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Genomic characterization of autozygosity in South African Merino sheep
Dissertation (MSc (Animal Science))--University of Pretoria, 2024.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2025
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| _version_ | 1867613652911128576 |
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| access_status_str | Open Access |
| author2 | Visser, Carina |
| author_browse | Visser, Carina |
| author_facet | Visser, Carina |
| collection | Thesis |
| dc_rights_str_mv | © 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Dissertation (MSc (Animal Science))--University of Pretoria, 2024. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/100913 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:39:33.692Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/100913 Genomic characterization of autozygosity in South African Merino sheep Visser, Carina micah.forsythe@gmail.com Lashmar, Simon Federick Forsythe, Micah Ellen UCTD Sustainable Development Goals (SDGs) Genetic parameters Inbreeding Runs of homozygosity Small stock Autozygosity Dissertation (MSc (Animal Science))--University of Pretoria, 2024. The South African (SA) Merino is a medium-framed, white wool breed, and is one of the most prominent breeds in the SA sheep industry. Because of its local importance, the SA Merino is the only SA sheep breed with sufficient single nucleotide polymorphism (SNP) genotypes to implement genomic selection (GS), and this provides comprehensive sample size (i.e. number) and composition (i.e. representation) of genotypic data to study the breed’s diversity and inbreeding. These estimates play a vital role as tools for breeders to maintain genetic progress whilst conserving diversity within flocks. This study aimed to perform a homozygosity-focused SNP investigation of the past and present inbreeding and autozygosity levels in the SA Merino sheep breed. A total of 1 738 animals (1 567 females and 171 males), genotyped using different versions of the Illumina® Ovine 50K SNP panel, were used to estimate various proxy-indicator parameters of genomic variability, runs of homozygosity (ROH) and heterozygosity-rich region (HRR) profiles, and conserved ROH-based selection signatures for the SA Merino breed. The reported observed (HO=0.351± 0.018) and expected (HE=0.365± 0.0001) heterozygosity, and their relationship to one another (i.e. HO<HE), as well as SNP-based inbreeding coefficient (FSNP=0.037±0.05) and effective population size (most recent Ne=305) indicated a slight loss in within-population genetic diversity, and low inbreeding levels. Additionally, high MAF values (0.2750.14) and LD (0.365±0.180) were observed within the SA Merino population. The autozygosity analysis identified a total of 43 147 ROH with a mean chromosome-wide ROH length per chromosome of 6.53Mb, and a corresponding mean FROH of 0.074±0.04 that further supported low inbreeding. Conserved ROH revealed selection signatures harbouring a total of 275 protein-coding genes (within a threshold of 16.4%) associated with various functions in sheep involving reproduction, fibre formation, and inflammatory responses. Overall, the results from this study conveyed that mating programs and intense selection are well managed within the breeding objectives of SA Merino sheep, and that sufficient levels of genetic diversity exists to facilitate sustainable production and genetic improvement in the future. Animal and Wildlife Sciences Msc (Animal Science) Unrestricted Faculty of Natural and Agricultural Sciences None 2025-02-14T11:15:56Z 2025-02-14T11:15:56Z 2025-04 2024-11 Dissertation * A2025 http://hdl.handle.net/2263/100913 https://doi.org/10.25403/UPresearchdata.28414508 en © 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf University of Pretoria |
| spellingShingle | UCTD Sustainable Development Goals (SDGs) Genetic parameters Inbreeding Runs of homozygosity Small stock Autozygosity Genomic characterization of autozygosity in South African Merino sheep |
| title | Genomic characterization of autozygosity in South African Merino sheep |
| title_full | Genomic characterization of autozygosity in South African Merino sheep |
| title_fullStr | Genomic characterization of autozygosity in South African Merino sheep |
| title_full_unstemmed | Genomic characterization of autozygosity in South African Merino sheep |
| title_short | Genomic characterization of autozygosity in South African Merino sheep |
| title_sort | genomic characterization of autozygosity in south african merino sheep |
| topic | UCTD Sustainable Development Goals (SDGs) Genetic parameters Inbreeding Runs of homozygosity Small stock Autozygosity |
| url | http://hdl.handle.net/2263/100913 https://doi.org/10.25403/UPresearchdata.28414508 |