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 |
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Authors: | Beng-Kah Song Ingo Hein Arnis Druka Robbie Waugh David Marshall Kalaivani Nadarajah Soon-Joo Yap Wickneswari Ratnam |
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Institution: | (1) School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia;(2) Genome Dynamics Program, Scottish Crop Research Institute, Dundee, DD2 5DA, UK;(3) School of BioScience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia;(4) School of Arts and Sciences, Monash University, Sunway Campus, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor, Malaysia;(5) Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor Darul Ehsan, Malaysia |
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Abstract: | 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.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Oryza rufipogon Yield QTL yld1 1 Comparative sequence analysis Microcolinearity |
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