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Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa
Thesis (MScAgric)--Stellenbosch University, 2022.
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| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867614015751979008 |
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| access_status_str | Open Access |
| author | Malan, Isaack Nichol |
| author2 | Molotsi, Annelin H. |
| author_browse | Malan, Isaack Nichol Molotsi, Annelin H. |
| author_facet | Molotsi, Annelin H. Malan, Isaack Nichol |
| author_sort | Malan, Isaack Nichol |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125101 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:45:19.124Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125101 Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa Malan, Isaack Nichol Molotsi, Annelin H. Cloete, Schalk W. P. Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Science. Fat-tailed sheep -- South Africa Sheep breeds -- South Africa Sheep breeds -- Genetics Genomics -- Genome mapping Phylogeny -- Genetic aspects Farms, Small -- Economic aspects -- South Africa Rural development -- South Africa UCTD Thesis (MScAgric)--Stellenbosch University, 2022. ENGLISH ABSTRACT: Indigenous fat-tailed sheep breeds are primarily kept by rural peoples, especially in developing countries. These livestock species contribute to household income, is a source of food security, plays a role in social and crop production (fertilizer) systems. The diversity within these indigenous breeds allows them to be productive under harsh environmental conditions, thus genetic and phenotypic characterization is pivotal for future sustainable farming practices. The aim of this study was to elucidate the genetic structure of indigenous fat-tailed sheep in South Africa and to trace selection pressure applied to fat-tailed sheep for adaptation. The first objective was to elucidate the genetic variation and population structure of indigenous fat-tailed sheep in South Africa. The second objective was to determine if selection pressure has been placed on these indigenous sheep breeds for adaptation traits. The first objective was achieved by sampling blood from indigenous sheep breeds (30 Damara, 30 Pedi, 30 Zulu, 20 Meatmaster and 54 Karakul animals). The extracted DNA was genotyped using the OvineSNP50K BeadChip. Genotype data from 48 Namaqua Afrikaners and 98 Merinos were included for comparative purposes. Several genetic parameters were analysed to determine the genetic diversity within and between the sheep populations: observed heterozygosity (Ho), expected heterozygosity (He), inbreeding coefficients (F) and Linkage disequilibrium (LD). The highest and lowest observed heterozygosity was seen in the Pedi and Damara sheep (0.4 and 0.34 respectively). The Merino exhibited the highest expected heterozygosity of 0.38 and the Namaqua Afrikaner the lowest at 0.345. The highest LD was reported in the Namaqua Afrikaner at r²= 0.45 and the lowest LD was observed in the Merino at r²= 0.37. The population structure of the indigenous sheep breeds was studied by conducting a Principal Component Analysis (PCA), where PC1 (6.8%) and PC2 (5.0%) describes the total genetic variation. A Bayesian approach was used to calculate maximum likelihood estimates in the FastSTRUCTURE program, which elucidate the true ancestral populations (K= 8) of the sheep breeds. Lastly, through hapFLK analysis, Reynolds genetic distances between the different sheep populations were calculated and a neighbour-joining population tree was generated. These could be used to determine the relatedness and dissimilarities (dendogram) found between the indigenous fat-tailed sheep. A close relationship could be seen between the Zulu and Damara sheep breeds. Despite the lower diversity, the Namaqua Afrikaner displays the highest genetic distance from the other indigenous fat-tailed breeds. The Pedi and Karakul populations also exhibited distinct clustering and separation. Admixture within the Meatmaster breed with the Merino was observed. This is to be expected as the Merino could have been used as a parental breed in the make-up of this composite (Meatmaster) sheep. To determine selection sweeps in the indigenous sheep breeds, the hapFLK approach was used and 13 regions were found to be under selection, spanning a total of 11 chromosomes. The candidate genes associated with the SNPs of interest was linked to traits involved in metabolic process such as DNA synthesis and transcription (CEP41, TLL1, EIF1B, SCN5A, SCN8A, SCN10A, SCN11A), immune response (BPIFC, CLDN12, CLDN14, TRL4), ultraviolet exposure and thermoregulation (SLX4, ASCL4, KCNJ5, LAMB1, GPR26, CX3CR1), energy metabolism (MYH9) and meat production (PDEZA, UTRN). These candidate genes give an insight into the adaptive traits of indigenous sheep in South Africa and further genotyping is needed to elucidate more of the robust characteristics exhibited by these locally acclimated genetic resources. AFRIKAANSE OPSOMMING: Inheemse vetstertskaaprasse word hoofsaaklik deur klein-skaapboere aangehou, veral in ontwikkelende lande. Hierdie