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Sci Rep. 2016 Jan 8;6:18917. doi: 10.1038/srep18917.

A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome.

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RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Department of Integrated Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
Institute of Evolutionary Biology, University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JT, UK.


Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving "the travelling salesman problem", and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map.

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