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Hong WJ, Kim YJ, Chandran AKN, Jung KH. Infrastructures of systems biology that facilitate functional genomic study in rice. RICE (NEW YORK, N.Y.) 2019; 12:15. [PMID: 30874968 PMCID: PMC6419666 DOI: 10.1186/s12284-019-0276-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Matsumoto T, Wu J, Itoh T, Numa H, Antonio B, Sasaki T. The Nipponbare genome and the next-generation of rice genomics research in Japan. RICE (NEW YORK, N.Y.) 2016; 9:33. [PMID: 27447712 PMCID: PMC4958085 DOI: 10.1186/s12284-016-0107-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/03/2016] [Indexed: 05/28/2023]
Abstract
The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits.
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Affiliation(s)
- Takashi Matsumoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Hisataka Numa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Baltazar Antonio
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takuji Sasaki
- Nodai Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
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Zhang Y, Verhoeff NI, Chen Z, Chen S, Wang M, Zhu Z, Ouwerkerk PBF. Functions of OsDof25 in regulation of OsC4PPDK. PLANT MOLECULAR BIOLOGY 2015; 89:229-42. [PMID: 26337938 PMCID: PMC4579267 DOI: 10.1007/s11103-015-0357-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/31/2015] [Indexed: 05/03/2023]
Abstract
Relative little is known about the functions of the so-called Dof zinc factors in plants. Here we report on the analysis of OsDof25 and show a function in regulation of the important C4 photosynthesis gene, OsC4PPDK in rice. Over-expression of OsDof25 enhanced the expression of OsC4PPDK in transient expression experiments by binding in a specific way to a conserved Dof binding site which was confirmed by yeast and in vitro binding studies. Expression studies using promoter GUS plants as well as qPCR experiments showed that OsDof25 expressed in different tissues including both photosynthetic and non-photosynthetic organs and that expression of OsDof25 was partially overlapping with the OsC4PPDK gene. Conclusive evidence for a role of OsDof25 in regulation of C4PPDK came from loss-of-function and gain-of-function experiments with transgenic rice, which showed that down-regulation or over-expression of OsDof25 correlated with OsC4PPDK expression and that OsDof25 has functions as transcriptional activator.
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Affiliation(s)
- Y Zhang
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - N I Verhoeff
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Z Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Wusi Rd 247, Fuzhou, 350003, Fujian, China
| | - S Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Wusi Rd 247, Fuzhou, 350003, Fujian, China
| | - Mei Wang
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- SU BioMedicine/TNO Quality of Life, Zernikedreef 9, P.O. Box 2215, 2301 CE, Leiden, The Netherlands
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - P B F Ouwerkerk
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
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Lu G, Wang X, Liu J, Yu K, Gao Y, Liu H, Wang C, Wang W, Wang G, Liu M, Mao G, Li B, Qin J, Xia M, Zhou J, Liu J, Jiang S, Mo H, Cui J, Nagasawa N, Sivasankar S, Albertsen MC, Sakai H, Mazur BJ, Lassner MW, Broglie RM. Application of T-DNA activation tagging to identify glutamate receptor-like genes that enhance drought tolerance in plants. PLANT CELL REPORTS 2014; 33:617-31. [PMID: 24682459 DOI: 10.1007/s00299-014-1586-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 05/26/2023]
Abstract
A high-quality rice activation tagging population has been developed and screened for drought-tolerant lines using various water stress assays. One drought-tolerant line activated two rice glutamate receptor-like genes. Transgenic overexpression of the rice glutamate receptor-like genes conferred drought tolerance to rice and Arabidopsis. Rice (Oryza sativa) is a multi-billion dollar crop grown in more than one hundred countries, as well as a useful functional genetic tool for trait discovery. We have developed a population of more than 200,000 activation-tagged rice lines for use in forward genetic screens to identify genes that improve drought tolerance and other traits that improve yield and agronomic productivity. The population has an expected coverage of more than 90 % of rice genes. About 80 % of the lines have a single T-DNA insertion locus and this molecular feature simplifies gene identification. One of the lines identified in our screens, AH01486, exhibits improved drought tolerance. The AH01486 T-DNA locus is located in a region with two glutamate receptor-like genes. Constitutive overexpression of either glutamate receptor-like gene significantly enhances the drought tolerance of rice and Arabidopsis, thus revealing a novel function of this important gene family in plant biology.
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Affiliation(s)
- Guihua Lu
- Beijing Kaituo DNA Biotech Research Center, Co., Ltd., Beijing, 102206, China,
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