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Genetic relationships among improved varieties of rice (Oryza sativa L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers

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Abstract

Morphological traits and two kinds of molecular markers were employed to study the genetic relationships among improved rice (Oryza sativa ) varieties of Indonesia since 1943. Dendrograms based on morphological traits and both molecular markers (simple sequence repeats, SSR and single nucleotide polymorphism, SNP) agreed in separating the varieties into two primary groups. Based on the morphological traits, a larger group (>60 %) contains varieties with smaller sizes compared with those in the smaller group (<40 %). SSR and SNP markers revealed that most of the varieties belonged to indica (88; 89 %) and japonica (9; 8 %) subspecies, and 3 % of varieties were not involved in two subspecies. The molecular markers revealed that the genetic diversity (H) stagnated between stage II (1967–1985) and stage III (1986–2003). However, during stage I (1943–1966), H was higher than in the other stages as revealed by SNP markers, while H in stage I was lower than in the other stages as revealed by SSR markers. In this study, the two molecular data sets were positively correlated and positive correlations between the phenotypic and molecular data depended on the kind of molecular marker: SNP had higher Mantel r values than SSRs. Besides, SSR markers seem to be appropriate for pedigree studies, while SNP markers could be used to reveal genomic relationships. These findings were attributable to the different properties of these two different markers. These results suggested that the diversity and differentiation of both the phenotypic and molecular marker variations were probably resulted from the crossing and selection in rice breeding in Indonesia. We suggest that Indonesia needs another strategy to improve new varieties to avoid a reduction in genetic diversity and similarity.

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Acknowledgments

We are grateful for the Dikti Scholarship and would like to thank the Government of the Indonesian Republic, who funded the first author for a Ph.D. program at the University of Tsukuba, and the ICRR for providing us seed material for this study.

Authors’ contributions

The first author contributes to substantive conception, laboratory and field work, design, analysis, interpretation of data and drafts the manuscript; the second, the third and the fourth authors contributed to revise it critically for important intellectual content; and the fourth author also as a final approval person of the version to be published.

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Authors and Affiliations

  1. Laboratory of Plant Genetics and Breeding Science, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan

    Kadapi Muhamad & Kazutoshi Okuno

  2. Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Kaworu Ebana

  3. QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Shuichi Fukuoka

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  1. Kadapi Muhamad
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  4. Kazutoshi Okuno
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Correspondence to Kazutoshi Okuno.

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Muhamad, K., Ebana, K., Fukuoka, S. et al. Genetic relationships among improved varieties of rice (Oryza sativa L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers. Genet Resour Crop Evol 64, 701–715 (2017). https://doi.org/10.1007/s10722-016-0392-1

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