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SNP-based genetic diversity and population structure of South African beef cattle breeds
Dissertation (MSc (Agric (Animal Breeding and Genetics))--University of Pretoria, 2021.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2022
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| _version_ | 1867613633907785728 |
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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 | © 2022 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 Breeding and Genetics))--University of Pretoria, 2021. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/83546 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:39:15.557Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| 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:2263/83546 SNP-based genetic diversity and population structure of South African beef cattle breeds Visser, Carina taylortonkin@gmail.com Van Marle-Koster, Este Tonkin, Taylor Animal Breeding and Genetics UCTD SNP (Single Nucleotide Polymorphism) Genetic diversity Population structure Beef cattle breeds Heterozygosity Allelic richness Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-12 Natural and agricultural sciences theses SDG-15 Dissertation (MSc (Agric (Animal Breeding and Genetics))--University of Pretoria, 2021. Evaluation of genetic diversity in cattle populations is important to understand breed structure and for maintaining diversity. The aim of this study was to assess SNP based genomic diversity and population structure of eight South African beef cattle breeds. In this study 2110 beef cattle genotypes, generated within the BGP, representing eight South African beef cattle breeds (Bonsmara, Beefmaster, Boran, Charolais, Hereford, Drakensberger, Nguni and Tuli) were included for analyses. Genotypic data were generated using the GGP 150k SNP array for all registered, genotyped animals participating in Logix Beef Recording. PLINK was used to estimate genetic diversity parameters within populations and biological types. GCTA and ADMIXTURE were used for population structure analysis. SNeP was used to estimate effective population size for all populations. Results indicated limited loss of heterozygosity for the Beefmaster, Boran, Drakensberg and Hereford breeds (𝐻𝑒>𝐻𝑜) and no loss of heterozygosity for Bonsmara, Charolais and Nguni breeds. Results further indicated no loss in genetic diversity for all eight populations. The eight populations were grouped into specific biological types namely indigenous (Drakensberger, Nguni and Tuli), composite (Beefmaster and Bonsmara) and exotic types (Boran, Charolais and Hereford) and population diversity parameters were estimated. Analysis of the percentage of low-MAF SNP (MAF<0.05) was done and revealed the indigenous breed group had the highest percentage of low-MAF SNP across the genome. Inbreeding estimates based on 𝐹𝐼𝑆 and 𝐹𝑅𝑂𝐻 indicated limited inbreeding across the populations (𝐹𝐼𝑆:-0.009 to 0.016 and 𝐹𝑅𝑂𝐻 : 0.001-0.005). ROH analysis revealed that any inbreeding was due to ancient inbreeding, based upon the high number of ROH segments that had a length of between 0 and 3.9 MB. Effective population size (𝑁𝑒) analysis showed a decline in the 𝑁𝑒 for all eight breeds. A principal component analysis (PCA) and admixture plot identified eight distinctive breeds with some admixture present. The indigenous populations clustered together due to common ancestry and time divergence. The study concluded that they SA beef populations in this study exhibit moderate to high levels of genetic diversity with low inbreeding. SA Studbook bs2026 Animal and Wildlife Sciences MSc Agric (Animal Breeding and Genetics) Unrestricted SDG-02: Zero hunger SDG-12: Responsible consumption and production SDG-15: Life on land 2022-02-01T08:20:58Z 2022-02-01T08:20:58Z 2022 2021-11 Dissertation * A2022 http://hdl.handle.net/2263/83546 en © 2022 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 | Animal Breeding and Genetics UCTD SNP (Single Nucleotide Polymorphism) Genetic diversity Population structure Beef cattle breeds Heterozygosity Allelic richness Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-12 Natural and agricultural sciences theses SDG-15 SNP-based genetic diversity and population structure of South African beef cattle breeds |
| title | SNP-based genetic diversity and population structure of South African beef cattle breeds |
| title_full | SNP-based genetic diversity and population structure of South African beef cattle breeds |
| title_fullStr | SNP-based genetic diversity and population structure of South African beef cattle breeds |
| title_full_unstemmed | SNP-based genetic diversity and population structure of South African beef cattle breeds |
| title_short | SNP-based genetic diversity and population structure of South African beef cattle breeds |
| title_sort | snp based genetic diversity and population structure of south african beef cattle breeds |
| topic | Animal Breeding and Genetics UCTD SNP (Single Nucleotide Polymorphism) Genetic diversity Population structure Beef cattle breeds Heterozygosity Allelic richness Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-12 Natural and agricultural sciences theses SDG-15 |
| url | http://hdl.handle.net/2263/83546 |