| Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice （Oryza rufipogon L.） in relation to the domestication of cultivated rice （O. sativa L.） |
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| 作者姓名： | Xiangqian Zhao ;Long Yang ;Yan Zheng ;Zhaohua Xu ;WeirenWu |
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| 作者单位： | [1]Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China; [2]College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China |
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| 基金项目： | the,National,Basic,Research,Program,(973,Program),of,China,the,National,Hi-Tech,Research,and,Development,Program,(863,Program),of,China |
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| 摘 要： | It is generally accepted that Oryza rufipogon is the progenitor of Asian cultivated rice （O. sativa）. However, how the two subspecies of O. sativa （indica and japonica） were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism （SSILP） markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups： one group （Group I） comprises all the O. rufipogon accesions from tropical （South and Southeast） Asia as well as the standard indica rice; the other group （Group II） comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. ruffpogon might occur after its speciation from other AA-genome species.
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| 关 键 词： | 野生水稻 种植技术 基因工程 多态现象 |
| 收稿时间： | 2 November 2008 |
Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. Sativa L.) |
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| Xiangqian Zhao,;Long Yang,;Yan Zheng,;Zhaohua Xu,;WeirenWu.Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. Sativa L.)[J].Journal of Genetics and Genomics,2009,36(7):435-442. |
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| Authors: | Xiangqian Zhao Long Yang Yan Zheng Zhaohua Xu Weiren Wu |
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| Institution: | 1. Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China;2. College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China;1. College of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130021, China;2. Norman Bethune College of Medicine, Jilin University, 71 Xinmin Street, Changchun 130021, China;3. School of Stomatology, Jilin University, 18-1 Ziqiang Street, Changchun 130000, China;1. The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA;2. Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, 41 Boggo Road, Dutton Park, QLD 4102, Australia;3. School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand;4. Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa;5. Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa;1. Department of Radiology, Xinhua Hospital, Shanghai Jiao Tong Medical University, Shanghai 200092, China;2. Department of Radiology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China;3. Department of General Surgery, First People''s Hospital of Yancheng, Jiangsu Province, China;1. Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Republic of Korea;2. Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea;1. Zhongshan Hospital, Medical College of Xiamen University, Xiamen 361004, PR China;2. Department of Basic Medicine, Medical College of Xiamen University/Cancer Research Center of Xiamen University, Xiamen 361102, PR China;3. Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8197, USA;4. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA |
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| Abstract: | It is generally accepted that Oryza rufipogon is the progenitor of Asian cultivated rice (O. sativa). However, how the two subspecies of O. sativa (indica and japonica) were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism (SSILP) markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SS1LP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups: one group (Group Ⅰ) comprises all the O. rufipogon accesions from tropical (South and Southeast) Asia as well as the standard indica rice; the other group (Group Ⅱ) comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China,respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. rufipogon might occur after its speciafion from other AA-genome species. |
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| Keywords: | Oryza sativa Oryza rufipogon evolution SSILP marker |
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