Theoretical and Applied Genetics

, Volume 127, Issue 4, pp 995–1004 | Cite as

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

  • Hiroshi Shinada
  • Toshio Yamamoto
  • Eiji Yamamoto
  • Kiyosumi Hori
  • Junichi Yonemaru
  • Shuichi Matsuba
  • Kenji Fujino
Original Paper

Abstract

Key message

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.

Supplementary material

122_2014_2274_MOESM1_ESM.pptx (260 kb)
Supplementary material 1 (PPTX 260 kb)
122_2014_2274_MOESM2_ESM.xlsx (96 kb)
Supplementary material 2 (XLSX 96 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Hiroshi Shinada
    • 1
    • 2
  • Toshio Yamamoto
    • 3
  • Eiji Yamamoto
    • 3
  • Kiyosumi Hori
    • 3
  • Junichi Yonemaru
    • 3
  • Shuichi Matsuba
    • 4
  • Kenji Fujino
    • 4
  1. 1.Rice Breeding Group, Kamikawa Agricultural Experiment StationLocal Independent Administrative Agency Hokkaido Research OrganizationPippuJapan
  2. 2.Beans Breeding Group, Tokachi Agricultural Experiment StationLocal Independent Administrative Agency Hokkaido Research OrganizationMemuroJapan
  3. 3.Rice Applied Genomics Research UnitNational Institute of Agrobiological SciencesTsukubaJapan
  4. 4.NARO Hokkaido Agricultural Research CenterNational Agricultural Research OrganizationSapporoJapan

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