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


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.


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


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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.


  1. Akimoto M, Shimamoto Y, Morishima H (1999) The extinction of genetic resources of Asian wild rice, Oryza rufipogon Griff.: a case study in Thailand. Genet Res Crop Evol 46:419–425CrossRefGoogle Scholar
  2. Appa Rao S, Bounphanousay C, Shiller JM, Jackson MT (2000) Collection and Classification of Rice Germplasm from the Lao PDR from 1995 to 2000. National Rice Research Program and Lao-IRRI Biodiversity Project, p 576Google Scholar
  3. Barbier P (1989a) Genetic variation and ecotypic differentiation in the wild rice species Oryza rufipogon. I. Population differentiation in life-history traits and isozymic loci. Jpn J Genet 64:259–271Google Scholar
  4. Barbier P (1989b) Genetic variation and ecotypic differentiation in the wild rice species Oryza rufipogon. II. Influence of the mating system and life-history traits on the genetic structure of populations. Jpn J Genet 64:273–285Google Scholar
  5. Bossart JL, Prowell DP (1998) Genetic estimates of population structure and gene flow: limitations, lessons and new directions. Trends Ecol Evol 13:202–206CrossRefGoogle Scholar
  6. Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47PubMedCrossRefGoogle Scholar
  7. Brown AHD (2000) The genetic structure of crop landraces and the challenge to conserve them in situ on farms. In: Brush SB (ed) Genes in the field: on-farm conservation of crop diversity. IDRC/IPGRI, Lewis, pp 29–48Google Scholar
  8. Cai HW, Wang XK, Morishima H (2004) Comparison of population genetic structures of common wild rice (Oryza rufipogon Griff.), as revealed by analyses of quantitative traits, allozymes, and RFLPs. Heredity 92:409–417PubMedCrossRefGoogle Scholar
  9. Chen WB, Nakamura I, Sato YI, Nakai H (1993) Distribution of deletion type in cpDNA of cultivated and wild rice. Jpn J Genet 68:597–603CrossRefGoogle Scholar
  10. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567CrossRefGoogle Scholar
  11. Cheng C, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on interspersion pattern of SINEs. Mol Biol Evol 20:67–75PubMedCrossRefGoogle Scholar
  12. Chu YE, Morishima H, Oka HI (1969) Reproductive barriers distributed in cultivated rice species and their wild relatives. Jpn J Genet 44:207–223Google Scholar
  13. Gao LZ (2004) Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation. Mol Ecol 13:1009–1024PubMedCrossRefGoogle Scholar
  14. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from Updated from Goudet (1995)
  15. Hamrick JL, Godt MJW (1989) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding and genetic resources. Sinauer Association Inc., Sunderland, pp 43–63Google Scholar
  16. Haig SM (1998) Molecular contributions to conservation. Ecology 79:413–425CrossRefGoogle Scholar
  17. Harlan JR (1975) Crops and man. American Society of Agronomy Inc., Madison, Wisconsin, p 295Google Scholar
  18. Jarvis DI, Hodgkin T (1999) Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Mol Ecol 8:S159–S173CrossRefGoogle Scholar
  19. Kuroda Y, Urairong H, Sato YI (2003) Population genetic structure of wild rice (Oryza rufipogon) in mainland Southeast Asia as revealed by microsatellite polymorphisms. Tropics 12:159–170CrossRefGoogle Scholar
  20. Kuroda Y, Urairong H, Sato YI (2005a) Differential heterosis in a natural population of Asian wild rice (Oryza rufipogon) due to reproductive strategy and edge effect. Genet Res Crop Evol 52:151–160CrossRefGoogle Scholar
  21. Kuroda Y, Sato YI, Bounphanousay C, Kono Y, Tanaka K (2005b) Gene flow from cultivated rice (Oryza sativa L.) to wild Oryza species (Oryza rufipogon Griff. and O. nivara Sharma & Shastry) on the Vientiane Plain of Laos. Euphytica 142:75–83CrossRefGoogle Scholar
  22. Lei X (2004) China could be first nation to approve sale of GM rice. Science 306:1458–1459PubMedCrossRefGoogle Scholar
  23. Lu BR, Snow AA (2005) Gene flow from genetically modified rice and its environmental consequences. Bioscience 55:669–678CrossRefGoogle Scholar
  24. McCouch SR, Temnykh S, Lukashova A, Coburn J, DeClerck G, Cartinhour S, Harrington S, Thomson M, Septiningsih E, Semon M, Moncada P, Li J (2001) Microsatellite markers in rice: abundance, diversity, and applications. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. Science Publishers Inc. International Rice Research Institute Los Baños, Philippines, pp 117–135Google Scholar
  25. Morishima H, Barbier P (1990) Mating system and genetic structure of natural populations in wild rice Oryza rufipogon. Plant Species Biol 5:31–39CrossRefGoogle Scholar
  26. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325PubMedGoogle Scholar
  27. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  28. Nei M (1987) Molecular Evolutionary genetics. Columbia Univ. Press, New YorkGoogle Scholar
  29. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170PubMedCrossRefGoogle Scholar
  30. Oka HI (1988) Origin of cultivated rice. Japan Scientific Societies Press /Elsevier, Tokyo, p 254Google Scholar
  31. Oka HI, Chang WT (1961) Hybrid swarms between wild and cultivated rice species, Oryza perennis and O. sativa. Evolution 15:418–430CrossRefGoogle Scholar
  32. Page RDM (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358Google Scholar
  33. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genomics 252:597–607Google Scholar
  34. Parker PG, Snow AA, Schug MD, Booton GC, Fuerst PA (1998). What molecules can tell us about populations: choosing and using a molecular marker. Ecology 79:361–382CrossRefGoogle Scholar
  35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:943–959Google Scholar
  36. Rousset F (1996) Equilibrium values of measures of population subdivision for stepwise mutation processes. Genetics 142:1357–1362PubMedGoogle Scholar
  37. Sharma SD, Shastry SVS (1965) Taxonomic studies in genus Oryza L. III. O. rufipogon Griff. sensu stricto and O. nivara Sharma et Shastry nom nov. Indian J Genet Plant Breed 25:157–167Google Scholar
  38. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462PubMedGoogle Scholar
  39. Song ZP, Lu BR, Zhu YG, Chen JK (2003a) Gene flow from cultivated rice to the wild species Oryza rufipogon under experimental field conditions. New Phytol 157:657–665CrossRefGoogle Scholar
  40. Song ZP, Xu X, Wang B, Chen JK, Lu BR (2003b). Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers. Theor Appl Genet 107:1492–1499CrossRefGoogle Scholar
  41. Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389–399PubMedGoogle Scholar
  42. Vargo EL, Husseneder C, Grace K (2003) Colony and population genetic structure of the Formosan subterranean termite, Coptotermes formosanus, in Japan. Mol Ecol 12:2599–2608PubMedCrossRefGoogle Scholar
  43. Vaughan DA (1994) The wild relatives of rice; a genetic resources handbook. International Rice Research Institute, Los Baños, Philippines, p 137Google Scholar
  44. Vaughan DA, Chang TT (1992) In situ conservation of rice genetic resources. Econ Bot 46:368–383Google Scholar
  45. Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates Inc., Sunderland, MassachusettsGoogle Scholar
  46. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  47. Westemeier RL, Brawn JD, Simpson SA, Esker TL, Jansen RW, Walk JW, Kershner EC, Bouzat JL, Paige KN (1998) Tracking the long-term decline and recovery of an isolated population. Science 282:1695–1698PubMedCrossRefGoogle Scholar
  48. Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395–420CrossRefGoogle Scholar

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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