Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
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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Subjects: | L10 - Génétique et amélioration des animaux, http://aims.fao.org/aos/agrovoc/c_8355, http://aims.fao.org/aos/agrovoc/c_7265, http://aims.fao.org/aos/agrovoc/c_1432, |
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dig-cirad-fr-5813112022-04-15T14:10:28Z http://agritrop.cirad.fr/581311/ http://agritrop.cirad.fr/581311/ 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 Rasmus, Cornélis Daniel, Chardonnet Philippe, Kraus R., Greyling B.J., Crooijmans Richard, Groenen M., Michaux Johan. 2016. Mammalian Biology, 81 (6) : 595-603.https://doi.org/10.1016/j.mambio.2016.07.047 <https://doi.org/10.1016/j.mambio.2016.07.047> Researchers 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, Rasmus Cornélis, Daniel Chardonnet, Philippe Kraus, R. Greyling, B.J. Crooijmans, Richard Groenen, M. Michaux, Johan eng 2016 Mammalian Biology L10 - Génétique et amélioration des animaux Afrique occidentale Afrique australe Afrique centrale http://aims.fao.org/aos/agrovoc/c_8355 http://aims.fao.org/aos/agrovoc/c_7265 http://aims.fao.org/aos/agrovoc/c_1432 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/581311/7/1-s2.0-S1616504716300982-main.pdf text Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1016/j.mambio.2016.07.047 10.1016/j.mambio.2016.07.047 info:eu-repo/semantics/altIdentifier/doi/10.1016/j.mambio.2016.07.047 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1016/j.mambio.2016.07.047 |
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L10 - Génétique et amélioration des animaux http://aims.fao.org/aos/agrovoc/c_8355 http://aims.fao.org/aos/agrovoc/c_7265 http://aims.fao.org/aos/agrovoc/c_1432 L10 - Génétique et amélioration des animaux http://aims.fao.org/aos/agrovoc/c_8355 http://aims.fao.org/aos/agrovoc/c_7265 http://aims.fao.org/aos/agrovoc/c_1432 |
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L10 - Génétique et amélioration des animaux http://aims.fao.org/aos/agrovoc/c_8355 http://aims.fao.org/aos/agrovoc/c_7265 http://aims.fao.org/aos/agrovoc/c_1432 L10 - Génétique et amélioration des animaux http://aims.fao.org/aos/agrovoc/c_8355 http://aims.fao.org/aos/agrovoc/c_7265 http://aims.fao.org/aos/agrovoc/c_1432 Smitz, Nathalie Van Hooft, Pim Heller, Rasmus Cornélis, Daniel Chardonnet, Philippe Kraus, R. Greyling, B.J. Crooijmans, Richard Groenen, M. Michaux, Johan Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing |
description |
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. |
format |
article |
topic_facet |
L10 - Génétique et amélioration des animaux http://aims.fao.org/aos/agrovoc/c_8355 http://aims.fao.org/aos/agrovoc/c_7265 http://aims.fao.org/aos/agrovoc/c_1432 |
author |
Smitz, Nathalie Van Hooft, Pim Heller, Rasmus Cornélis, Daniel Chardonnet, Philippe Kraus, R. Greyling, B.J. Crooijmans, Richard Groenen, M. Michaux, Johan |
author_facet |
Smitz, Nathalie Van Hooft, Pim Heller, Rasmus Cornélis, Daniel Chardonnet, Philippe Kraus, R. Greyling, B.J. Crooijmans, Richard Groenen, M. Michaux, Johan |
author_sort |
Smitz, Nathalie |
title |
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing |
title_short |
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing |
title_full |
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing |
title_fullStr |
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing |
title_full_unstemmed |
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing |
title_sort |
genome-wide single nucleotide polymorphism (snp) identification and characterization in a non-model organism, the african buffalo (syncerus caffer), using next generation sequencing |
url |
http://agritrop.cirad.fr/581311/ http://agritrop.cirad.fr/581311/7/1-s2.0-S1616504716300982-main.pdf |
work_keys_str_mv |
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