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Analysis of indica- and japonica-specific markers of Oryza sativa and their applications

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Abstract

Asian rice, Oryza sativa L., is one of the most important crop species. Genetic analysis has established that rice consists of several genetically differentiated variety groups, with two main groups, namely, O. sativa ssp. japonica kata and ssp. indica kata. To determine the genetic diversity of indica and japonica rice, 45 rice varieties, including domesticated rice and Asia common wild rice (O. rufipogon Griff.), were analyzed using sequence-related amplified polymorphism, target region amplified polymorphism, simple sequence repeat, and intersimple sequence repeat marker systems. A total of 90 indica- and japonica-specific bands between typical indica and japonica subspecies were identified, which greatly helped in determining whether domesticated rice is of the indica or japonica type, and in analyzing the consanguinity of hybrid rice with japonica, which were bred from indica and japonica crossed offspring. These specific bands were both located in the coding and non-encoding region, and usually connected with quantitative trait loci. Utilizing the indica-japonica-specific markers, japonica consanguinity was detected in sterile hybrid rice lines. Many indica-japonica-specific bands were found in O. rufipogon. This result supports the multiple-origin model for domesticated rice. Javanica exhibited a greater number of indica-japonica-specific bands, which indicates that it is a subspecies of O. sativa L.

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Acknowledgments

This work is supported by the National High Technology Research and Development Program of China (no. 2010AA101305), the Key Programs for Science and Technology Development of Hunan Province of China (no. 2009FJ1004-1,2,4), the Hunan Provincial Natural Science Foundation of China (no. 10JJ3092), and the Specialized Research Fund for the Doctoral Program of Higher Education of China (no. 20094306120005).

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Authors and Affiliations

  1. College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China

    Xiao-Jun Dai, Liang Zhou, Li-Jun Ou, Man-Zhong Liang, Wen-Jia Li, Gong-Ping Kang & Liang-Bi Chen

  2. Hunan Yahua Seeds Science Research Institute, Changsha, 410119, Hunan, China

    Xiao-Jun Dai & Yuan-Zhu Yang

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  1. Xiao-Jun Dai
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  2. Yuan-Zhu Yang
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  3. Liang Zhou
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  5. Man-Zhong Liang
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Correspondence to Liang-Bi Chen.

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Dai, XJ., Yang, YZ., Zhou, L. et al. Analysis of indica- and japonica-specific markers of Oryza sativa and their applications. Plant Syst Evol 298, 287–296 (2012). https://doi.org/10.1007/s00606-011-0543-y

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  • DOI: https://doi.org/10.1007/s00606-011-0543-y

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