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Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism
Thesis (MScAgric)--Stellenbosch University, 2022.
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| Format: | Thesis |
| Language: | English |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867613945662013440 |
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| access_status_str | Open Access |
| author | Bosman, Robin Nicole |
| author2 | Lashbrook, Justin G. |
| author_browse | Bosman, Robin Nicole Lashbrook, Justin G. |
| author_facet | Lashbrook, Justin G. Bosman, Robin Nicole |
| author_sort | Bosman, Robin Nicole |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125144 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:44:12.049Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125144 Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism Bosman, Robin Nicole Lashbrook, Justin G. Stellenbosch University. Faculty of AgriSciences. Dept. of Viticulture & Oenology & Institute for Wine Biotechnology. Grapes -- Breeding Grapes -- Genome mapping Grapes -- Genetics -- Data processing Plant metabolites -- Biotechnology Plant molecular biology Grapevines -- Metabolism Phenols UCTD Thesis (MScAgric)--Stellenbosch University, 2022. ENGLISH ABSTRACT: Plants produce secondary (specialised) metabolites which play roles in plant defence against pathogens and herbivores, as well as protecting plants against abiotic stress and in attracting seed dispersers and pollinators. Specialised metabolites also influence the quality traits of crops such as grapevine, where metabolites such as terpenes and phenylpropanoids contribute to the aroma, colour, astringency, and nutritional value of grapevine. Furthermore, these traits are complex and controlled by multiple genes, the vast majority of which are unknown or uncharacterised. QTL studies may be used to investigate the genetic markers associated with these traits, which can then be utilised in breeding programs. Similar studies in grapevine have mostly focused on developing markers for disease resistance and table grape qualities such as berry size, and shape and seedlessness, while very few markers are available for organoleptic properties like colour and aroma. To that end, this study aimed to identify and investigate genomic regions that associate with modulation of specialised metabolism in grapevine. The volatile organic compounds and phenolic compounds present in a grapevine mapping population at veraison were quantified. This metabolic data was used to identify quantitative trait loci associated with the metabolites, and significant QTL were further investigated in silico to identify candidate genes. Lastly, genomic investigation of selected candidate genes was performed to determine underlying genomic factors influencing specialised metabolite accumulation. Significant QTLs were identified for various phenolic compounds. Two tandem genes on chromosome 2, VvMYBA1 and VvMYBA2 were associated with the accumulation of anthocyanins confirming this well-established locus to be the master regulator for grapevine anthocyanin accumulation. Additionally, VvHCT was identified and proposed as a candidate gene involved in caftaric acid accumulation. Several significant QTLs were associated with terpenes and candidate genes were proposed for sesquiterpenes and monoterpenes. Most monoterpenes and two C13-norisoprenoids associated with the VvDXS1 locus. A SNP in VvDXS1 is a well-known marker for monoterpene accumulation in grapevine and genotyping results showed that this SNP is also associated with monoterpene accumulation within the mapping population. Additional candidate genes, the terpene synthases VvGer and VvTer were proposed for geraniol and cyclic monoterpene accumulation, respectively. Molecular and genomic investigation of VvGer and VvTer revealed that these genes were in tandemly duplicated clusters displaying high levels of hemizygosity. Copy number analysis further showed that VvTer and VvGer copy numbers varied within the mapping population. Significantly, VvTer copy number correlated with VvTer gene expression and cyclic monoterpene accumulation in the mapping population, while VvGer copy number had no correlation with gene expression or geraniol accumulation. This study contributes to our fundamental understanding of grapevine specialised metabolism by identifying several established and novel loci associated with specialised metabolism. Additionally, the potential impact of gene duplication and copy number variation in a VvTPS gene on terpene accumulation is explored. Future work from this study could potentially lead to development of genetic markers for various organoleptic grapevine traits such as colour and aroma. AFRIKAANSE OPSOMMING: Plante produseer sekondêre (gespesialiseerde) metaboliete wat 'n rol speel in die verdediging teen patogene en herbivore, asook die beskerming