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.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 523470
Title Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
Author(s) Smitz, Nathalie; Hooft, W.F. van; Heller, Rasmus; Cornélis, Daniel; Chardonnet, Philippe; Kraus, Robert; Greyling, Ben; Crooijmans, R.P.M.A.; Michaux, Johan
DOI http://dx.doi.org/10.5061/dryad.q8q11
Department(s) Resource Ecology
PE&RC
Animal Breeding and Genetics
WIAS
Publication type Dataset
Publication year 2016
Keyword(s) population genomics - conservation - disease ecology - molecular markers - Syncerus caffer
Toponym Africa
Abstract This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed
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