Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
smitz, nathalie; Van Hooft, pim; Heller, Rasmuset al.
[en] 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.
Disciplines :
Zoology
Author, co-author :
smitz, nathalie
Van Hooft, pim
Heller, Rasmus
Cornelis, Daniel
Chardonnet, Philippe
Kraus, Robert
Greyling, Ben
Crooijmans, Richard
Groenen, Martien
Michaux, Johan ; Université de Liège > Département des sciences de la vie > Génétique et physiologie des microalgues
Language :
English
Title :
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
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