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Introgression of the chromosomal region with the Pi-cd locus from Oryza meridionalis into O. sativa L. during rice domestication

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Abstract

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The genotype of the Pi-cd locus found in blast-resistant rice variety Kitakurin, which is a cultivated rice from Japan belonging to Oryza sativa japonica, is identical to that of its wild relative O. meridionalis.

Abstract

Crop domestication from wild relatives to cultivated species has encompassed significant phenotypic changes. However, little is known about the genetic changes involved in domestication. Here, we surveyed the origin of the Pi-cd locus across Oryza species with AA genomes by comparison with the genome sequences of Hoshinoyume (HS), which does not carry the Pi-cd blast resistance gene, and Kitakurin (KK), which carries the Pi-cd blast resistance gene. We found that variety-specific transposons were enriched at the Pi-cd locus. The genotype of the Pi-cd locus characterized by transposons in HS and KK was specific to each Oryza species with the AA genome. The Kitaake (KT) genotype at the Pi-cd locus found in KK was identical only to that of O. meridionalis and distributed only in subgroups of japonica in the World Rice Collection and tropical japonica in the Japanese Rice Collection, whereas it was not present in O. rufipogon accessions. The distinct distributions of genotypes of the Pi-cd locus clearly demonstrated that the Pi-cd locus was introgressed from O. meridionalis into O. sativa, specific to tropical japonica.

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Acknowledgements

The wild rice accessions used in this study were supplied by the National Institute of Genetics supported by the National Bioresource Project (NBRP), AMED, Japan. 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).

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

    Kenji Fujino, Mari Obara & Tomohito Ikegaya

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

    Yuji Hirayama

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  1. Kenji Fujino
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KF conceived and designed the experiments and wrote the manuscript. KF, YH, MO, TI performed the experiments and analyzed the data. KF, YH, MO, TI approved the final manuscript.

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Correspondence to Kenji Fujino.

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Fujino, K., Hirayama, Y., Obara, M. et al. Introgression of the chromosomal region with the Pi-cd locus from Oryza meridionalis into O. sativa L. during rice domestication. Theor Appl Genet 132, 1981–1990 (2019). https://doi.org/10.1007/s00122-019-03332-1

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