Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
A genome wide scan for signatures of selection in six South African cattle populations
Thesis (PhD)--University of Pretoria, 2015.
Saved in:
| Other Authors: | |
|---|---|
| Format: | Thesis |
| Language: | English |
| Published: |
University of Pretoria
2015
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613577194504192 |
|---|---|
| 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 | © 2015 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 | Thesis (PhD)--University of Pretoria, 2015. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/50670 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:38:21.509Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| 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:2263/50670 A genome wide scan for signatures of selection in six South African cattle populations Van Marle-Koster, Este qwabes@arc.agric.za Maiwashe, A. Makina, Sithembile Olga UCTD Call rate Minor allele frequency Linkage disequilibrium Effective population size SNP makers Cattle breeds Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-12 Natural and agricultural sciences theses SDG-15 Thesis (PhD)--University of Pretoria, 2015. South African (SA) indigenous and locally developed cattle breeds possess adaptive traits that are usually associated with tolerance to various diseases, extreme temperatures and humidity and to change in the availability of feed. These breeds are also adapted to low-input management system and have shown the ability to survive, produce and reproduce under harsh environments. Thus, these breeds hold potential in the changing South African production environments. However, little is still known about the nature or extent of the genetic variation underlying these breeds. Therefore, in this study, the Bovine SNP50 BeadChip was used to characterize the genetic diversity and population structure of SA cattle breeds, determine the level of linkage disequilibrium and conduct a genome wide scan for signatures of selection among the Afrikaner (n=44), Nguni (n=54), Drakensberger (n=47), and Bonsmara (n=46) using the Angus (n=31) and Holstein (n=29) cattle as reference groups since they have been characterized in other countries using similar tools. The first experiment performed included the evaluation of the Bovine SNP50 BeadChip to determine its utility for genome wide studies of South African cattle. Results of this experiment revealed that over 50 % of the SNPs were polymorphic (e.g. Nguni = 35 843), indicating that the Bovine SNP50 assay would be useful for genome wide studies among South African cattle breeds. The genetic diversity and population structure analyses indicated that the Afrikaner cattle had the lowest level of genetic diversity (He=0.24) while the Drakensberger cattle (He=0.30) had the highest among indigenous and locally-developed breeds. As expected, the average genetic distance was the greatest between indigenous breeds and Bos taurus breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The analyses of the extent of linkage disequilibrium (LD) showed that Afrikaner, Angus and Holstein had higher LD compared to Nguni, Drakensberger and Bonsmara cattle at all tested genomic distances. The higher LD within the Afrikaner cattle suggested that this breed has experienced considerable selection forces in contrast to what is expected of indigenous breeds and would require lower marker (50 000) density relative to what will be required for the Nguni, Drakensberger (150 000) and Bonsmara (75 000) cattle for genome wide studies. Lastly, a genome wide scan for signatures of selection revealed a number of genes (KRT222, KRT24, KRT25, KRT26 and KRT27) and one heat shock protein (HSPB9) on chromosome (BTA) 19 at 41,447,971-41,926,734 bp in the Nguni that have been previously associated with adaptation to tropical environments in Zebu cattle. Furthermore, a number of genes associated with nervous system (WNT5B, FMOD, PRELP, ATP2B), immune response (CYM, CDC6, CDK10), production (MTPN, IGFBP4, TGFB1, AJAP1) and reproductive (ADIPOR2, OVOS2, RBBP8) performances were detected to be under selection in this study. The results presented on this thesis forms the basis for effective management of South African cattle breeds. tm2015 bs2026 Animal and Wildlife Sciences PhD Unrestricted SDG-02: Zero hunger SDG-12: Responsible consumption and production SDG-15: Life on land 2015-11-25T09:47:10Z 2015-11-25T09:47:10Z 2015/09/01 2015 Thesis Makina, SO 2015, A genome wide scan for signatures of selection in six South African cattle populations, PhD Thesis, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/50670> S2015 http://hdl.handle.net/2263/50670 en © 2015 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 Call rate Minor allele frequency Linkage disequilibrium Effective population size SNP makers Cattle breeds Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-12 Natural and agricultural sciences theses SDG-15 A genome wide scan for signatures of selection in six South African cattle populations |
| title | A genome wide scan for signatures of selection in six South African cattle populations |
| title_full | A genome wide scan for signatures of selection in six South African cattle populations |
| title_fullStr | A genome wide scan for signatures of selection in six South African cattle populations |
| title_full_unstemmed | A genome wide scan for signatures of selection in six South African cattle populations |
| title_short | A genome wide scan for signatures of selection in six South African cattle populations |
| title_sort | genome wide scan for signatures of selection in six south african cattle populations |
| topic | UCTD Call rate Minor allele frequency Linkage disequilibrium Effective population size SNP makers Cattle breeds 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/2263/50670 |