Plant Systematics and Evolution

, Volume 282, Issue 1–2, pp 21–29 | Cite as

Genome-type-specific variation of the 19th intron sequence within the RNA polymerase I largest subunit gene in the genus Oryza

  • H. Takahashi
  • T. Sato
  • Y.-I. Sato
  • I. NakamuraEmail author
Original Article


Rice PolA1 gene, encoding for the largest subunit of RNA polymerase I, spans ca. 15 kb containing 21 exons and presents as a single-copy-per-haploid genome. The genus Oryza comprises 22 wild species and 9 recognized genome types: AA, BB, CC, EE, FF, GG, BBCC, CCDD, and HHJJ. We analyzed sequences of the 19th intron (PI19) within PolA1 genes in 17 Oryza species. The AA species, containing two cultivated species, showed similar length of PI19 to that of CC species (287–296 bp). The longer PI19s were found in BB (502 bp) and FF (349 bp) species, although EE (217 bp) and GG (222 bp) species had shorter sequences. The size differences of the PI19s are particularly useful to discriminate between diploid (BB and CC) and allotetraploid (BBCC) species using simple PCR analysis. The evolutionary relationship among seven genomes was inferred based on the comparison of their PI19 sequences.


DNA marker Harr-plot analysis Rice RNA polymerase I PolA1 gene Phylogeny Oryzasativa 



We are grateful to Dr. Masahiro Mii, Chiba University, for his encouragement and helpful advice on the research. This work was funded by Sato Project, Research Institute of Humanity and Nature (Contribution No. 13 of Sato Project, RIHN). Accessions of wild-rice species were supplied by Dr. Nori Kurata, National Bio Resources Project, National Institute of Genetics, Japan.


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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • H. Takahashi
    • 1
  • T. Sato
    • 2
  • Y.-I. Sato
    • 3
  • I. Nakamura
    • 1
    Email author
  1. 1.Graduate School of Science and TechnologyChiba UniversityChibaJapan
  2. 2.Graduate School of Life ScienceTohoku UniversitySendaiJapan
  3. 3.Research Institute for Humanity and NatureKyotoJapan

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