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Conservation Genetics

, Volume 8, Issue 1, pp 149–158 | Cite as

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

  • Yosuke KurodaEmail author
  • Yo-Ichiro Sato
  • Chay Bounphanousay
  • Yasuyuki Kono
  • Koji Tanaka
Original Paper

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.

Keywords

Cultivated rice Gene flow Genetic structure Simple sequence repeat (SSR) Wild rice 

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Notes

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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Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Yosuke Kuroda
    • 1
    • 2
    Email author
  • Yo-Ichiro Sato
    • 3
  • Chay Bounphanousay
    • 4
  • Yasuyuki Kono
    • 5
  • Koji Tanaka
    • 5
  1. 1.Graduate School of Asian and African Area StudiesKyoto University Sakyo-kuKyotoJapan
  2. 2.National Institute of Agrobiologial SciencesTsukuba, IbarakiJapan
  3. 3.Research Institute for Humanity and NatureKyotoJapan
  4. 4.National Agricultural Research CenterVientianeLaos
  5. 5.Center for Southeast Asian StudiesKyoto UniversityKyotoJapan

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