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Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos

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Abstract

Microsatellite (SSR) markers can reveal a high level of polymorphic loci, and are increasingly being used in population genetic structure studies. On the Vientiane plain of Laos all components of the rice crop complex exist, wild annual (O. nivara), wild perennial (O. rufipogon) and weedy relatives of rice as well as rice itself. To understand gene flow in the rice complex, the genetic structures of O. rufipogon (10 populations), O. nivara (10 populations) and O. sativa (24 samples) from across the Vientiane Plain, Laos, were compared. Higher genetic differentiation was detected among O. nivara populations (G ST =  0.77, R ST = 0.71) than O. rufipogon populations (G ST = 0.29, R ST = 0.28), whereas genetic diversity for all populations of these two wild species showed similar values (H T = 0.77 and 0.64 in O. rufipogon and O. nivara, respectively). Based on neighbor-joining tree constructed on the basis of genetic distance (D A), three genetic clusters were detected, corresponding to (1) O. sativa samples, (2) O. nivara populations and (3) O. rufipogon populations. Pairwise tests confirmed the genetic differentiation of the three species. Although none of the wild rice individuals used in this study had any cultivated-specific phenotypic traits, genetic admixture analysis detected more than 10% O. sativa membership in three O. rufipogon and one O. nivara populations, indicating that O. sativa alleles may cryptically persist in natural populations of O. rufipogon and O. nivara on the Vientiane Plain.

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Acknowledgements

This research was supported in part by a grant from the Toyota foundation. We would like to acknowledge here the generosity of the Lao government, the National Agricultural Research Center (NARC, Laos), the National Agriculture and Forestry Institute (NAFRI, Laos), the Ministry of Agriculture (MAF, Laos), and the Lao-IRRI project for permission to conduct a field survey in the Vientiane plain of Laos.

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Authors and Affiliations

  1. Graduate School of Asian and African Area Studies, Kyoto University Sakyo-ku, Kyoto, 603-8501, Japan

    Yosuke Kuroda

  2. National Institute of Agrobiologial Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan

    Yosuke Kuroda

  3. Research Institute for Humanity and Nature, Kita-ku, Kyoto, 602-0878, Japan

    Yo-Ichiro Sato

  4. National Agricultural Research Center, 811, Vientiane, Laos

    Chay Bounphanousay

  5. Center for Southeast Asian Studies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan

    Yasuyuki Kono & Koji Tanaka

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  1. Yosuke Kuroda
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  2. Yo-Ichiro Sato
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  3. Chay Bounphanousay
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  4. Yasuyuki Kono
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  5. Koji Tanaka
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Correspondence to Yosuke Kuroda.

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Kuroda, Y., Sato, YI., Bounphanousay, C. et al. Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos. Conserv Genet 8, 149–158 (2007). https://doi.org/10.1007/s10592-006-9156-3

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