RDA derived <Emphasis Type="Italic">Oryza minuta</Emphasis>-specific clones to probe genomic conservation across <Emphasis Type="Italic">Oryza</Emphasis> and introgression into rice (<Emphasis Type="Italic">O. sativa</Emphasis> L.) |
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| Authors: | Junghyun Shim Olivier Panaud Clémentine Vitte Merlyn S Mendioro Darshan S Brar |
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| Institution: | 1.Plant Breeding, Genetics, and Biotechnology Division,International Rice Research Institute (IRRI),Metro Manila,Philippines;2.Laboratoire Génome et Développement des Plantes,Université de Perpignan,Perpignan,France;3.UMR de Génétique Végétale,INRA - Univ Paris-Sud - CNRS - AgroParisTech,Gif-sur-Yvette,France;4.Institute of Biological Sciences,University of the Philippines Los Ba?os,Los Ba?os,Philippines |
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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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