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SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference
Thesis (MSc)--Stellenbosch University, 2021.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2021
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| _version_ | 1867613911536107520 |
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| access_status_str | Open Access |
| author | Engelbrecht, Marius Adriaan |
| author2 | Kinnear, Craig |
| author_browse | Engelbrecht, Marius Adriaan Kinnear, Craig |
| author_facet | Kinnear, Craig Engelbrecht, Marius Adriaan |
| author_sort | Engelbrecht, Marius Adriaan |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2021. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/110431 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:40.048Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/110431 SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference Engelbrecht, Marius Adriaan Kinnear, Craig Moller, Marlo Glanzmann, Brigitte Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences: Molecular Biology and Human Genetics. Kruger National Park UCTD African buffalo Bovine tuberculosis Molecular genetics Genome research Hluhluwe-iMfolozi Park Thesis (MSc)--Stellenbosch University, 2021. ENGLISH 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. AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar Masters 2021-04-30T08:27:27Z 2021-04-30T08:27:27Z 2021-03 Thesis http://hdl.handle.net/10019.1/110431 en_ZA Stellenbosch University 95 pages application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Kruger National Park UCTD African buffalo Bovine tuberculosis Molecular genetics Genome research Hluhluwe-iMfolozi Park Engelbrecht, Marius Adriaan SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference |
| title | SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference |
| title_full | SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference |
| title_fullStr | SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference |
| title_full_unstemmed | SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference |
| title_short | SNP discovery and selection in Cape buffalo for bTB association study, using an African buffalo genome reference |
| title_sort | snp discovery and selection in cape buffalo for btb association study using an african buffalo genome reference |
| topic | Kruger National Park UCTD African buffalo Bovine tuberculosis Molecular genetics Genome research Hluhluwe-iMfolozi Park |
| url | http://hdl.handle.net/10019.1/110431 |
| work_keys_str_mv | AT engelbrechtmariusadriaan snpdiscoveryandselectionincapebuffaloforbtbassociationstudyusinganafricanbuffalogenomereference |