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

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Abstract

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.

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Acknowledgments

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).

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Authors and Affiliations

  1. Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Higashi-5, Kita-15, Naganuma, Hokkaido, 0691317, Japan

    Kenji Fujino & Hiroshi Sekiguchi

  2. Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 3058602, Japan

    Jianzhong Wu, Takeshi Izawa & Takashi Matsumoto

  3. Research Division I, Institute of the Society for Techno-innovation of Agriculture Forestry and Fisheries, Tsukuba, Ibaraki, 3050854, Japan

    Tomoko Ito

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  1. Kenji Fujino
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  2. Jianzhong Wu
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  3. Hiroshi Sekiguchi
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  4. Tomoko Ito
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  5. Takeshi Izawa
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  6. Takashi Matsumoto
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Correspondence to Kenji Fujino.

Additional information

Communicated by M. Yano.

K. Fujino and J. Wu contributed equally to this work.

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Fujino, K., Wu, J., Sekiguchi, H. et al. Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L.. Mol Genet Genomics 284, 137–146 (2010). https://doi.org/10.1007/s00438-010-0555-2

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  • DOI: https://doi.org/10.1007/s00438-010-0555-2

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