high throughput rice functional analyses using both forward and reverse genetic approaches.
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Affiliation(s)
- Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
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Hirochika H, Guiderdoni E, An G, Hsing YI, Eun MY, Han CD, Upadhyaya N, Ramachandran S, Zhang Q, Pereira A, Sundaresan V, Leung H. Rice mutant resources for gene discovery. Plant Mol Biol 2004; 54:325-34. [PMID: 15284490 DOI: 10.1023/b:plan.0000036368.74758.66] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
With the completion of genomic sequencing of rice, rice has been firmly established as a model organism for both basic and applied research. The next challenge is to uncover the functions of genes predicted by sequence analysis. Considering the amount of effort and the diversity of disciplines required for functional analyses, extensive international collaboration is needed for this next goal. The aims of this review are to summarize the current status of rice mutant resources, key tools for functional analysis of genes, and our perspectives on how to accelerate rice gene discovery through collaboration.
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Affiliation(s)
- Hirohiko Hirochika
- Molecular Genetics Department, National Institute of Agrobiological Sciences, Tsukuba City, Ibaraki 305-8602, Japan.
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18
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Affiliation(s)
- P F Lee
- Graduate Institute of Botany, National Taiwan University, Taipei, Taiwan, Republic of China
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19
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Chen ZY, Hsing YI, Lee PF, Chow TY. Nucleotide sequences of a soybean cDNA encoding an 18 kilodalton late embryogenesis abundant protein. Plant Physiol 1992; 99:773-4. [PMID: 16668955 PMCID: PMC1080534 DOI: 10.1104/pp.99.2.773] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- Z Y Chen
- Institute of Botany, Academia Sinica, Taipei, Taiwan, Republic of China
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20
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Hsing YI, Chen ZY, Chow TY. Nucleotide sequences of a soybean complementary DNA encoding a 50-kilodalton late embryogenesis abundant protein. Plant Physiol 1992; 99:354-5. [PMID: 16668877 PMCID: PMC1080450 DOI: 10.1104/pp.99.1.354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- Y I Hsing
- Institute of Botany, Academia Sinica, Taipei, Taiwan, Republic of China
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21
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Chang WC, Hsing YI. Plant regeneration through somatic embryogenesis in root-derived callus of ginseng (Panax ginseng C. A. Meyer). Theor Appl Genet 1980; 57:133-135. [PMID: 24302495 DOI: 10.1007/bf00253888] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/27/1979] [Indexed: 06/02/2023]
Abstract
Callus culture was initiated from expiants of mature root tissues of ginseng (Panax ginseng C.A. Meyer) on MS medium enriched with 2,4-D. The ageing callus produced numerous embryoids in this medium. Reculture of these embryoids in media (1/2 MS or B5) supplemented with benzyladenine and gibberellic acid resulted in profuse plantlet regeneration.
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Affiliation(s)
- W C Chang
- Academia Sinica, Institute of Botany, Taipei, Taiwan (Republic of China)
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22
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Chang WC, Hsing YI. DPX-3778 promotes proliferation of tobacco callus in vitro. Planta 1978; 140:293-294. [PMID: 24414569 DOI: 10.1007/bf00390263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/1978] [Accepted: 02/07/1978] [Indexed: 06/03/2023]
Abstract
DPX-3778, the triethanolamine salt of 3-(p-chlorophenyl)-6-methoxy-s-triazine-2,4(1H,3H) dione, at concentrations of 0.124-2.48 μM enhanced ca. 4-5-fold the proliferation of tobacco (Nicotiana tabacum L. cv. Wisconsin 38) callus cultured in the presence of indole-3-acetic acid and kinetin, and retarded its senescence.
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Affiliation(s)
- W C Chang
- Institute of Botany, Academia Sinica, 115, Taipei, Taiwan, Republic of China
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