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


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.


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)


  1. Ando I, Sato H, Aoki N, Suzuki Y, Hirabayashi H, Kuroki M, Shimizu H, Ando T, Takeuchi Y (2010) Genetic analysis of the low-amylose characteristics of rice cultivars Oborozuki and Hokkai-PL9. Breed Sci 60:187–194CrossRefGoogle Scholar
  2. Chakhonkaen S, Pitnjam K, Saisuk W, Ukoskit K, Muangprom A (2012) Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute. Rice 5:19CrossRefGoogle Scholar
  3. Courtois B, Frouin J, Greco R, Bruschi G, Droc G, Hamelin C, Ruiz M, Clément G, Evrard J-C, van Coppenole S, Katsantonis D, Oliveira M, Negrão S, Matos C, Cavigiolo S, Lupotto E, Piffanelli P, Ahmadi N (2012) Genetic diversity and population structure in a European collection of rice. Crop Sci 52:1663–1675CrossRefGoogle Scholar
  4. Felsenstein J (1989) PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164–166Google Scholar
  5. Fujino K, Sekiguchi H (2005a) Mapping of QTLs conferring extremely early heading in rice (Oryza sativa L.). Theor Appl Genet 111:393–398PubMedCrossRefGoogle Scholar
  6. Fujino K, Sekiguchi H (2005b) Identification of QTLs conferring genetic variation for heading date among rice varieties at the northern-limit of rice cultivation. Breed Sci 55:141–146CrossRefGoogle Scholar
  7. Fujino K, Sekiguchi H (2008) Mapping of quantitative trait loci controlling heading date among rice cultivars in the northern-most region of Japan. Breed Sci 58:367–373CrossRefGoogle Scholar
  8. Fujino K, Sekiguchi H (2011) Origins of functional nucleotide polymorphisms in a major quantitative locus, qLTG3-1, controlling low-temperature germinability in rice. Plant Mol Biol 75:1–10PubMedCrossRefGoogle Scholar
  9. Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799PubMedCrossRefGoogle Scholar
  10. Fujino K, Yamanouchi U, Yano M (2013) Roles of Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation. Theor Appl Genet 126:611–618PubMedCrossRefGoogle Scholar
  11. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638PubMedCentralPubMedCrossRefGoogle Scholar
  12. Giarrocco LE, Marassi MA, Salerno GL (2007) Assessment of the genetic diversity in Argentine rice cultivars with SSR markers. Crop Sci 47:853–860CrossRefGoogle Scholar
  13. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30PubMedCrossRefGoogle Scholar
  14. Hori K, Sugimoto K, Nonoue Y, Ono K, Matsubara K, Yananouchi U, Takeuchi Y, Yano M (2010) Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theor Appl Genet 120:1547–1557PubMedCentralPubMedCrossRefGoogle Scholar
  15. Hori K, Ogiso-Tanaka E, Matsubara K, Yamanouchi U, Ebana K, Yano M (2013) Hd16, a gene for casein kinase I, is involved in the control of flowering time by the modulating the day-length response. Plant J 76:36–46PubMedGoogle Scholar
  16. Huang X, Kurata N, Wei X, Wang ZX, Wang Z, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhna Q, Li C, Fujiyama A, Lu T, Feng Q, Qian Q, Li J, Han B (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–503PubMedCrossRefGoogle Scholar
  17. Kuroki M, Saito K, Matsuba S, Yokogami N, Shimizu H, Ando I, Sato Y (2007) A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8. Theor Appl Genet 115:593–600PubMedCrossRefGoogle Scholar
  18. Lu H, Redus MA, Coburn JR, Rutger JN, McCouch SR et al (2005) Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci 45:66–76CrossRefGoogle Scholar
  19. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res 8:4321–4326PubMedCentralPubMedCrossRefGoogle Scholar
  20. Nagasaki H, Ebana K, Shibaya T, Yonemaru J, Yano M (2010) Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population. Breed Sci 60:648–655CrossRefGoogle Scholar
  21. Nonoue Y, Fujino K, Hirayama Y, Yamanouchi U, Lin SY, Yano M (2008) Detection of quantitative trait loci controlling extremely early heading in rice. Theor Appl Genet 116:715–722PubMedCrossRefGoogle Scholar
  22. Pitchard JK, Stephens M, Donnely P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959Google Scholar
  23. Shinada H, Iwata N, Sato T, Fujino K (2013) Genetical and morphological characterization of cold tolerance at fertilization stage in rice. Breed Sci 63:197–204PubMedCentralPubMedCrossRefGoogle Scholar
  24. Spada A, Mantengazza R, Biloni E, Caporali E, Sala F (2004) Italian rice varieties: historical data, molecular markers and pedigrees to reveal their genetic relationships. Plant Breed 123:105–111CrossRefGoogle Scholar
  25. Takeuchi Y, Hori K, Suzuki K, Nonoue Y, Takemoto-Kuno Y, Maeda H, Sato H, Hirabayashi H, Ohta H, Ishi T, Kato H, Nemoto H, Imbe T, Ohtubo K, Yano M, Ando I (2008) Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3. Breed Sci 58:437–445CrossRefGoogle Scholar
  26. Wade MJ, Winther RG, Agrawal A, Goodnight CJ (2001) Alternative definitions of epistasis: dependence and interaction. Trends Ecol Evol 16:498–504CrossRefGoogle Scholar
  27. Yadong H, Millet BP, Beaubien KA, Dahl SK, Steffenson BJ, Smith KP, Muehibauer GJ (2012) Haplotype diversity and population structure in cultivated and wild barley evaluated for Fusarium head blight responses. Theor Appl Genet 126:619–636Google Scholar
  28. Yamamto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T, Yano M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genom 11:267CrossRefGoogle Scholar
  29. Yonemaru J, Yamamoto T, Ebana K, Yamamoto E, Nagasaki H, Shibaya T, Yano M (2012) Genome-wide haplotype changed produced by artificial selection during modern rice breeding in Japan. Plos One 7–3:e32982CrossRefGoogle Scholar

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

Personalised recommendations