Molecular Breeding

, Volume 34, Issue 3, pp 1007–1021 | Cite as

Genome-wide single nucleotide polymorphisms and insertion–deletions of Oryza sativa L. subsp. japonica cultivars grown near the northern limit of rice cultivation

  • Sho Takano
  • Shuichi Matsuda
  • Noriko Kinoshita
  • Naomi Shimoda
  • Takashi Sato
  • Kiyoaki Kato


Single nucleotide polymorphisms (SNPs) and insertions–deletions (InDels) are valuable molecular markers for molecular breeding among genetically closely related cultivars. Rice (Oryza sativa L. subsp. japonica) cultivars grown in Hokkaido (45–42°N), the northernmost region of rice paddy cultivation in Japan, have been bred for over 100 years for adaptation to low summer temperatures together with high yield and good eating quality. In this study, for 10 closely related rice cultivars released in Hokkaido and cultivar Koshihikari, we identified genome-wide SNPs and InDels by next-generation sequencing. More than 29 million reads from the Hokkaido cultivars, each 101 nucleotides long, were uniquely mapped to the Nipponbare reference genome. The average of the total nucleotide length of all uniquely mapped reads corresponded to 10.9 times (3,978 Mb with genome coverage of 90.7 %) the Nipponbare reference genome. An average of 99,955 putative SNPs (1.8 times the number in Koshihikari) and 14,617 putative InDels (also 1.8 times the number in Koshihikari) were detected in Hokkaido cultivars relative to the Nipponbare genome, which enabled analyses of the inheritance of pedigree haplotypes of four cultivars, SNPs and InDels among closely related Hokkaido cultivars, and haplotype blocks unique to Hokkaido cultivars. The comprehensive SNP and InDel data provide DNA marker resources and will facilitate quantitative trait locus analysis of biparental mapping of very closely related Hokkaido cultivars. Furthermore, the haplotype blocks unique to Hokkaido cultivars represent ideal genetic regions for improvement of cultivars to be grown near the northern and southern limits of rice cultivation.


Single nucleotide polymorphism Insertion Deletion Next-generation sequencing Oryza sativa L. 



This study was supported in part by the Suhara Memorial Foundation, the Tojuro Iijima Foundation for Food Science and Technology, and Adaptable and Seamless Technology Transfer Program through Target-driven R&D (A-STEP), Japan Science and Technology Agency (JST). Seeds of Hokkaido cultivars were provided by the Central Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization, and seeds of Koshihikari were provided by the National Institute of Agrobiological Sciences Genebank. We thank Noboru Shinbashi, Harumi Kikuchi, Toshio Yamamoto, Satoshi Natsume, Hiroki Takagi, Ryohei Terauchi, Kei Sonoyama, Toshihiko Maekawa, Yuuji Hirayama, Hitoshi Kiuchi, Tsutomu Nishimura, and Hirokazu Sato for their valuable suggestions throughout the study.

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Sho Takano
    • 1
  • Shuichi Matsuda
    • 1
  • Noriko Kinoshita
    • 1
  • Naomi Shimoda
    • 1
  • Takashi Sato
    • 2
  • Kiyoaki Kato
    • 1
  1. 1.Department of Agro-Environmental ScienceObihiro University of Agriculture and Veterinary MedicineObihiroJapan
  2. 2.Rice Breeding Group, Kamikawa Agricultural Experiment StationLocal Independent Administrative Agency Hokkaido Research OrganizationPippuJapan

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