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Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers

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Abstract

Indica–japonica variation represents the most significant genetic differentiation in Asian cultivated rice (Oryza sativa L. subsp. indica Kato or subsp. japonica Kato). Understanding the differentiation and distribution patterns of cultivated rice along altitude gradients will facilitate strategic utilization and conservation of rice germplasm from mountainous regions. In this study, we analyzed 203 varieties and 14 wild accessions of rice collected from localities across an altitude gradient between 450 and 2,350 m above sea level in Yunnan, China, applying the “InDel molecular index” developed recently. Results from PCA of the InDel data demonstrated significant genetic differentiation of rice varieties from Yunnan into indica and japonica types. A few cultivars and nearly all wild rice accessions showed only moderate or no differentiation. Further analyses demonstrated a clear distribution pattern of the rice varieties in the mountainous region: indica varieties were grown across the entire altitude gradient in the sampling areas, but most japonica varieties were found above 1,400 m. These results clearly indicated that indica rice could be cultivated in areas at much higher altitudes than those categorized by the traditional methods. The knowledge opens a new dimension for introducing indica rice varieties to mountainous regions at higher altitudes and for selecting rice germplasm in these regions. In addition, the pattern of significant indica–japonica differentiation in rice varieties from Yunnan suggested the exotic origin of cultivated rice, which did not support the hypothesis that Yunnan is a part of the center of origin of rice, although it is certainly one of the centers of genetic diversity for rice.

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Acknowledgments

This study was supported by the 973 Program (Grant No. 2006CB100205) from the Chinese Ministry of Science and Technology, Shanghai Commission of Science and Technology (Grant No. 08JC1401700), and Italian Ministry of Environment and Environmental Protection, within the research project “Application of biotechnology to the protection of the environment in collaboration with China (years 2005–2007)”.

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Authors and Affiliations

  1. Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, 200433, Shanghai, China

    Zhiyuan Xiong, Shujie Zhang, Xin Jin, Yue Wu, Huanxin Yan, Xiao Yang, Ping Liu & Bao-Rong Lu

  2. Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Key Laboratory of Plant Pathology, Yunnan Agricultural University, 650201, Kunming, China

    Yunyue Wang & Min Tu

  3. School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

    Brian V. Ford-Lloyd

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  1. Zhiyuan Xiong
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Correspondence to Bao-Rong Lu.

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Zhiyuan Xiong and Shujie Zhang contributed equally to this work.

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Xiong, Z., Zhang, S., Wang, Y. et al. Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers. Genet Resour Crop Evol 57, 891–902 (2010). https://doi.org/10.1007/s10722-009-9528-x

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