Veterinary Science Collected Works - Research Publications
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ItemNo Preview AvailableA Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds(PUBLIC LIBRARY SCIENCE, 2009-03-03)The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.
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ItemNo Preview AvailableA presentation of the differences between the sheep and goat genetic maps(E D P SCIENCES, 2005)The current autosomal version (4.2) of the sheep genetic map comprises 1175 loci and spans approximately 3540 cM. This corresponds to almost complete coverage of the sheep genome. Each chromosome is represented by a single linkage group, with the largest gap between adjacent loci being 19.8 cM. In contrast the 1998 goat genetic map (the most recently published) is much less well developed spanning 2737 cM and comprising only 307 loci. Only one of the goat chromosomes appears to have complete coverage (chromosome 27), and 16 of the chromosomes are comprised of two or more linkage groups, or a linkage group and one or more unlinked markers. The two maps share 218 loci, and the maps have been aligned using the shared loci as reference points. Overall there is good agreement between the maps in terms of homologous loci mapping to equivalent chromosomes in the two species, with only four markers mapping to non-equivalent chromosomes. However, there are lots of inversions in locus order between the sheep and goat chromosomes. Whilst some of these differences in locus order may be genuine, the majority are likely to be a consequence of the paucity of genetic information for the goat map.
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ItemUsing comparative genomics to reorder the human genome sequence into a virtual sheep genome(BMC, 2007)BACKGROUND: Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? RESULTS: A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser. CONCLUSION: We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited.