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Genetic diversity of Indo-China rice varieties using ISSR, SRAP and InDel markers

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Abstract

Rice is believed to have originated from Indo-China, area between China and India, and then spread throughout the world. The Indochina region mainly includes countries like Thailand, Laos and Vietnam, which are the world’s major rice exporters. Rice varieties grown in this area are highly diverse due to their different environment, ecosystem and climatic conditions. The objective of this study was to evaluate the genetic relationship of Indochina rice varieties using intersimple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP) and insertion–deletion (InDel) markers. Forty-six rice varieties, including 16, 4, 11 and 15 from Thailand, China, Laos and Vietnam, respectively were used in this study. Seventeen of the 20 ISSR primers showed 82.96% polymorphism. At the same time, 17 of the 30 primer pairs of SRAP marker showed clear DNA amplification, which resulted in 84.79% polymorphism. Ninety-seven of 133 InDel markers have about 99.47% polymorphism. Three markers showed average PIC score ranging from 0.20 to 0.26. When the analysis was conducted using UPGMA clustering method, it was found that the combined data from three markers gave a better result than each marker separately. The results from clustering analysis showed that all accessions can be grouped based on their location and can be categorized into two major groups. Useful results from this study could bring substantial benefits and ultimately help the rice breeders to develop elite rice varieties in future.

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Acknowledgements

This research was supported from graduate scholarship provided by the National Research Council of Thailand (NRCT) in the 2018 fiscal year and the Graduate Scholarship from the Graduate School of Kasetsart University and the Bilateral Research Co-operation, Faculty of Science, Kasetsart University to Miss Pattaraborn Moonsap.

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Authors and Affiliations

  1. Faculty of Science, Department of Genetics, Kasetsart University, 50 Ngam, Wong Wan Rd., Ladyaw, Chatuchak, Bangkok, 10900, Thailand

    Pattaraborn Moonsap & Chatchawan Jantasuriyarat

  2. Faculty of Science, Department of Zoology, Kasetsart University, 50 Ngam, Wong Wan Rd., Ladyaw, Chatuchak, Bangkok, 10900, Thailand

    Nutthalak Laksanavilat & Piyama Tasanasuwan

  3. Rajamangala University of Technology Isan, 744 Suranari Rd., Muang District, Nakhon Ratchasima, 30000, Thailand

    Sittipun Sinumporn

  4. Faculty of Agriculture, Department of Agronomy, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand

    Sureeporn Kate-Ngam

  5. Centre for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, 10900, Thailand

    Chatchawan Jantasuriyarat

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  1. Pattaraborn Moonsap
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  2. Nutthalak Laksanavilat
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  5. Sureeporn Kate-Ngam
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  6. Chatchawan Jantasuriyarat
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Correspondence to Chatchawan Jantasuriyarat.

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Corresponding editor: H. A. Ranganath

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Moonsap, P., Laksanavilat, N., Sinumporn, S. et al. Genetic diversity of Indo-China rice varieties using ISSR, SRAP and InDel markers. J Genet 98, 80 (2019). https://doi.org/10.1007/s12041-019-1123-0

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  • DOI: https://doi.org/10.1007/s12041-019-1123-0

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