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Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

Author

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  • Shahril Ab Razak

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Nor Helwa Ezzah Nor Azman

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Rahiniza Kamaruzaman

    (Rice Breeding Program, Rice Research Centre, MARDI Seberang Perai, Kepala Batas, Pulau Pinang, Malaysia)

  • Shamsul Amri Saidon

    (Rice Breeding Program, Rice Research Centre, MARDI Seberang Perai, Kepala Batas, Pulau Pinang, Malaysia)

  • Muhammad Fairuz Mohd Yusof

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Siti Norhayati Ismail

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Mohd Azwan Jaafar

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Norzihan Abdullah

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

Abstract

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159-MR167) to 0.723 (MRIA-Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

Suggested Citation

  • Shahril Ab Razak & Nor Helwa Ezzah Nor Azman & Rahiniza Kamaruzaman & Shamsul Amri Saidon & Muhammad Fairuz Mohd Yusof & Siti Norhayati Ismail & Mohd Azwan Jaafar & Norzihan Abdullah, 2020. "Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 56(2), pages 62-70.
    • Handle: RePEc:caa:jnlcjg:v:56:y:2020:i:2:id:58-2019-cjgpb
    DOI: 10.17221/58/2019-CJGPB
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    References listed on IDEAS

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    1. Youyong Zhu & Hairu Chen & Jinghua Fan & Yunyue Wang & Yan Li & Jianbing Chen & JinXiang Fan & Shisheng Yang & Lingping Hu & Hei Leung & Tom W. Mew & Paul S. Teng & Zonghua Wang & Christopher C. Mundt, 2000. "Genetic diversity and disease control in rice," Nature, Nature, vol. 406(6797), pages 718-722, August.
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