Conservation Genetics

, Volume 7, Issue 6, pp 909–917 | Cite as

Comparison of genetic variation in populations of wild rice, Oryza rufipogon, plants and their soil seed banks

  • Gui-hua Liu
  • Li-ming Luo
  • Bin Wang
  • Wei Li
  • Zhiping Song


Wild rice, Oryza rufipogon, has endangered species conservation status and it is subject to in situ conservation in China. To understand the potential of the seed bank in species conservation and population restoration, this study compared the genetic diversity of O. rufipogon plants with that of its soil seed banks in two marshes. A total of 11 pairs of rice SSR primers were used and 9 were polymorphic. Allele frequencies of the seeds differed significantly from those of surface plants and varied between soil layers. Relatively more alleles and higher genetic diversity (H e) were found in plant populations, relative to seed banks. The numbers of germinable seeds and the level of genetic variation in seed banks decreased with the increasing of soil depth, indicating a rapid seed loss. Genetic differentiation was detected between sites and between plant and seed populations, as well as among seeds of different soil strata. Rapid seed loss, partly dormancy loss, and nonrandom seed mortality are discussed as the possible contributors to the pattern of reduced genetic variation within seed banks, compared to plants. These could also be responsible for the considerable genetic differentiation between populations. The seed population held about 72% of the total genetic variation of O. rufipogon in each marsh, indicating the potential of seed banks for restoring population variabilities if the plant populations were lost.


conservation genetic diversity Oryza rufipogon seed bank SSR 


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We thank Dr. Anthony J. Davy for correcting the English and providing valuable comments, You-ping Liu for field assistance, Shu-fei Chen for glasshouse work and Dr. Hong-wen Huang for SSR assays. Financial support was provided by the National Natural Science Foundation of China (Grant No. 30300019), the Innovation Key project of CAS (KSCX2-1-10), and the State Key Basic Research and Development Plan of China (2002CB412300).


