Advertisement

Tropical Plant Biology

, Volume 3, Issue 4, pp 227–239 | Cite as

Genetic Structure of Oryza rufipogon Griff. Natural Populations in Malaysia: Implications for Conservation and Genetic Introgression of Cultivated Rice

  • Mee Siing Ngu
  • K. K. Sabu
  • Li Sze Lim
  • M. Z. Abdullah
  • Ratnam Wickneswari
Article

Abstract

Thirty polymorphic Oryza sativa microsatellite loci (SSRs) were used to study population genetic structure of O. rufipogon Griff. natural populations in Malaysia. A total of 445 alleles were detected with an average of 14.8 alleles per locus in 176 individuals of O. rufipogon sampled from the states of Penang, Kedah, Kelantan and Terengganu where the natural populations are still found. The Kelantan population in the northeast of Peninsular Malaysia had the highest level of genetic diversity as measured by the mean number of alleles per locus, Aa = 7.67, average number of effective alleles, Ae = 5.50, percentage of polymorphic loci, P = 100%, observed heterozygosity, Ho = 0.631 and expected heterozygosity, He = 0.798. In contrast, the Terengganu population in the east showed the lowest level of genetic diversity measured by the same criteria (Aa = 4.23, Ae = 2.10, P = 100%, Ho = 0.549 and He = 0.449). Model–based clustering analysis using the STRUCTURE 2.2 program placed all the individuals into 12 clusters that corresponded to the geographic sampling locations. Neighbour-joining tree was constructed based on Nei’s genetic distance to further assess the genetic structure of the O. rufipogon individuals, showed good agreement (93.8%) with the model-based cluster analysis. However, the neighbour-joining tree identified sub-populations that STRUCTURE could not identify. The classification of individuals from the same populations under the same cluster supported the population differentiation. These two analyses seemed to indicate expansion of populations from the northeast of Peninsular Malaysia (Tumpat, Pasir Mas and Kota Bahru, Kelantan) not only to the immediate south of the region i.e. Terengganu but also into the northwest (i.e. Penang and Kedah) with the former being more recent. Oryza rufipogon accession IRGC105491 and O. sativa ssp. indica cultivar MR219, which were included in this study for comparisons with the local wild rice accessions, indicated that introgression of cultivated rice could change genetic composition and affect the population genetic structure of wild rice. This possibility should be carefully considered in plans to conserve this wild rice.

Keywords

Genetic diversity Genetic introgression Population structure Oryza rufipogon SSR markers 

Abbreviations

RAPD

Randomly amplified polymorphic DNA

RFLP

Restriction fragment length polymorphism

SSR

Microsatellite or simple sequence repeat

QTL

Quantitative trait locus

DNA

Deoxyribonucleic acid

PCR

Polymerase chain reaction

Notes

Acknowledgements

This study was funded by the Ministry of Science, Technology and Innovation (MOSTI), Malaysia (IRPA Grant No. 01-03-03-BTK003/ER001). We would like to thank Malaysian Agricultural Research and Development Institute (MARDI) staff (Ismail b. Muhamod Nor, Latefi b. Mahmud, Haji Adnan b. Boerhannoeddin) for their assistance in germplasm collection. We would also like to thank Dr Gao Lizhi for helping to design this study initially and Prof. Dr. Gail Taylor for critically reading an earlier version of this manuscript.

Supplementary material

12042_2010_9060_MOESM1_ESM.pdf (679 kb)
ESM 1 (PDF 678 kb)

