Genome Sequences of Oryza Species

  • Masahiko Kumagai
  • Tsuyoshi Tanaka
  • Hajime Ohyanagi
  • Yue-Ie C. Hsing
  • Takeshi Itoh


This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.


Genome sequencing Reference genome Annotation Next-generation sequencing technology Resequencing Biodiversity Comparative genomics 



This work was supported by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics-based Technology for Agricultural Improvement, IVG2001).


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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Masahiko Kumagai
    • 1
  • Tsuyoshi Tanaka
    • 1
  • Hajime Ohyanagi
    • 2
  • Yue-Ie C. Hsing
    • 3
  • Takeshi Itoh
    • 1
  1. 1.Advanced Analysis CenterNational Agriculture and Food Research OrganizationTsukubaJapan
  2. 2.King Abdullah University of Science and Technology (KAUST)Computational Bioscience Research Center (CBRC)ThuwalKingdom of Saudi Arabia
  3. 3.Academica SinicaInstitute of Plant and Microbial BiologyTaipeiTaiwan

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