Finding selection footprints in the swine genome using massive parallel sequencing.

A.J. Amaral, L. Feretti, H.J.W.C. Megens, R.P.M.A. Crooijmans, H. Nie, M.A.M. Groenen

Research output: Contribution to conferencePoster

Abstract

We investigated whether selection footprints can be identified from GA (Genome analyzer) sequences generated from pooled Reduced Representation Libraries and covering approximately 2% of the genome of Large White, Landrace, Pietrain, Duroc and Wild Boar. Methods were developed to estimate Nucleotide Diversity (ND) considering that, GA sequences were obtained from pooled DNA, singletons were removed and the sequencing error rate. The average ND ranged from 0.0008 to 0.002 depending on chromosome and breed. Genomic locations that have been, putatively, under selection were identified. We found signals of positive selection on SSC8 in the region containing the KIT gene, for white breeds but not for Duroc and Wild Boar. Signals of balancing selection were found for regions on SSC7 containing genes from the MHC complex and from the olfactory receptors complex. Enrichment analysis of KEGG-pathways showed that for regions under positive selection, swine breeds showed higher enrichment of pathways related to growth whereas Wild Boar showed higher enrichment of pathways related to immunity and robustness. Balancing selection resulted in the significant enrichment of pathways related to the olfactory receptors activities in all swine breeds and Wild Boar. Our results raise the possibility of using GA sequencing of pools for identification of selection footprints and present the first global map of regions under selection in the swine genome
Original languageEnglish
Publication statusPublished - 2009
EventNGS2009 conference on Next generation sequencing: Challenges and opportunities -
Duration: 1 Oct 20093 Oct 2009

Conference

ConferenceNGS2009 conference on Next generation sequencing: Challenges and opportunities
Period1/10/093/10/09

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    Amaral, A. J., Feretti, L., Megens, H. J. W. C., Crooijmans, R. P. M. A., Nie, H., & Groenen, M. A. M. (2009). Finding selection footprints in the swine genome using massive parallel sequencing.. Poster session presented at NGS2009 conference on Next generation sequencing: Challenges and opportunities, .