References

  1. Abdullah MZ (1997) Progress report on field collection and preservation in Malaysia. In: Reports of the reviewing and planning workshop on safeguarding and preservation of the biodiversity of the rice genepool, Penang, 8–12 December 1997Google Scholar
  2. Abdullah MZ, Vaughan DA, Mohamad O (1991) Wild relatives of rice in Malaysia: their characteristics, distribution, ecology and potential in rice breeding. MARDI report 145Google Scholar
  3. Abdullah MZ, Vaughan DA, Watanabe H, Okuno K (1996) The origin of weedy rice in Peninsular Malaysia. MARDI Res J 24(2):169–174Google Scholar
  4. 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 Resour Crop Evol 46:419–425CrossRefGoogle Scholar
  5. Bakar BB, Bakar MA, Man AB (2000) Weedy rice (Oryza sativa L.) in Peninsular Malaysia. In: Baki BB, Chin DV, Motimer M (eds) Wild and weedy rice in rice ecosystems in Asia—a review. International Rice Research Institute, Phillipines, pp 57–60Google Scholar
  6. Barbier P (1989) 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 64:273–285CrossRefGoogle Scholar
  7. Blair MW, Hedetale V, McCouch SR (2001) Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.). Theor Appl Genet 105:449–457CrossRefGoogle Scholar
  8. Chen LJ, Lee DS, Song ZP, Suh HS, Lu B-R (2004) Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives. Ann Bot 93:67–73CrossRefPubMedGoogle Scholar
  9. Coburn JR, Temnykh SV, McCouch SR (2001) Chromosome-specific panels of microsatellite markers for semi-automated genotyping of rice (Oryza sativa L.). Crop Sci 42:2092–2099CrossRefGoogle Scholar
  10. Dinesh RR, Kiran AG, Thomas G (2010) Population genetic structure and conservation priorities of Oryza rufipogon Griff. Populations in Kerala, India. Curr Sci 98(1):65–68Google Scholar
  11. Dong YB, Pei XW, Yuan QH, Wu HJ, Wang XJ, Jia SR, Peng YF (2010) Ecological, morphological and genetic diversity in Oryza rufipogon Griff. (Poaceae) from Hainan Island, China. Genet Resour Crop Evol 57:915–926CrossRefGoogle Scholar
  12. Ellstrand NC, Prentice HC, Hancock JF (1999) Gene flow and introgression from domesticated plants into their wild relatives. Annu Rev Ecol Syst 30:539–563CrossRefGoogle 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 13:1009–1024CrossRefPubMedGoogle Scholar
  14. Gao LZ, Hong DY (2000) Allozyme variation and population genetic stucture of common wild rice Oryza rufipogon Griff. in China. Theor Appl Genet 101:494–502CrossRefGoogle Scholar
  15. Gao LZ, Zhang CH (2005) Comparisons of microsatellite variability and population structure of two endangered wild rice species, Oryza rufipogon and O. officinalis, and their conservation implications. Biodivers Conserv 14:1663–1679CrossRefGoogle Scholar
  16. Gao LZ, Hong DY, Ge S (2001) Intra-population genetic structure of Oryza rufipogon Griff. in Yunnan, China. J Plant Res 114:107–113CrossRefGoogle Scholar
  17. Gao LZ, Schaal BA, Zheng CH, Jia JZ, Dong YS (2002) Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. Using microsatellite and allozyme markers. Theor Appl Genet 106:173–180PubMedGoogle Scholar
  18. Gao H, Williamson S, Bustamante CD (2007) A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics 176:1635–1651CrossRefPubMedGoogle Scholar
  19. Gliddon C, Belhassen E, Gouyon PH (1987) Genetic neighborhoods in plants with diverse systems of mating and different pattern of growth. Heredity 7:29–32CrossRefGoogle Scholar
  20. Grillo MA, Li C, Fowlkes AM, Briggeman TM, Zhou A, Schemske DW, Sang T (2008) Genetic architecture for the adaptive origin of annual wild rice, Oryza nivara. Evolution 63:870–883CrossRefGoogle Scholar
  21. Gupta PK, Balyan IS, Sharma PC, Ramesh B (1996) Microsatellites in plants: a new class of molecular markers. Curr Sci 70:45–54Google Scholar
  22. Hamrick JL, Godt MJ (1996) Conservation genetics of endemic plant species. In: Avise JC, Hamrick JL (eds) Conservation genetics. Chapman and Hall, New York, p 281Google Scholar
  23. Huang XQ, Börner A, Röder MS, Ganal MW (2002) Assesing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellites markers. Theor Appl Genet 105:699–707CrossRefPubMedGoogle Scholar
  24. Kuroda Y, Urairong H, Sato YI (2002) Population genetic structure of wild rice (Oryza rufipogon) in mainland Southeast Asia as revealed by microsatellite polymorphisms. Tropics 12(2):159–170CrossRefGoogle Scholar
  25. Kuroda Y, Sato YI, Bounphanousay C, Kono Y, Tanaka K (2005) Gene flow from cultivated rice (Oryza sativa L.) to wild Oryza species (Oryza rufipogon Griff. and O. nivara Sharma et Shastry) on the Vientiane plain of Laos. Euphytica 142:75–83CrossRefGoogle Scholar
  26. Kuroda Y, Appa Rao S, Bounphanousay C, Kingphanh K, Iwata A, Tanaka K, Sato YI (2006) Diversity of wild and weedy rice in Laos. In: Schiller JM, Chanphengxay MB, Linquist B, Appa Rao S (eds) Rice in Laos. International Rice Research Institute, Philipines, pp 215–233Google Scholar
