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A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes
Thesis (MScAgric)--Stellenbosch University, 2023.
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| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2023
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| _version_ | 1867614134217998336 |
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| access_status_str | Open Access |
| author | Old, Jessica Anne |
| author2 | Dzama, Kennedy |
| author_browse | Dzama, Kennedy Old, Jessica Anne |
| author_facet | Dzama, Kennedy Old, Jessica Anne |
| author_sort | Old, Jessica Anne |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2023. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/127112 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:47:12.516Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/127112 A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes Old, Jessica Anne Dzama, Kennedy Molotsi, Annelin H. Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Science. Cattle -- Breeding -- Genetic aspects Genotype-environment interaction Genomics Copy number variations (CNV) UCTD Thesis (MScAgric)--Stellenbosch University, 2023. ENGLISH ABSTRACT: With an ever-increasing demand for milk and meat products, and with climate change posing a threat to the productive efficacy of cattle across the globe, there is a need for the application of genomic tools for animal breeding. The valuable genomic variation exhibited in cattle is important for identifying major genes and quantitative trait loci (QTL), to be used as molecular markers in the genomic selection of animals. One of the key steps of selective breeding in cattle is the characterisation of genetic variation responsible for phenotypic differences. Copy number variations (CNVs), such as duplications, deletions, and insertions, are increasingly being shown to be one of the main contributors to genomic diversity and subsequent phenotypic differences observed among animals. Copy number variation can cause major changes in gene expression, phenotypic traits, and evolutionary adaptation, through gene dosage and transcript structure alterations. Several CNV- based studies have identified gene variations that could potentially be responsible for the phenotypic differences, but the sheer number of studies on this topic makes it difficult for one to come to a definite conclusion. This systematic review summarised the relevant findings of cattle CNV research, and identified the important genes involved therewith, to help researchers remain up to date with current and ongoing research in cattle-CNV studies. This review revealed that cattle CNV research has increased considerably since 2008. The extent and distribution of the publications reflect the worldwide growing importance of understanding the cattle genome for genetic improvement of livestock. However, there is a lack of research in developing countries, a lack of emphasis on Bos indicus (12%) and Bos taurus africanus (4%) cattle, and a lack of standardised reporting across cattle CNV studies. Copy number variations can alter the gene expression and consequently influence phenotypic expression. This systematic review identified several important CNV-related genes in the published articles that influence economically important traits in cattle. These genes were related to adaptation and immunity (ABCC4, BOLA gene family, IGLL1, OR family, WC1, ZNF280B, BSP30A, DEFB, ULBP gene family, CATHL gene family, and HSP gene family), milk yield, milk composition and reproduction (DGAT1, IFNT, PAG, PRAME, PRL, AP3B1, IGLL1, SLC27A6, ITFG1, MTHFSD, PRP, and PTK2), meat yield, meat quality and growth (IGF2, PLA2G2D, CAST, IGF1R, APOL3, PTPRC, KCNJ12, CAPN1, AGBL3, CTNNA1, MSTN, ADRA1B, ATRN, LRRC49, MYH3, SORCS2, and TG), feed efficiency (PRKG1, FABP2, and EIF2S1), and coat colour, coat patterns and hair morphology (KIT, AP3B1, MC1R, PRLR, and FGF18). This knowledge is relevant from a molecular perspective to the practical application in animal breeding, and offers breeders the means to consider genomic selection of animals at a younger age. The productive efficacy of cattle is vulnerable, thus, the use of molecular assisted selective breeding is essential for overcoming current and future challenges in cattle productivity. AFRIKAANSE OPSOMMING: Met ʼn al-toenemende aanvraag vir suiwel en vleis produkte, en met klimaatsverandering wat regoor die wêreld ʼn bedreiging inhou vir die produktiewe doeltreffendheid van beeste, is daar ʼn behoefte aan die toepassing van genomiese