, Volume 176, Issue 2, pp 269–279 | Cite as

RDA derived Oryza minuta-specific clones to probe genomic conservation across Oryza and introgression into rice (O. sativa L.)

  • Junghyun Shim
  • Olivier Panaud
  • Clémentine Vitte
  • Merlyn S. Mendioro
  • Darshan S. Brar


Molecular markers have been successfully used in rice breeding however available markers based on Oryza sativa sequences are not efficient to monitor alien introgression from distant genomes of Oryza. We developed O. minuta (2n = 48, BBCC)-specific clones comprising of 105 clones (266–715 bp) from the initial library composed of 1,920 clones against O. sativa by representational difference analysis (RDA), a subtractive cloning method and validated through Southern blot hybridization. Chromosomal location of O. minuta-specific clones was identified by hybridization with the genomic DNA of eight monosomic alien additional lines (MAALs). The 37 clones were located either on chromosomes 6, 7, or 12. Different hybridization patterns between O. minuta-specific clones and wild species such as O. punctata, O. officinalis, O. rhizomatis, O. australiensis, and O. ridleyi were observed indicating conservation of the O. minuta fragments across Oryza spp. A highly repetitive clone, OmSC45 hybridized with O. minuta and O. australiensis (EE), and was found in 6,500 and 9,000 copies, respectively, suggesting an independent and exponential amplification of the fragment in both species during the evolution of Oryza. Hybridization of 105 O. minuta specific clones with BB- and CC-genome wild Oryza species resulted in the identification of 4 BB-genome-specific and 14 CC-genome-specific clones. OmSC45 was identified as a fragment of RIRE1, an LTR-retrotransposon. Furthermore this clone was introgressed from O. minuta into the advanced breeding lines of O. sativa.


Oryza minuta-specific clones Representational difference analysis Highly repetitive sequence Genomic conservation MAALs Introgression 



The senior author is thankful to the Rural Development Administration, Korea, for financial support. The authors are also grateful to Dr. Bill Hardy, senior science editor, IRRI, for editing this manuscript, to Dr. M. Ashikari for allowing to sequence 105 O. minuta-specific clones, and to K. McNally, S. Heuer, and R.A. Shim for their useful comments on it.

Supplementary material

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Supplementary material 1 (DOC 61 kb)
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Supplementary material 2 (DOC 31 kb)
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Supplementary material 3 (DOC 164 kb)
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Supplementary material 4 (DOC 173 kb)


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Junghyun Shim
    • 1
  • Olivier Panaud
    • 2
  • Clémentine Vitte
    • 3
  • Merlyn S. Mendioro
    • 4
  • Darshan S. Brar
    • 1
  1. 1.Plant Breeding, Genetics, and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
  2. 2.Laboratoire Génome et Développement des PlantesUniversité de PerpignanPerpignanFrance
  3. 3.UMR de Génétique VégétaleINRA - Univ Paris-Sud - CNRS - AgroParisTechGif-sur-YvetteFrance
  4. 4.Institute of Biological SciencesUniversity of the Philippines Los BañosLos BañosPhilippines

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