Functional & Integrative Genomics

, Volume 9, Issue 1, pp 97–108 | Cite as

The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

  • Beng-Kah Song
  • Ingo Hein
  • Arnis Druka
  • Robbie Waugh
  • David Marshall
  • Kalaivani Nadarajah
  • Soon-Joo Yap
  • Wickneswari Ratnam
Original Paper


Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1.


Oryza rufipogon Yield QTL yld1.1 Comparative sequence analysis Microcolinearity 



We specifically thank Dr. Nils Rostoks and other staff in the Scottish Crop Research Institute, Dundee, Scotland for their help and encouragement. This work is supported by the Malaysian Ministry of Science and Technology, grant number IRPA 01-03-03-0001-BTK/ER/001 and the Scottish Executive Environment and Rural Affairs Department.

Supplementary material

10142_2008_91_MOESM1_ESM.doc (278 kb)
Supplementary Table 1 Annotation comparison between the GenBank, TIGR and reannotation of the RM5 region in japonica genome and O. rufipogon genome (DOC 278 KB).


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Beng-Kah Song
    • 1
    • 4
  • Ingo Hein
    • 2
  • Arnis Druka
    • 2
  • Robbie Waugh
    • 2
  • David Marshall
    • 2
  • Kalaivani Nadarajah
    • 3
  • Soon-Joo Yap
    • 5
  • Wickneswari Ratnam
    • 1
  1. 1.School of Environmental and Natural Resource Sciences, Faculty of Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  2. 2.Genome Dynamics ProgramScottish Crop Research InstituteDundeeUK
  3. 3.School of BioScience and Biotechnology, Faculty of Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  4. 4.School of Arts and SciencesMonash University, Sunway CampusBandar SunwayMalaysia
  5. 5.Malaysia Genome Institute, UKM-MTDC Smart Technology CentreUniversiti Kebangsaan Malaysia (UKM)BangiMalaysia

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