SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference

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dc.contributor.advisorKinnear, Craigen_ZA
dc.contributor.advisorMoller, Marloen_ZA
dc.contributor.advisorGlanzmann, Brigitteen_ZA
dc.contributor.authorEngelbrecht, Marius Adriaanen_ZA
dc.contributor.otherStellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences: Molecular Biology and Human Genetics.en_ZA
dc.date.accessioned2021-04-30T08:27:27Z
dc.date.available2021-04-30T08:27:27Z
dc.date.issued2021-03
dc.descriptionThesis (MSc)--Stellenbosch University, 2021.en_ZA
dc.description.abstractENGLISH ABSTRACT: The African buffalo (Syncerus caffer) is an important herd-based bovid in Africa, which is ubiquitous across almost the entire continent. These animals also act as a maintenance host for the ever-present threat that is bovine tuberculosis (bTB). The animal facilitates the spread and continued existence of the health problem that is bTB amongst wildlife and domestic cattle populations throughout Africa, causing problems in terms of conservation and economic loss. The disease is endemic to the southern part of Africa, especially South Africa, where two major national parks, The Kruger National Park (KNP) and Hluhluwe-iMfolozi Park (HiP), are host to it. There are also spill-over events of the disease from animals to humans, which is especially problematic in South Africa where tuberculosis (TB) in humans is already a major health concern. This study aimed to use 40 high-quality low-coverage African buffalo whole genome sequences in conjunction with a species-specific reference genome to create a panel of single nucleotide polymorphisms (SNPs) for use in further research in genetic association in buffalo bTB susceptibility. The sequences were from 40 Cape buffalo from 4 South African national parks, namely KNP, HiP and two bTB unexposed regions, the Mokala National Park (MNP) and Addo Elephant National Park (AENP). From this we produced a panel of 3698 high quality SNPs across 26 immune related genes in the African buffalo genome. One hundred and forty-three of these SNPs in three genes from the panel was used in a preliminary targeted association test with bTB exposure, which produced 10 SNPs associated with TB exposure. This may aid in future research and subsequent association studies.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Geen opsomming beskikbaaraf_ZA
dc.description.versionMastersen_ZA
dc.format.extent95 pagesen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/110431
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subjectKruger National Parken_ZA
dc.subjectUCTDen_ZA
dc.subjectAfrican buffaloen_ZA
dc.subjectBovine tuberculosisen_ZA
dc.subjectMolecular geneticsen_ZA
dc.subjectGenome researchen_ZA
dc.subjectHluhluwe-iMfolozi Parken_ZA
dc.titleSNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome referenceen_ZA
dc.typeThesisen_ZA
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