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Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation

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Abstract

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The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world.

Abstract

Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

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Acknowledgments

This work was supported in part by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry).

Conflict of interest

The authors declare that they have no conflict of interest.

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Author notes

  1. Hiroshi Shinada

    Present address: Beans Breeding Group, Tokachi Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization, Shinsei Minami 9-2, Memuro, Hokkaido, 082-0071, Japan

Authors and Affiliations

  1. Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization, Minami 1-5, Pippu, Hokkaido, 078-0397, Japan

    Hiroshi Shinada

  2. Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Toshio Yamamoto, Eiji Yamamoto, Kiyosumi Hori & Junichi Yonemaru

  3. NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido, 062-8555, Japan

    Shuichi Matsuba & Kenji Fujino

Authors
  1. Hiroshi Shinada
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  2. Toshio Yamamoto
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  3. Eiji Yamamoto
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  4. Kiyosumi Hori
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  5. Junichi Yonemaru
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  6. Shuichi Matsuba
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  7. Kenji Fujino
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Corresponding author

Correspondence to Kenji Fujino.

Additional information

Communicated by L. Jiang.

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Shinada, H., Yamamoto, T., Yamamoto, E. et al. Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation. Theor Appl Genet 127, 995–1004 (2014). https://doi.org/10.1007/s00122-014-2274-2

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  • DOI: https://doi.org/10.1007/s00122-014-2274-2

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