hulpbronne vir diere teling. Die waardevolle genomiese variasie wat in beeste waargeneem is, is belangrik vir die identifisering van hoof gene en kwantitatiewe eienskap loci, wat dan gebruik kan word as molekulêre merkers in die genomiese seleksie van diere. Een van die belangrikste stappe van selektiewe teling in beeste is die karakterisering van geneties variasie wat verantwoordelik is vir fenotipies verskille. Kopie Getal Variasies (KGV’s), soos duplikasies, verwyderde gene en invoegings, word toenemend geïdentifiseer as een van die hoof bydraers tot genomiese diversiteit en die daaropvolgende fenotipiese verskille wat tussen diere waargeneem word. KGV’s kan groot veranderinge in geen uitdrukking, fenotipiese eienskappe en evolusionêre aanpassing veroorsaak. Hierdie veranderinge is as gevolg van geen dosis en transkripsie struktuur veranderinge. Verskeie KGV-gebaseerde studies het geen variasies, wat moontlik vir die fenotipiese verskille verantwoordelik kan wees, geïdentifiseer. Maar die blote aantal studies op hierdie onderwerp maak dit moeilik om tot ʼn definitiewe gevolgtrekking te kom. Hierdie sistematiese ontleding som die relevante bevindings van bees-KGV navorsing op, en identifiseer die belangrike gene wat daarin betrokke is, om navorsers te help om op datum te bly met huidige en aangaande navorsing in bees-KGV studies. Hierdie ontleding het aan die lig gebring dat bees-KGV navorsing aansienlik toegeneem het sedert 2008. Die omvang en die sprei van die publikasies reflekteer dat dit wêreldwyd toenemend belangrik is om die bees genoom te verstaan vir die genetiese verbetering van vee. Maar daar is egter ʼn gebrek aan navorsing in ontwikkelende lande, ʼn gebrek aan beklemtoning van Bos indicus (12%) en Bos taurus africanus (4%) bees, en ʼn gebrek aan gestandaardiseerde verslagdoening regoor bees-KGV studies. KGV’s kan die geen uitdrukking verander en gevolglik die fenotipiese uitdrukking beïnvloed. Hierdie sistematiese ontleding het verskeie belangrike KGV-verwante gene, wat ekonomiese belangrike eienskappe in beeste beïnvloed, in die gepubliseerde artikels geïdentifiseer. Dié gene hou verband met aanpassing en immuniteit (ABCC4, BOLA geen familie, IGLL1, OR familie, WC1, ZNF280B, BSP30A, DEFB, ULBP geen familie, CATH geen familie, en die HSP geen familie), melk opbrengs, melk samestelling en voortplanting (DGAT1, IFNT, PAG, PRAME, PRL, AP3B1, IGLL1, SLC27A6, ITFG1, MTHFSD, PRP, en PTK2), vleis opbrengs, vleis kwaliteit en groei (IGF2, PLA2G2D, CAST, IGF1R, APOL3, PTPRC, KCNJ12, CAPN1, AGBL3, CTNNA1, MSTN, ADRA1B, ATRN, LRRC49, MYH3, SORCS2, en TG), voer doeltreffendheid (PRKG1, FABP2, en EIF2S1), en pels kleur, pels patrone en haar morfologie (KIT, AP3B1, MC1R, PRLR, en FGF18). Hierdie kennis is relevant vanaf ʼn molekulêre perspektief tot die praktiese toepassing in diere teling, en bied telers ʼn middel om die genomiese seleksie van diere op ʼn jonger ouderdom te oorweeg. Die produktiewe doeltreffendheid van beeste is vatbaar, dus is die gebruik van molekulêre geassisteerde selektiewe teling noodsaaklik om die huidige en toekomstige uitdagings in bees produktiwiteit te oorkom. Masters 2023-03-03T11:17:58Z 2023-05-18T07:04:51Z 2023-03-03T11:17:58Z 2023-05-18T07:04:51Z 2023-03 Thesis http://hdl.handle.net/10019.1/127112 en_ZA Stellenbosch University xv, 135 pages : illustrations (some color), maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Cattle -- Breeding -- Genetic aspects Genotype-environment interaction Genomics Copy number variations (CNV) UCTD Old, Jessica Anne A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes |
| title | A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes |
| title_full | A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes |
| title_fullStr | A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes |
| title_full_unstemmed | A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes |
| title_short | A systematic review of the role of genomic copy number variation in cattle (Bos taurus) production and associated genes |
| title_sort | systematic review of the role of genomic copy number variation in cattle bos taurus production and associated genes |
| topic | Cattle -- Breeding -- Genetic aspects Genotype-environment interaction Genomics Copy number variations (CNV) UCTD |
| url | http://hdl.handle.net/10019.1/127112 |
| work_keys_str_mv | AT oldjessicaanne asystematicreviewoftheroleofgenomiccopynumbervariationincattlebostaurusproductionandassociatedgenes AT oldjessicaanne systematicreviewoftheroleofgenomiccopynumbervariationincattlebostaurusproductionandassociatedgenes |