Molecular Genetics and Genomics

, Volume 284, Issue 2, pp 137–146 | Cite as

Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L.

  • Kenji Fujino
  • Jianzhong Wu
  • Hiroshi Sekiguchi
  • Tomoko Ito
  • Takeshi Izawa
  • Takashi Matsumoto
Original Paper


Flowering time is a major determinant for the local adaptation of crops. Hd1 is a key flowering-time gene in rice and is orthologous to the Arabidopsis CONSTANS gene. To elucidate the role of Hd1 in selection, we examined the Hd1 alleles of 60 landraces of Asian cultivated rice (Oryza sativa L.) originating from all regions of Asia, which comprised three cultivar groups, indica, japonica, and aus. The identified alleles were classified into four allele groups. The functional Hd1 alleles in allele groups I and II corresponded to indica and japonica, respectively. Non-functional alleles in these groups were not clearly associated with cultivar groups or locations. Allele groups III and IV corresponded to the aus cultivar group. The ancestry of each cultivar group was identified by the coalescent approach for Hd1 molecular evolution using the haplotype patterns of 14 regions over the 1.1 Mb chromosomal region surrounding Hd1 and the pSINE patterns of two loci, 1.4 and 4.4 Mb apart from Hd1. The haplotype patterns clearly revealed that Hd1 allele migration was caused by multiple and complex introgression events between cultivar groups. The Hd1 haplotypes among dozens of accessions of the wild species O. rufipogon were strongly divergent and only two of the haplotype clusters in O. rufipogon were closely related to those in cultivated rice. This strongly suggested that multiple introgression events have played an important role in the shaping and diversification of adaptation in addition to primary selection steps at the beginning of domestication.


Adaptation CONSTANS Flowering time Hd1 Introgression Rice 



The seeds of the landraces and wild rice accessions used in this study were provided by the National Institute of Agrobiological Sciences and National Institute of Genetics, Japan, respectively. This research was supported partly by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation, QTL5003).

Supplementary material

438_2010_555_MOESM1_ESM.ppt (378 kb)
Supplementary material 1 (PPT 378 kb)


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Kenji Fujino
    • 1
  • Jianzhong Wu
    • 2
  • Hiroshi Sekiguchi
    • 1
  • Tomoko Ito
    • 3
  • Takeshi Izawa
    • 2
  • Takashi Matsumoto
    • 2
  1. 1.Plant Breeding and Production Division, Agricultural Research InstituteHOKUREN Federation of Agricultural CooperativesNaganumaJapan
  2. 2.Plant Genome Research UnitNational Institute of Agrobiological SciencesTsukubaJapan
  3. 3.Research Division IInstitute of the Society for Techno-innovation of Agriculture Forestry and FisheriesTsukubaJapan

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