Molecular Diversity Analysis of Different Hybrid Rice (Oryza sativa L.) Varieties through RAPD and SSR Markers

International Journal of Biotech Trends and Technology (IJBTT)
© 2020 by IJBTT Journal
Volume - 10 Issue - 3                          
Year of Publication : 2020
Authors : Absana Islam, Shamim Ara Sumi, Abdul Wahab, M. E. Hoque
DOI :  10.14445/22490183/IJBTT-V10I3P602


MLA Style:Absana Islam, Shamim Ara Sumi, Abdul Wahab, M. E. Hoque"Molecular Diversity Analysis of Different Hybrid Rice (Oryza sativa L.) Varieties through RAPD and SSR Markers" International Journal of Biotech Trends and Technology 10.3 (2020): 6-13.

APA Style:Absana Islam, Shamim Ara Sumi, Abdul Wahab, M. E. Hoque(2020). Molecular Diversity Analysis of Different Hybrid Rice (Oryza sativa L.) Varieties through RAPD and SSR Markers. International Journal of Biotech Trends and Technology, 10(3), 6-13.


Rice (Oryza sativa L.) is one of the principal cereal crops around the globe. A study was conducted to assess molecular diversity of four rice hybrid varieties released from a private seed company using PCR-based Random Amplified Polymorphic DNA (RAPD) and Single Sequence Repeat (SSR) markers. A total of 20 RAPD primers and 4 SSR primers were used to determine polymorphism among the rice hybrids. Some total 76 DNA bands were amplified through RAPD primers. Among them 24 were polymorphic bands. The rate of polymorphism was obtained about 30.20%. Genetic diversity ranged from 0.083 to 0.438 and the frequency of major allele ranged from 0.625 to 0.917. The PIC value ranged from 0.063 to 0.340 with the average value 0.150. The PIC value indicated that the studied rice hybrids had low molecular diversity. The dendrogram indicating the relative genetic similarity of the rice hybrids was constructed which followed three major clusters (A, B and C) among the studied material. Two SSR primers showed polymorphic bands which can be used as an evidence of variety protection data. These experimental findings can be used for the protection of hybrids in commercial purpose and in managing rice genetic resource in Bangladesh.