teen abiotiese stres en om saadverspreiders en bestuiwers te lok. Gespesialiseerde metaboliete beïnvloed ook die kwaliteitseienskappe van gewasse soos winger, waar metaboliete soos terpene en fenielpropanoïede bydra tot die aroma, kleur, strenghed en voedingswaarde van wingerd. Hierdie eienskappe is kompleks en word beheer deur veelvuldige gene, waarvan die oorgrote meerderheid onbekend of ongekarakteriseer is. Kwantitatiewe kenmerk lokusse (KKLs) studies kan gebruik word om die genetiese merkers wat met hierdie eienskappe geassosieer word te ondersoek, wat dan weer in teelprogramme gebruik kan word. Soortgelyke studies in wingerd het meestal gefokus op die ontwikkeling van merkers vir siekteweerstand en tafeldruif-eienskappe soos bessiegrootte, en vorm en pitloosheid, terwyl baie min merkers beskikbaar is vir organoleptiese eienskappe soos kleur en geur. Vir daardie doel het hierdie studie daarop gemik om genomiese streke te identifiseer en te ondersoek wat assosieer met die regulering van gespesialiseerde metabolisme in wingerd. Die vlugtige organiese verbindings en fenoliese verbindings wat tydens veraison teenwoording is in 'n wingerd kartering populasie is gekwantifiseer. Hierdie metaboliese data was gebruik om KKLs wat met die metaboliete geassosieer is te identifiseer en betekenisvolle KKLs was verder in silico ondersoek om kandidaatgene te identifiseer. Laastens is genomiese ondersoek van geselekteerde kandidaatgene uitgevoer om onderliggende genomiese faktore wat gespesialiseerde metabolietakkumulasie beïnvloed, te bepaal. Beduidende KKLs is vir verskeie fenoliese verbindings geïdentifiseer. Twee tandemgene op chromosoom 2, VvMYBA1 en VvMYBA2 was geassosieer met die versameling van antosianiene wat bevestig dat hierdie goed gevestigde lokus die hoof reguleerder is vir wingerd-antosianien akkumulasie. Daarbenewens is VvHCT geïdentifiseer en voorgestel as 'n kandidaat-geen betrokke by kaftariensuur-akkumulasie. Verskeie beduidende KKLS is geassosieer met terpene en kandidaatgene vir sesquiterpene en monoterpene is voorgestel. Die meeste monoterpene en twee C13-norisoprenoïede het geassosieer met die VvDXS1 lokus. 'n Enkelnukleotied polimorfisme (ENP) in VvDXS1 is 'n bekende merker vir monoterpeen akkumulasie in wingerd en genotipering resultate het getoon dat hierdie ENP ook geassosieer word met monoterpeen akkumulasie binne die kartering populasie. Addisionele kandidaat-gene, die terpeen-sinteses VvGer en VvTer is onderskeidelik vir geraniol- en sikliese monoterpeen-akkumulasie voorgestel. Verdere molekulêre en genomiese ondersoeke van VvGer en VvTer het aan die lig gebring dat hierdie gene in tandem gedupliseerde klusters was, wat hoë vlakke van hemisigotisiteit toon. Kopiegetalontleding het verder gewys dat VvTer- en VvGer-kopiegetalle gewissel het binne die karteringpopulasie. Dit is betekenisvol dat VvTer-kopiegetal met VvTer-geenuitdrukking en sikliese monoterpeen akkumulasie in die karteringpopulasie gekorreleer het, terwyl VvGer-kopiegetal geen korrelasie met geenuitdrukking of geraniol-akkumulasie gehad het nie. Hierdie studie dra by tot ons fundamentele begrip van wingerd-gespesialiseerde metabolisme deur die identifisering van verskeie gevestigde en nuwe lokusse wat met gespesialiseerde metabolisme geassosieer word. Daarbenewens is die potensiële impak van geenduplisering en kopiegetalvariasie in 'n VvTPS-geen op terpeenakkumulasie ondersoek. Toekomstige werk van hierdie studie kan moontlik lei tot die ontwikkeling van genetiese merkers vir verskeie organoleptiese wingerd-eienskappe soos kleur en aroma. Masters 2022-03-10T20:54:55Z 2022-04-29T12:55:53Z 2022-03-10T20:54:55Z 2022-03 Thesis http://hdl.handle.net/10019.1/125144 en Stellenbosch University xiii, 107 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Grapes -- Breeding Grapes -- Genome mapping Grapes -- Genetics -- Data processing Plant metabolites -- Biotechnology Plant molecular biology Grapevines -- Metabolism Phenols UCTD Bosman, Robin Nicole Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism |
| title | Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism |
| title_full | Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism |
| title_fullStr | Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism |
| title_full_unstemmed | Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism |
| title_short | Genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism |
| title_sort | genomic investigation and characterisation of genetic regions associated with grapevine specialised metabolism |
| topic | Grapes -- Breeding Grapes -- Genome mapping Grapes -- Genetics -- Data processing Plant metabolites -- Biotechnology Plant molecular biology Grapevines -- Metabolism Phenols UCTD |
| url | http://hdl.handle.net/10019.1/125144 |
| work_keys_str_mv | AT bosmanrobinnicole genomicinvestigationandcharacterisationofgeneticregionsassociatedwithgrapevinespecialisedmetabolism |