  1. Alvarez-Buylia ER, Chaos A, Piv nero D, Garay AA (1996) Demographic genetics of a pioneer tropical tree species: Patch dynamics, seed dispersal, and seed banks. Evolution 50: 1155–1166CrossRefGoogle Scholar
  2. Bakker JP, Poschlod P, Strykstra RJ, Bekker RM, Thompson K (1996) Seed banks and seed dispersal: Important topics in restoration ecology. Acta Bot. Neerl. 45: 461–490Google Scholar
  3. Cabin RJ (1996) Genetic comparisons of seed bank and seedling populations of a perennial mustard, Lesquerella fendleri. Evolution 50: 1830–1841CrossRefGoogle Scholar
  4. Cabin BJ, Mitchell RJ, Marshall DL (1998) Do surface plant and soil seed bank population differ genetically? A multipopulation study of the desert mustard Lesquerelia fendleri (Brassicaceae). Am. J. Bot. 85: 1098–1109CrossRefGoogle Scholar
  5. Chang ER, Jefferies RL, Carleton TJ (2001) Relationship between vegetation and soil seed banks in an arctic coastal marsh. J. Ecol. 89: 367–384CrossRefGoogle Scholar
  6. Del Castillo RF (1994) Factors influencing the genetic structure of Phacelia dubia, a species with a seed bank and large fluctuations in population size. Heredity 72: 446–458Google Scholar
  7. Ellner S, Hairston Jr NG (1994) Role of overlapping generations in maintaining genetic variation in a fluctuations environment. Am. Nat. 143: 403–417CrossRefGoogle Scholar
  8. Ellstrand NC (1992) Gene flow by pollen: Implications for plant conservation genetics. Oikos 63: 77–86Google Scholar
  9. Ellstrand NC, Elam DR (1993) Population genetic consequences of small population size: Implications for plant conservation. Ann. Rev. Ecol. Syst. 24: 217–242CrossRefGoogle Scholar
  10. Gao LZ, Chen W, Jiang WZ, Ge S, Hong DY, Wang XQ (2000) Genetic erosion in the Northern marginal population of the common wild rice Oryza rufipogon Griff. and its conservation, revealed by the change of population genetic structure. Hereditas 133: 47–53CrossRefPubMedGoogle Scholar
  11. Kalinowski ST (2005) HP-RARE1.0: A computer program for performing rarefaction on measures of allelic richness. Mol. Ecol. Notes 5: 187–189CrossRefGoogle Scholar
  12. Kalisz S, McPeek MA (1992) Demography of an age-structured annual: Resampled projection matrices, elasticity analyses, and seed bank effects. Ecology 73: 1082–1093CrossRefGoogle Scholar
  13. Kalisz S, McPeek MA (1993) Extinction dynamics, population growth and seed banks – an example using an age-structured annual. Oecologia 95: 314–320CrossRefGoogle Scholar
  14. Leck MA, Parker VT, Simpson RL (1989) Ecology of soil seed banks. Academic Press, San Diego, CAGoogle Scholar
  15. Levin DA (1990) The seed bank as a source of genetic novelty in plants. Am. Nat. 135: 563–572CrossRefGoogle Scholar
  16. Li J, Chen JK, Zhou J, He GQ (1999) Dynamics and evaluation of Oryza rufipogon and Ranalisma rostratum population in ex situ conservation of communities. Acta Phytoecol. Sinica 23: 275–282. (In Chinese with English abstract)Google Scholar
  17. Liu GH, Zhou J, Huang DS, Li W (2004) Spatial and temporal dynamics of a restored population of Oryza rufipogon in Huli Marsh, South China. Restor. Ecol. 12: 456–463CrossRefGoogle Scholar
  18. Liu GH, Zhou J, Li W, Cheng Y (2005) The seed bank in a subtropical freshwater marsh: Implications for wetland restoration. Aquat. Bot. 81: 1–11CrossRefGoogle Scholar
  19. Mahy G, Vekemans X, Jacquemart AL (1999) Patterns of allozymic variation within Calluna vulgaris populations at seed bank and adult stages. Heredity 82: 432–440CrossRefPubMedGoogle Scholar
  20. Middleton BA (2003) Soil seed banks and the potential restoration of forested wetlands after farming. J. Appl. Ecol. 40: 1025–1034CrossRefGoogle Scholar
  21. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590PubMedGoogle Scholar
  22. Nunney L (2002) The effective size of annual plant populations: The interaction of a seed bank with fluctuating population size in maintaining genetic variation. Am. Nat. 160: 195–204CrossRefPubMedGoogle Scholar
  23. Oka HI (1988) Origin of Cultivated Rice. Japanese Scientific Societies Press, TokyoGoogle Scholar
  24. Qian J (2003) Conservation Biology Study on the Northern Populations of Oryza rufipogon: Experimental ecology and Spatial Genetic Analysis. PhD thesis, Fudan University, Shanghai ChinaGoogle Scholar
  25. Rohlf FJ (1993) NTSYS-pc, numerical taxonomy and multivariate analysis, ver. 1.80. Exeter Setauket, New YorkGoogle Scholar
  26. Smith LM, Kadlec JA (1983) Seed banks and their role during drawdown of a North American marsh. J. Appl. Ecol. 20: 673–684CrossRefGoogle Scholar
  27. Sokal RR, Rohlf FJ (1981) Biometry. WH Freeman, San Francisco, CAGoogle Scholar
  28. Song ZP, Xu X, Wang B, Chen JK, Lu BR (2003) Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers. Theor. Appl. Genet. 107: 1492–1499CrossRefPubMedGoogle Scholar
  29. Song ZP, Lu BR, Chen JK (2004b) Pollen flow of cultivated rice measured under experimental conditions. Biodivers. Conserv. 13: 579–590CrossRefGoogle Scholar
  30. Song ZP, Lu BR, Wang B, Chen JK (2004a) Fitness estimation through performance comparison of F-1 hybrids with their parental species Oryza rufipogon and O. sativa. Ann. Bot. 93: 311–316CrossRefGoogle Scholar
  31. Song ZP, Li B, Chen JK, Lu BR (2005) Genetic diversity and conservation of Common wild rice (Oryza rufipogon) in China. Plant Species Biol. 20(2): 83–92CrossRefGoogle Scholar
  32. Templeton AR, Levin DA (1979) Evolutionary consequences of seed pools. Am. Nat. 114: 232–249CrossRefGoogle Scholar
  33. Tonsor SJ, Kalisz S, Fisher J, Holtsford TP (1993) A life-history based study of population genetic structure: Seed bank to adults in Plantago lanceolata. Evolution 47: 833–843CrossRefGoogle Scholar
  34. van der Valk AG, Davis CB (1978) The role of seed banks in the vegetation dynamics of prairie glacial marshes. Ecology 59: 322–335CrossRefGoogle Scholar
  35. Veasey EA, Karasawa MG, Santos PP, Rosa MS, Manani RE, Oliveira GCX (2004) Variation in the loss of seed dormancy during after-ripening of wild and cultivated rice species. Ann. Bot. 94: 875–882CrossRefPubMedGoogle Scholar
  36. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370CrossRefGoogle Scholar
  37. Wilson SD, Moore DRJ, Keddy PA (1993) Relationships of marsh seed banks to vegetation patterns along environmental gradients. Freshw. Biol. 29: 361–370CrossRefGoogle Scholar
  38. Xie ZW, Ge S, Hong DY (1999) Preparation of DNA from silica gel a dried mini-amount of leaves of Oryza rufipogon for RAPD study and total DNA bank construction. Acta Bot. Sinica 41: 807–812Google Scholar
  39. Yeh FC, Yang RC, Boyle T (1999) POPGENE, Microsoft window-based freeware for population genetic analysis. /softlib/ MSLFILES/HPGL.EXE
  40. Zhou J (1995) Studies on Conservation Biology of Three Northern Populations of Common Wild Rice (Oryza rufipogon) (in Chinese). PhD thesis, Wuhan University, Wuhan, ChinaGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Gui-hua Liu
    • 1
  • Li-ming Luo
    • 1
  • Bin Wang
    • 1
  • Wei Li
    • 1
  • Zhiping Song
    • 2
  1. 1.Laboratory of Aquatic Plant Biology, Wuhan Botanical GardenThe Chinese Academy of SciencesWuhanChina
  2. 2.Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity ScienceFudan UniversityShanghaiChina

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