veespesies dra by tot huishoudelike inkomste, is 'n bron van voedselsekerheid, speel ' n rol in sosiale en gewasproduksie (kunsmis) stelsels. Die diversiteit binne hierdie inheemse rasse laat hulle toe om produktief te wees onder strawwe omgewingstoestande, dus is genetiese en fenotipiese karakterisering deurslaggewend vir toekomstige volhoubare boerderypraktyke. Die doel van hierdie studie was om die genetiese struktuur van inheemse vetstertskape in Suid-Afrika toe te lig en om seleksiedruk wat op vetstertskape toegepas word vir aanpassing op te spoor. Die eerste doelwit was om die genetiese variasie en populasiestruktuur van inheemse vetstertskape in Suid-Afrika toe te lig. Die tweede doelwit was om te bepaal of seleksiedruk op hierdie inheemse skaaprasse geplaas is vir aanpassingseienskappe. Die eerste doelwit is bereik deur bloedmonsters van inheemse skaaprasse (30 Damara-, 30 Pedi-, 30 Zoeloe-, 20 Meatmaster- en 54 Karakoel-diere) te neem. Die onttrekte DNA is genotipeer met behulp van die OvineSNP50K BeadChip. Genotipe data van 48 Namakwa-Afrikaners en 98 Merino's is vir vergelykende doeleindes ingesluit. Verskeie genetiese parameters is ontleed om die genetiese diversiteit binne en tussen die skaappopulasies te bepaal: waargenome heterosigositeit (Ho), verwagte heterosigositeit (He), intelingskoëffisiënte (F) en Koppelingsonewewig (LD). Die hoogste en laagste waargenome heterosigositeit is by die Pedi- en Damara-skape (0.4 en 0.34 onderskeidelik) gesien. Die Merino het die hoogste verwagte heterosigositeit van 0.38 getoon en die Namaqua Afrikaner die laagste op 0.345. Die hoogste LD is by die Namaqua Afrikaner by r2= 0.45 gerapporteer en die laagste LD is in die Merino by r2= 0.37 waargeneem. Die bevolkingstruktuur van die inheemse skaaprasse is bestudeer deur 'n Hoofkomponent Analise (PCA) uit te voer, waar PC1 (6.8%) en PC2 (5.0%) die totale genetiese variasie beskryf. 'n Bayesiese benadering is gebruik om maksimum waarskynlikheid skattings te bereken in die FastSTRUCTURE program, wat die ware voorvaderlike populasies (K= 8) van die skaaprasse toelig. Laastens, deur middel van hapFLK -analise, is Reynolds genetiese afstande tussen die verskillende skaappopulasies bereken en 'n naburige populasieboom is gegenereer. Dit kan gebruik word om die verwantskap en ongelykhede (dendogram) wat tussen die inheemse vetstertskape gevind word, te bepaal. ’n Noue verhouding kon tussen die Zoeloe- en Damara-skaaprasse gesien word. Ten spyte van die laer diversiteit vertoon die Namakwa-Afrikaner die hoogste genetiese afstand van die ander inheemse vetstertrasse. Die Pedi- en Karakoel-bevolkings het ook duidelike groepering en skeiding getoon. Vermenging binne die Meatmaster-ras met die Merino is waargeneem. Dit is te verwagte aangesien die Merino as ouerras in die samestelling van hierdie saamgestelde (Meatmaster) skaap gebruik was. Om seleksiedruk in die inheemse skaaprasse te bepaal, is die hapFLK- benadering gebruik en daar is gevind dat 13 streke onder seleksie is, wat oor 'n totaal van 11 chromosome strek. Die kandidaatgene wat met die SNP's van belang geassosieer word, is gekoppel aan eienskappe betrokke by metaboliese proses soos DNA-sintese en transkripsie (CEP41, TLL1, EIF1B, SCN5A, SCN8A, SCN10A, SCN11A), immuunrespons (BPIFC, CLDN12, CLDN14, TRL4), ultravioletblootstelling en termoregulering (SLX4, ASCL4, KCNJ5, LAMB1, GPR26, CX3CR1), energiemetabolisme (MYH9) en vleisproduksie (PDEZA, UTRN). Hierdie kandidaatgene gee 'n insig in die aanpasbare eienskappe van inheemse skape in Suid-Afrika en verdere genotipering is nodig om meer van die robuuste eienskappe wat deur hierdie plaaslik geakklimatiseerde genetiese hulpbronne vertoon word, toe te lig. Masters 2022-03-10T07:38:14Z 2022-04-29T12:54:00Z 2022-03-10T07:38:14Z 2022-03 Thesis http://hdl.handle.net/10019.1/125101 en_ZA Stellenbosch University viii, 64 pages : illustrations (some color) application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Fat-tailed sheep -- South Africa Sheep breeds -- South Africa Sheep breeds -- Genetics Genomics -- Genome mapping Phylogeny -- Genetic aspects Farms, Small -- Economic aspects -- South Africa Rural development -- South Africa UCTD Malan, Isaack Nichol Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa |
| title | Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa |
| title_full | Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa |
| title_fullStr | Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa |
| title_full_unstemmed | Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa |
| title_short | Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa |
| title_sort | analysis of genetic diversity and population structure of indigenous fat tailed sheep in south africa |
| topic | Fat-tailed sheep -- South Africa Sheep breeds -- South Africa Sheep breeds -- Genetics Genomics -- Genome mapping Phylogeny -- Genetic aspects Farms, Small -- Economic aspects -- South Africa Rural development -- South Africa UCTD |
| url | http://hdl.handle.net/10019.1/125101 |
| work_keys_str_mv | AT malanisaacknichol analysisofgeneticdiversityandpopulationstructureofindigenousfattailedsheepinsouthafrica |