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Establishment of adaptability to the northern-limit of rice production


The domestication of cultivated crops from their wild relatives narrowed down their genetic diversity in a bottleneck effect. Subsequently, the cultivation areas of crops have expanded all over the world into various environmental conditions from the original area along with human migration after domestication. Here, we demonstrated the genetic changes in the adaptation of rice to Hokkaido (41°2–45°3N latitude), Japan, from the tropics of their origin in Asian cultivated rice, Oryza sativa L. Although cultivated rice originated from the tropics, Hokkaido is one of the northern-limits of rice cultivation worldwide. Population genomics focusing on the local populations showed the varieties had genetically distinct classes with limited genetic diversity. In addition, some varieties in the class carried unique genotypes for flowering time, exhibiting extremely early flowering time. Certain mutations in unique genotypes can split off the varieties that are able to grow in Hokkaido. Furthermore, the changes in the genotype for flowering time during rice cultivation in Hokkaido demonstrated novel combinations of genes for flowering time owing to the intensive artificial selection on natural variation and rice breeding programs to achieve stable rice production in Hokkaido.

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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) (to KF) and JSPS KAKENHI Grant number 25450015 (to KF).


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) (to KF) and JSPS KAKENHI Grant number 25450015 (to KF).

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Conceived and designed the experiments and wrote the manuscript: KF. Performed the experiments, analyzed the data, and approved the final manuscript: TI, MO, KF.

Correspondence to Kenji Fujino.

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Fujino, K., Obara, M. & Ikegaya, T. Establishment of adaptability to the northern-limit of rice production. Mol Genet Genomics 294, 729–737 (2019).

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  • Natural variation
  • Plant breeding programs
  • Artificial selection
  • Adaptability
  • Flowering time
  • Rice