Abstract
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.
Highlights
Sex chromosomes are 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
We applied our approach to refine the map of the Y chromosome of a dioecious plant, Silene latifolia, which has heteromorphic sex chromosomes (X and Y)
The non-recombining region includes at least two sex-determining loci, a gynoecium suppression function (GSF) and a stamen promoting function (SPF). These loci were initially inferred by crosses between dioecious plants and related species, and by studying deletions of parts of the Y chromosome found in asexual and hermaphroditic mutants; more recent work, with more flower phenotype mutations, confirmed these conclusions[12,13]
Summary
Sex chromosomes are 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. Radiation hybrid (RH) mapping has been very useful in mammals, such as humans[1] and dogs[2], and in other animals (e.g. the sea bream[3]) It is based on the frequencies of double-strand breaks between genetic or cytological markers after irradiation with a specific radiation dose[4], and the dose dependency prevents the use of deletion mutants from different experiments. The non-recombining region includes at least two sex-determining loci, a gynoecium suppression function (GSF) and a stamen promoting function (SPF) These loci were initially inferred by crosses between dioecious plants and related species, and by studying deletions of parts of the Y chromosome found in asexual and hermaphroditic mutants (deleted for SPF and GSF factors, respectively, as reviewed in ref 9); more recent work, with more flower phenotype mutations, confirmed these conclusions[12,13]. Such studies demonstrate that the Y has lost genes[25] and it is estimated that the coding sequences of as many as 23%
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