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


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.


Genetic diversity Genetic introgression Population structure Oryza rufipogon SSR markers 



Randomly amplified polymorphic DNA


Restriction fragment length polymorphism


Microsatellite or simple sequence repeat


Quantitative trait locus


Deoxyribonucleic acid


Polymerase chain reaction



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)


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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

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