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

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Abstract

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines

    Junghyun Shim & Darshan S. Brar

  2. Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France

    Olivier Panaud

  3. UMR de Génétique Végétale, INRA - Univ Paris-Sud - CNRS - AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France

    Clémentine Vitte

  4. Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines

    Merlyn S. Mendioro

Authors
  1. Junghyun Shim
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  2. Olivier Panaud
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  3. Clémentine Vitte
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  4. Merlyn S. Mendioro
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  5. Darshan S. Brar
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Corresponding author

Correspondence to Darshan S. Brar.

Additional information

The O. minuta-specific clones are being maintained as inserts in the form of plasmids in E. coli at −80°C and are available for sharing with interested scientists. The 105 clones were sequenced and deposited in Genbank (NCBI).

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Shim, J., Panaud, O., Vitte, C. et al. RDA derived Oryza minuta-specific clones to probe genomic conservation across Oryza and introgression into rice (O. sativa L.). Euphytica 176, 269–279 (2010). https://doi.org/10.1007/s10681-010-0245-5

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  • DOI: https://doi.org/10.1007/s10681-010-0245-5

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