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A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle
Dissertation (Msc Agric Animal Science (Animal Breeding and Genetics))--University of Pretoria, 2020.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2020
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| _version_ | 1867613564168044544 |
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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 | © 2019 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, 2020. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/75190 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:38:08.659Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| 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:2263/75190 A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle Van Marle Koster, Este u14108934@tuks.co.za van der Westhuizen, Robert Reding, Jason Jack UCTD Genomics Genome-wide association study (GWAS) Fertility traits Maternal traits Bonsmara cattle Quantitative trait loci Single nucleotide polymorphisms Genomic selection Calving interval Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-08 Natural and agricultural sciences theses SDG-12 Dissertation (Msc Agric Animal Science (Animal Breeding and Genetics))--University of Pretoria, 2020. Reproductive wastage is of major economic importance and limits overall herd efficiency. Fertility traits are lowly heritable but are an essential component in selection programs for the genetic improvement of all livestock species. In order to gain a better understanding of the underlying genetic basis of these traits a GWAS was conducted to investigate fertility and maternal traits within the SA Bonsmara breed. Traits of interest were age at first calving (AFC), inter-calving period (ICP), scrotal circumference (SC) and weaning weight maternal (WWMAT). Estimated breeding values, pedigrees and genotypes for 3 291 SA Bonsmara animals were available for the study. Three different commercial arrays underwent quality control (QC), principal component analysis (PCA), with the amalgamation of the three arrays via imputation to a density of 128 793 SNPs and finally an association analysis by single SNP regression. Gene annotation was done for significant SNPs (≤1x10-8), with four associated with ICP (BTA 4, BTA11, BTA17, BTA19), twenty with AFC (BTA1, BTA2, BTA4, BTA5, BTA7, BTA8, BTA9, BTA11, BTA12, BTA16, BTA20, BTA24, BTA27, BTA28, BTA29), twenty-two with SC (BTA1, BTA2, BTA3, BTA4, BTA5, BTA6, BTA8, BTA10, BTA11, BTA15, BTA16, BTA20, BTA22, BTA24, BTA26, BTA28) and forty-four with WWMAT on all chromosomes except BTA10, BTA13, BTA16, BTA17, BTA23, BTA24, BTA25 and BTA26. The three SNPs significantly associated with AFC on BTA3 were all in gene regions. Of the six SNPs associated with WWMAT on BTA15, five were identified in four genes, with two SNPs annotating to the same gene (LRRC4C). Three genes for SC, eight genes for AFC and nineteen genes for WWMAT were identified. Genes associated with SC (PPP3CA), AFC (AKT3, GRM8, KIF1B, OVOS2) and WWMAT (BMP1, LRRC4C, MACROD1, RBM47, THSD7B) were reported for cattle in other studies. Genes associated with AFC (AKT3; BTA16) and SC (PPP3CA, TRPM6; BTA6, BTA8) where shown to share serine/threonine biological pathway processes. Chromosomes and SNPs that yielded novel associations with previously uncharacterised genes and previously not reported in literature may possibly be unique to the SA Bonsmara beef breed and will require further investigation. bs2026 Animal and Wildlife Sciences MsAgric Animal Breeding and Genetics Unrestricted SDG-02: Zero hunger SDG-08: Decent work and economic growth SDG-12: Responsible consumption and production 2020-07-13T14:02:36Z 2020-07-13T14:02:36Z 2020 2020 Dissertation * S2019 http://hdl.handle.net/2263/75190 en © 2019 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 Genomics Genome-wide association study (GWAS) Fertility traits Maternal traits Bonsmara cattle Quantitative trait loci Single nucleotide polymorphisms Genomic selection Calving interval Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-08 Natural and agricultural sciences theses SDG-12 A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle |
| title | A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle |
| title_full | A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle |
| title_fullStr | A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle |
| title_full_unstemmed | A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle |
| title_short | A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle |
| title_sort | genome wide association study of fertility and maternal traits in south african bonsmara cattle |
| topic | UCTD Genomics Genome-wide association study (GWAS) Fertility traits Maternal traits Bonsmara cattle Quantitative trait loci Single nucleotide polymorphisms Genomic selection Calving interval Natural and agricultural sciences theses SDG-02 Natural and agricultural sciences theses SDG-08 Natural and agricultural sciences theses SDG-12 |
| url | http://hdl.handle.net/2263/75190 |