Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Record number 402816
Title The Porcine HapMap Project: Genome-Wide Assessment Of Nucleotide Diversity, Haplotype Diversity And Footprints Of Selection In The Pig
Author(s) Groenen, M.A.M.; Amaral, A.J.; Megens, H.J.W.C.; Larson, B.A.; Archibald, A.L.; Muir, W.M.; Malhi, Y.; Crooijmans, R.P.M.A.; Ferretti, L.; Perez-Encizo, M.; Schook, L.B.
Source In: Book of Abstracts of the Plant and Animal Genome XVIII Conference, San Diego, California, USA, 9-13 Januari 2010. - - p. w609 - w609.
Event Plant and Animal Genome XVIII Conference, San Diego, California, USA, 2010-01-09/2010-01-13
Department(s) Animal Breeding and Genetics
WIAS
Publication type Abstract in scientific journal or proceedings
Publication year 2010
Abstract The Porcine HapMap Consortium The pig has a complex and long history of domestication and breed formation and has been domesticated independently multiple times and has likely experienced introgression of local Wild boar after the spread of agriculture. Using the Illumina GA sequencing platform thousand s of SNPs were identified in the porcine genome and used these to develop the Illumin porcine 60K iSelect Beadchip. This chip has enabled whole-genome characterization of linkage disequilibrium and haplotype structure in commercial and local breeds and comparison with the Wild boar. The chip has also allowed an investigation into whole-genome patterns of variation, including signatures of selection associated with domestication and breed formation as well as elucidating demographic events such as population bottlenecks, and providing insights into the complex origin of domesticated populations by examining patterns of haplotype sharing. Signatures of selection were also identified using Illumina short read sequences generated from pooled reduced representation libraries of different breeds and covering approximately 2% of the genome. Signals of positive selection were identified and a GO term/KEGG pathway enrichment analysis provided evidence for specific gene families under selection in domesticated pigs and Wild boar. Currently approximately 2,000 pigs were been genotyped with the porcine 60K beadchip, including approximatley 50 pig breeds, and about 20 different Wild boar populations distributed throughout Eurasia. In addition, museum and archeological samples were included to provide a wider insight into domestication and geographic history. Inclusion of a range of other Suidae as outgroup species, supported an estimation of ancestral alleles and the origin and relative age of the porcine SNPs.
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