  27. Li J, Thomson MJ, McCouch SR (2004) Fine mapping of a grain weight QTL in the peri-centromeric region of rice chromosome 3. Genetics 168:187–2195CrossRefGoogle Scholar
  28. Liu K, Muse V (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129CrossRefPubMedGoogle Scholar
  29. McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207CrossRefPubMedGoogle Scholar
  30. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  31. Nei M (1983) Genetic polymorphism and the role of mutation in evolution. In: Koehn PK, Nei M (eds) Evolution of genes and proteins. Sinauer Assoc, Sunderland, p 165Google Scholar
  32. Oka HI, Morishima H (1967) Variations in the breeding systems of a wild rice, Oryza perennis. Evolution 21:249–258CrossRefGoogle Scholar
  33. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  34. Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432CrossRefPubMedGoogle Scholar
  35. Shishido R, Kikuchi M, Nomura K, Ikehashi H (2006) Evaluation of genetic diversity of wild rice (Oryza rufipogon Griff.) in Myanmar using simple sequence repeats (SSRs). Genet Resour Crop Evol 53:179–186CrossRefGoogle Scholar
  36. Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47:264–279CrossRefGoogle Scholar
  37. Song ZP, Lu BR, Zhu YG, Chen JK (2002) Pollen competition between cultivated and wild rice species (Oryza sativa and O. rufipogon). New Phytol 253:289–296CrossRefGoogle Scholar
  38. 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
  39. Song ZP, Xu X, Wang B, Chen JK, Lu BR (2003b) Genetic diversity in the northern Oryza rufipogon populations estimated by SSR markers. Theor Appl Genet 107:1492–1499CrossRefPubMedGoogle Scholar
  40. Sun XP, Yang QW (2009) Comparative study on genetic diversity of wild rice (Oryza rufipogon Griff.) in China and three countries in Southeast Asia. Acta Agro Sinica 35(4):679–684CrossRefGoogle Scholar
  41. Sun CQ, Wang XK, Li ZC, Yoshimura A, Iwata N (2001) Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers. Theor Appl Genet 102:157–162CrossRefGoogle Scholar
  42. Sweeney M, Thomson MJ, Pfeil B, McCouch SR (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18:283–294CrossRefPubMedGoogle Scholar
  43. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471CrossRefPubMedGoogle Scholar
  44. Thomson MJ, Septiningsih EJD, EM HSE, McCouch SR (2006) Substitution mapping of dth11, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics 172:2501–2514CrossRefPubMedGoogle Scholar
  45. Vaughan DA (1994) The wild relatives of rice: a genetic resources handbook. International Rice Research Institute, ManilaGoogle Scholar
  46. Vaughan DA, Watanabe H, Abdullah MZ, Okuno K (1995) Genetic diversity of weedy rice in Malaysia. Rice Genetics Newsletter 12:176 http://www.gramene.org/newsletters/rice_genetics/rgn12/v12p176.html
  47. Vaughan DA, Lu BR, Tomookan N (2008) Was Asian rice (oryza sativa) domesticated more than once? Rice 1:16–24Google Scholar
  48. Wang F, Yuan QH, Shi L, Qian Q, Liu WG, Kuang BG, Zeng DL, Liao YL, Cao B, Jia SR (2006) A large-scale field study of transgene flow from cultivated rice (Oryza sativa) to common wild rice (O. rufipogon) and barnyard grass (Echinochloa crusgalli). Plant Biotechnol J 4:667–676CrossRefPubMedGoogle Scholar
  49. Wang MX, Zhang HL, Zhang DL, Qi YW, Fan ZL, Pan DJ, Cao YS, Qiu ZE, Yu P, Yang QW, Wang XK, Li ZC (2008) Genetic structure of Oryza rufipogon Griff. in China. Heredity 101:527–535CrossRefPubMedGoogle Scholar
  50. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  51. Wright S (1931) Evolution in mendelian populations. Genetics 16:97–159PubMedGoogle Scholar
  52. Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tansley SD, McCouch SR (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relatives, Oryza rufipogon. Genetics 150:899–909PubMedGoogle Scholar
  53. Xie J, Agrama HA, Kong D, Zhunag J, Hu B, Wan Y, Yan W (2010) Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon). Genet Resour Crop Evol 57:597–609CrossRefGoogle Scholar
  54. Yeh FC, Boyle TJB (1997) Population genetic analysis of co-dominant and dominant markers and quatitative traits. Bel J Bot 129:157Google Scholar
  55. Zainuddin H, Azmi M, Othman AS (2010) Morphologizal study of the relationships between weedy rice accessions (Oryza sativa complex) and commercial rice varietis in Penang’s rice granary area. Trop Life Sci Res 21(2):47–62Google Scholar
  56. Zhou HF, Xie ZW, Ge S (2003) Microsatellites analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. Theor Appl Genet 107:332–339CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Mee Siing Ngu
    • 1
  • K. K. Sabu
    • 2
  • Li Sze Lim
    • 1
  • M. Z. Abdullah
    • 3
  • Ratnam Wickneswari
    • 1
  1. 1.School of Environmental and Natural Resources Sciences, Faculty Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  2. 2.Tropical Botanic Garden and Research InstituteThiruvananthapuramIndia
  3. 3.Faculty of Agrotechnology & Food SciencesUniversity Malaysia TerengganuKuala TerengganuMalaysia

Personalised recommendations