[1] BER (Bangladesh Economic Review). 2013. “Ministry of Finance, Finance Division. Economic Advisory wing”. Government of the People`s Republic of Bangladesh.
[2] HIES. (2010). “Household Income and Expenditure Survey, Bangladesh Bureau of statistics, Ministry of Planning,” Government of the People`s Republic of Bangladesh, Dhaka.
[3] PANAP, (2007). “Hybrid Rice in Asia: Sowing the Seeds of Dependency, A Fact Sheet on Hybrid Rice”. Pesticide Action Network Asia and the Pacific (PANAP), Penang, Malaysia.
[4] Lin J. Y. (1991). The household Responsibility System Reform and Adoption of Hybrid Rice in China. J. Develop. Econom. 36: 353-372.
[5] Lin J. Y. (1994). Impact of Hybrid Rice on Input Demand and Productivity. Agricultural Economics. 10: 154-164.
[6] Virmani S. S., Siddiq E. A. and Muralidaran K. (1998). Advances in Hybrid Rice Technology, IRRI, Los Banos.
[7] Mailer R. J., Scarth R., and Fristensky B. (1994) Discrimination among cultivars of rapeseed (Brassica napus L.) using DNA polymorphism amplified from arbitrary primers. Theor. Appl. Genet. 87: 697-704.
[8] Marshall P., Marchand M. C., Lisieczko Z. and Landry B. S. (1994). A simple method to estimate the percentage of hybridity in canola (Brassica napus) F1 hybrids. Theor. Appl. Genet. 89: 853858.
[9] Karkousis A., Barr A. R., Chalmers K. J., Ablett G. A., Holton T. A., Henry R. J., Lim P. and Langridge P. (2003). Potential of SSR markers for plant breeding and variety identification in Australian Barley germplasm. Aust. J. Agric. Res. 54: 1197-1210.
[10] Agarwal M., Sahi C., Katiyar-Agarwal S., Agarwal S., Young T., Gallie, Sharma V. M., Ganesan K. and Grover A. (2003). Molecular characterization of rice hsp101: Complementation of yeast hsp104 mutation by disaggregation of protein granules and differential expression in indica and japonica rice types. Plant Mol. Biol. 51: 543-53.
[11] Liu G., Bernhardt J., Jia M. H., Wamishe Y. and Jia Y. (2007). Molecular characterization of rice recombinant inbred line population derived from a japonica-indica cross. Euphytica. 159: 73-82.
[12] Prabakaran A., Paramasivam K., Rajesh T. and Rajarajan D. (2010). Molecular characterization of rice land races using SSR markers. Elec. J. Plant Breed. 1: 512-516.
[13] Yasmin F., Islam M. R., Rehana S., Mazumder R. R., Anisuzzaman M., Khatun H., Rayhan R. and Gregorio G. B. (2012). Molecular characterization of inbred and hybrid rice genotypes of Bangladesh. SABRAO J. Breed. Genet. 44: 163-175.
[14] Williams J. G. K., Kubelik A. E., Levak K.J., Rafalski J. A. and Tingey S. V. (1990). Genetic analysis using random amplified polymorphic DNA markers. Methods Enzymology. 1218: 704-740.
[15] Tautz D. (1989). Hypervariabflity of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463-6471.
[16] Morgante M. and Olivieri A. (1993). PCR-amplified microsatellites as markers in plant genetics. Plant J. 3:175-182.
[17] Powell W., Machray G. C. and Provan J. (1996). Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1:215- 222.
[18] Lapitan V. C., Brar D. S., Abe T. and Redofia E. D. (2007). Assessment of genetic diversity of Philippine rice cultivars carrying good quality traits using SSR markers. Breed. Sci. 57: 263-270.
[19] Liu, K.J., and Muse, S.V., 2005, PowerMarker: An integrated analysis environment for genetic marker analysis, Bioinformatics,21, 2128–2129
[20] Rholf, F., 2002, Numerical Taxonomy and Multivariate Analysis System Version 2.2, New York, USA: Department of Ecology and Evolution, State University of New York.
[21] Sneath, P.H.A. and Sokal, R.R. (1973). Numemical taxonomy: the principles and practice of numerical classification. San Francisco: Freeman. p. 573.
[22] Yeh F. C., Yang R. C. and Boyle T. (1999). POPGENE VERSION 1.31: Microsoft Window-based free Software for Population Genetic Analysis.
[23] Botstein D., White R. L., Skolnick M. and Davis R. W. (1980). Construction of genetic linkage map in man using restriction fragment length polymorphisms. Amer. J. Hum. Genet. 32: 314- 333.
[24] Nei M. and Chesser R. K. (1983). Estimation of fixation indices and gene diversities. Annual Hum. Genet. 47: 253- 259.
[25] Nei M. (1972). Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA. 70(12). 3321-3323.
[26] Kanawapee N., Sanitchon J., Srihaban P. and Theerakulpisut P. (2011). Genetic diversity analysis of rice cultivars (Oryza sativa L.) differing in salinity tolerance based on RAPD and SSR markers. Elect. J Biotech. 6: 25-31.
[27] Ramadan E. A., Elmoghazy A. M. and El-Mowafi H. F. (2015). Molecular markers based genetic diversity analysis for drought tolerance in rice (Oryza Sativa L.) Using SSR Markers. Int. J. Sci. Res. Agric. Sci. 2: 137- 146.
[28] Thompson J. A., Nelson R. L. and Vodkin L. O. (1998). Identification of diverse soybean germplasm using RAPD markers. Crop Sci. 38:1348-1355.
[29] Islam A. S. M. F., Ali M. R., Gregorio G. B. and Islam M. R. (2012). Genetic diversity analysis of stress tolerant rice (Oryza sativa L.). Afr. J. Biotecnol. 11(85): pp. 15123- 15129.
[30] Rahman L., Molla M. R, Sultana S., Islam M. N., Ahmed N. U., Rahman M. S. and Nazim-ud-Dowla M. (2007). PLANT VARIETIES OF BANGLADESH: Morphological and Molecular Characterization. Published by Seed Wing, Ministry of Agriculture, Government of the Peoples’ Republic of Bangladesh, 1: 486.
[31] Garris, A. J., Tai T. H., Coburn J., Kresovich S. and McCouch S. (2005). Genetic structure and diversity in Oryza sativa L. Genetics. 169:1631-1638.
[32] Thomson M. J., Septiningsih E. M., Suwardjo F., Santoso T. J., Silitonga T. S. and McCouch S. R. (2007). Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet. 114: 559-568.
[33] Muhammad A., Samina K., Muhammad A. B., Anjuman A. and Yusuf Z. (2005). Genetic diversity among rice genotypes of Pakistan through Random Amplified Polymorphic DNA (RAPD) analysis. Pakistan J. Bot. 37(3): 585-592.
[34] Malik A. R., Zahida H. P. and Muhammad S. M. (2008). Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L.) using RAPD markers. Electronic J. Biotechnol. 11(3): 1? 10.
[35] Deepu V., Rajani J., Nair G. M. and Nair A. J. (2013). Molecular characterization of selected cultivars of rice, Oryza sativa L. using Random Amplified Polymorphic DNA (RAPD) markers. Inter. Food Res. J. 20(2): 919-923.
[36] Yeasmin S., Islam M. M. and Begum S. N. (2013). Molecular characterizations of some rice genotypes using RAPD markers. Bangladesh J. Nuclear Agric. 29: 1-11.
[37] Rabab Dauob, Georges Makhoul, Hafez Mahfoud, "Genetic Diversity among Grapevine (Vitis Vinifera L.) Cultivars of Tartous Province (Syria) using Microsatellite Markers" SSRG International Journal of Agriculture & Environmental Science 5.6 (2018): 54-8.

Molecular Diversity, RAPD and SSR Markers, Polymorphism, Rice hybrid.