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Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics. PLANTS 2019; 8:plants8090310. [PMID: 31470516 PMCID: PMC6783850 DOI: 10.3390/plants8090310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023]
Abstract
Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more than half of the world's population; however, the functions of most of the genes in its genome are yet to be analyzed. Various mutant populations represent extremely valuable resources in order to achieve this goal. Here, we have reviewed different insertional mutagenesis approaches that have been used in rice, and have discussed their principles, strengths, and limitations. Comparisons between transfer DNA (T-DNA), transposons, and entrapment tagging approaches have highlighted their utilization in functional genomics studies in rice. We have also summarised different forward and reverse genetics approaches used for screening of insertional mutant populations. Furthermore, we have compiled information from several efforts made using insertional mutagenesis approaches in rice. The information presented here would serve as a database for rice insertional mutagenesis populations. We have also included various examples which illustrate how these populations have been useful for rice functional genomics studies. The information provided here will be very helpful for future functional genomics studies in rice aimed at its genetic improvement.
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Chang CL, Serapion JC, Hung HH, Lin YC, Tsai YC, Jane WN, Chang MC, Lai MH, Hsing YIC. Studies of a rice sterile mutant sstl from the TRIM collection. BOTANICAL STUDIES 2019; 60:12. [PMID: 31292815 PMCID: PMC6620220 DOI: 10.1186/s40529-019-0260-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/30/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Rice (Oryza sativa) is one of the main crops in the world, and more than 3.9 billion people will consume rice by 2025. Sterility significantly affects rice production and leads to yield defects. The undeveloped anthers or abnormal pollen represent serious defects in rice male sterility. Therefore, understanding the mechanism of male sterility is an important task. Here, we investigated a rice sterile mutant according to its developmental morphology and transcriptional profiles. RESULTS An untagged T-DNA insertional mutant showed defective pollen and abnormal anthers as compared with its semi-sterile mutant (sstl) progeny segregates. Transcriptomic analysis of sterile sstl-s revealed several biosynthesis pathways, such as downregulated cell wall, lipids, secondary metabolism, and starch synthesis. This downregulation is consistent with the morphological characterization of sstl-s anthers with irregular exine, absence of intine, no starch accumulation in pollen grains and no accumulated flavonoids in anthers. Moreover, defective microsporangia development led to abnormal anther locule and aborted microspores. The downregulated lipids, starch, and cell wall synthesis-related genes resulted in loss of fertility. CONCLUSIONS We illustrate the importance of microsporangia in the development of anthers and functional microspores. Abnormal development of pollen grains, pollen wall, anther locule, etc. result in severe yield reduction.
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Affiliation(s)
- Chia-Ling Chang
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
| | - Jerry C. Serapion
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
| | - Han-Hui Hung
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413 Taiwan
| | - Yan-Cheng Lin
- Department of Life Science, National Taiwan University, Taipei, 106 Taiwan
| | - Yuan-Ching Tsai
- Department of Agronomy, National Chiayi University, Chiayi, 600 Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413 Taiwan
| | - Yue-ie C. Hsing
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
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Sagart L, Hsu TF, Tsai YC, Wu CC, Huang LT, Chen YC, Chen YF, Tseng YC, Lin HY, Hsing YIC. A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals. RICE (NEW YORK, N.Y.) 2018; 11:57. [PMID: 30306280 PMCID: PMC6179969 DOI: 10.1186/s12284-018-0247-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Genetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue. RESULTS We report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000-5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving. CONCLUSION We suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE.
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Affiliation(s)
- Laurent Sagart
- Centre de Recherches Linguistiques sur l’Asie Orientale/Centre National de la Recherche Scientifique, INaLCO, 2 rue de Lille, 75007 Paris, France
| | - Tze-Fu Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yuan-Ching Tsai
- Department of Agronomy, National Chiayi University, Chiayi, 600 Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, 106 Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yu-Chi Chen
- Taiwan International Cooperation and Development Fund, Taipei, 111 Taiwan
| | - Yi-Fang Chen
- Soil and Water Conservation Bureau, Council of Agriculture, Nantou, 540 Taiwan
| | - Yu-Chien Tseng
- Department of Agronomy, National Chiayi University, Chiayi, 600 Taiwan
| | - Hung-Ying Lin
- Department of Agronomy, Iowa State University, Ames, Iowa 50011-1085 USA
| | - Yue-ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
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Wu HP, Wei FJ, Wu CC, Lo SF, Chen LJ, Fan MJ, Chen S, Wen IC, Yu SM, Ho THD, Lai MH, Hsing YIC. Large-scale phenomics analysis of a T-DNA tagged mutant population. Gigascience 2018; 6:1-7. [PMID: 28854617 PMCID: PMC5570018 DOI: 10.1093/gigascience/gix055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/04/2017] [Indexed: 01/26/2023] Open
Abstract
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.
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Affiliation(s)
- Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Institute of Plant Biology, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Jen Fan
- Department of Biotechnology, Asia University, 500, Lioufeng Road, Taichung 413, Taiwan
| | - Shu Chen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Ien-Chie Wen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Department of Agronomy, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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Meng X, Yu H, Zhang Y, Zhuang F, Song X, Gao S, Gao C, Li J. Construction of a Genome-Wide Mutant Library in Rice Using CRISPR/Cas9. MOLECULAR PLANT 2017. [PMID: 28645639 DOI: 10.1016/j.molp.2017.06.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xiaoguang Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Songsong Gao
- Beijing ViewSolid Biotechnology, Beijing 102206, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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