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Genetic diversity of some upland and lowland rice cultivars in Bangladesh using RAPD, ISSR and SSR markers

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Abstract

In order to increase the molecular tools and markers needed to detect genetic diversity of rice, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Simple Sequence Repeat (SSR) markers were used to reveal genetic diversity in 22 upland and lowland rice cultivars from Bangladesh. DNA from fresh leaves of young plants was extracted and subjected to the DNA polymorphism studies using the above mentioned markers. Among ten RAPD primers tested, four showed high polymorphism (90.90 %) with an average of 8.25 bands per primer with band size of approximately 220–1531 bp. Four ISSR primers out of ten produced high polymorphism (90.47 %) with an average of 10.5 bands per primer with band size of approximately 222–1750 bp. Among seven SSR primers tested, three amplified polymorphic bands with an average number of 4.0 bands per primer (ranging from approximately 233–950 bp) and 100 % polymorphism. Based on combined dataset generated by RAPD, ISSR and SSR markers, the highest similarity was showed between BRRI dhan 27 and BRRI dhan 29 (similarity coefficient value 0.89) and the lowest similarity was recorded between BR-3 and BRRI dhan 19 (similarity coefficient value 0.25). The UPGMA dendrogram based on genetic similarity grouped the cultivars into several clusters. Results obtained from PCA analysis were similar with UPGMA dendrogram. The evaluation of genetic similarity and cluster analysis provides useful guides for assisting plant breeders in selecting suitable genetically diverse parents for the future breeding programs.

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Acknowledgments

The authors are gratefully acknowledged to Professor Joarder DNA and Chromosome Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi and USDA (Grant No. 09.111.014.10.01.002.2009-13) and Ministry of Science and Technology (MoST), Bangladesh (Grant No. BS 58 (2010-2011)), for financial support. The authors also acknowledge the support and encouragement of the Principal, Vivekananda College, Thakurpukur, West Bengal, India.

Authors’ contribution

Shah Md. Mahbub Alam, Sadia siddika, Md. Enamul Haque, Md. Asadul Islam and Biswanath Sikdar designed the workplan, performed the experiments and wrote the paper. Ashutosh Mukherjee performed statistical analysis.

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Authors and Affiliations

  1. Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh

    Shah Md. Mahbub Alam, Sadia Siddika, Md. Enamul Haque, Md. Asadul Islam & Biswanath Sikdar

  2. Department of Botany, Vivekananda College, 269, Diamond Harbour Road, Thakurpukur, Kolkata, 700063, West Bengal, India

    Ashutosh Mukherjee

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  1. Shah Md. Mahbub Alam
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  2. Sadia Siddika
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  3. Md. Enamul Haque
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  6. Biswanath Sikdar
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Correspondence to Biswanath Sikdar.

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Alam, S.M.M., Siddika, S., Haque, M.E. et al. Genetic diversity of some upland and lowland rice cultivars in Bangladesh using RAPD, ISSR and SSR markers. Nucleus 59, 15–23 (2016). https://doi.org/10.1007/s13237-015-0148-x

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  • DOI: https://doi.org/10.1007/s13237-015-0148-x

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