Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Publication Type:Journal Article
Year of Publication:2016
Authors:N. Smitz, Van Hooft, P., Heller, R., Cornélis, D., Chardonnet, P., Kraus, R., Greyling, B., Crooijmans, R., Groenen, M., Michaux, J.
Journal:Mammalian Biology - Zeitschrift für Säugetierkunde
Pagination:595 - 603
Keywords:Molecular markers

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 İI\} 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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Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith