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Genomic characterisation of the South African Wagyu populations
Dissertation (MSc (Agric) Animal Science: Animal Breeding and Genetics))--University of Pretoria, 2024.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2024
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| _version_ | 1867613627922513920 |
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| access_status_str | Open Access |
| author2 | Van Marle-Koster, Este |
| author_browse | Van Marle-Koster, Este |
| author_facet | Van Marle-Koster, Este |
| 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 (Agric) Animal Science: Animal Breeding and Genetics))--University of Pretoria, 2024. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/98829 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:39:09.918Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| 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:2263/98829 Genomic characterisation of the South African Wagyu populations Van Marle-Koster, Este u18016635@tuks.co.za Visser, Carina Pieterse, Tanya UCTD Sustainable Development Goals (SDGs) Wagyu cattle Diversity Inbreeding Japanese Black Akaushi Dissertation (MSc (Agric) Animal Science: Animal Breeding and Genetics))--University of Pretoria, 2024. A genomic characterisation was performed on South African (SA) Wagyu cattle based on pedigree and genomic data. The pedigree-based analysis was performed on records of SA animals between 2000 and 2022, with a minimum of 50% Akaushi (AK: 5 108), Japanese Black (JB: 42 237) and combined Wagyu genetic content (AK and JB combined > 50%; 51 632). The genotypic analysis was performed on the available single nucleotide polymorphism (SNP) genotypes of fullblood and purebred animals. Subtotals of 205 and 439 genotypes were available for the SA Akaushi and Japanese Black Wagyu breeds, while 731 Australian Japanese Black genotypes were made available due to potential genetic linkage between the Japanese Black populations. The genotypes were generated using the Unistel BovineSNP50 v3 BeadChip or Neogen GGP Bovine 100K SNP array. The pedigree-based population analysis was performed using PopReport (Groeneveld et al., 2009). Pedigree completeness, generation interval, average inbreeding and effective population size were evaluated. Pedigree completeness for the SA Wagyu population was low, with an overall completeness of 33.14%. There is a positive trend for an increase in pedigree recording over the past 6 generations. Genotypic analysis with the use of Principal Component analysis (PCA) indicated that the SA Akaushi and Japanese Black populations are two separate populations, and they were treated separately in the subsequent genomic analysis. The population structure investigated with the use of ADMIXTURE (Alexander et al., 2009) supported the results of the PCA. Additionally, genomic parameters indicated a slightly higher genomic variation (He = 0.30) within the SA Japanese Black compared to the Australian subset (He = 0.28). Inbreeding coefficients were negative for the Akaushi and both Japanese Black subsets. The genomic inbreeding (FROH) revealed higher levels of inbreeding in the SA Akaushi population (0.17) in comparison to the Japanese Black populations from SA (0.07) and Australia (0.09), respectively. This study provides a benchmark of the population structure and genomic diversity of the SA Wagyu. It is important to note the distinct genomic difference between the Akaushi and Japanese Black Wagyu and this information can be applied in future genetic management and selection of SA Wagyu. Animal and Wildlife Sciences MSc (Agric) Animal Science: Animal Breeding and Genetics Unrestricted Faculty of Natural and Agricultural Sciences SDG-15: Life on land 2024-10-30T07:15:24Z 2024-10-30T07:15:24Z 2025-04-15 2024-10-02 Dissertation * A2025 http://hdl.handle.net/2263/98829 10.25403/UPresearchdata.27231888 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) Wagyu cattle Diversity Inbreeding Japanese Black Akaushi Genomic characterisation of the South African Wagyu populations |
| title | Genomic characterisation of the South African Wagyu populations |
| title_full | Genomic characterisation of the South African Wagyu populations |
| title_fullStr | Genomic characterisation of the South African Wagyu populations |
| title_full_unstemmed | Genomic characterisation of the South African Wagyu populations |
| title_short | Genomic characterisation of the South African Wagyu populations |
| title_sort | genomic characterisation of the south african wagyu populations |
| topic | UCTD Sustainable Development Goals (SDGs) Wagyu cattle Diversity Inbreeding Japanese Black Akaushi |
| url | http://hdl.handle.net/2263/98829 |