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Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars
Thesis (PhD)--Stellenbosch University, 2025.
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613846730964992 |
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| access_status_str | Open Access |
| author | Van Heerden, Carel Jacobus |
| author2 | Burger, Johan T. |
| author_browse | Burger, Johan T. Van Heerden, Carel Jacobus |
| author_facet | Burger, Johan T. Van Heerden, Carel Jacobus |
| author_sort | Van Heerden, Carel Jacobus |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/132345 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:42:38.497Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/132345 Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars Van Heerden, Carel Jacobus Burger, Johan T. Prins, Renee Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics & Institute of Plant Biotechnology. Grapes -- Breeding -- South Africa Grape powdery mildew disease -- Genetics Grapes -- Genetics -- Variation Grapes -- Disease and pest resistance DNA fingerprinting -- Technique Fungal diseases of plants -- Genetic aspects Plant genomes UCTD Thesis (PhD)--Stellenbosch University, 2025. Van Heerden, C. J. 2025. Genetic Analysis of Downy and Powdery Mildew Resistance in Grapevine: A Comparative Study of 'Regent' and 'Red Globe' Cultivars. Unpublished doctoral dissertation. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/42cce74c-1740-4276-be19-39033e8a4e89 ENGLISH ABSTRACT: Fungal pathogens, causing powdery and downy mildew infections, have a large negative impact on grape production worldwide. Quantitative trait loci (QTL) mapping projects have identified several loci linked to the genetic factors responsible for resistance to these pathogens. Numerous studies focused on the cultivar ‘Regent’, which carries the resistance loci to downy mildew on chromosome 18 (Rpv3), as well as powdery mildew on chromosome 15 (Ren3, Ren9). This study aimed to determine the effectiveness of the reported resistance in ‘Regent’ to both diseases in South Africa and to validate the associated QTL effects and chromosome positions. First, a microsatellite-based genetic map was created for both ‘Regent’ (resistant) and ‘Red Globe’ (susceptible) using the first-generation offspring of a cross between these two cultivars. Using a QTL mapping approach, the position of the loci conferring resistance was determined. A major resistance locus was identified for each of the diseases at the expected map positions. Markers flanking these resistance genes were identified along with their specific alleles that are linked to the resistance alleles to facilitate marker-assisted selection in further resistance breeding efforts using ‘Regent’. In a second focus, next-generation sequencing (NGS) of both ‘Regent’ and ‘Red Globe’ provided a view of the DNA sequence diversity between these two genomes. The genome data revealed a higher single nucleotide polymorphism (SNP) density in ‘Regent’ than ‘Red Globe’ as expected, based on the non-vinifera ancestry of ‘Regent’. A per-gene analysis of the SNPs between resistant and susceptible cultivars in the target QTL regions provided a better view/understanding of the diversity of the genes located at Rpv3, Ren3 and Ren9. Thirdly, DNA fingerprints based on 20 microsatellites were generated for a selection of grape cultivars and breeding lines often used in the table breeding programme, as well as a small selection of wine cultivars. Unique fingerprints were assigned to 98 of the 113 cultivars and breeding lines tested, while seven additional fingerprints were assigned to seven groups of cultivars. These fingerprints confirm the breeding history of most cultivars but also reveal some inconsistencies. Included in the selection of microsatellites were some of the markers linked to the resistance loci, which confirmed that eight of the nine downy mildew resistant cultivars included in this dataset had the same conserved Rpv3 haplotype found in ‘Regent’ while ‘Ajvaz’ retained only part of the haplotype that could reduce potential linkage drag at this locus if used in future resistance breeding. In addition to the confirmation of the efficacy of the resistance loci, this study improved the resolution of the QTL interval containing the Ren3 locus. This provided a foundation for more recent work by other authors who showed that Ren3 and Ren9 loci are tightly linked at the originally described larger Ren3 locus. The results of the fingerprint study have since been incorporated into the table breeding programme as well as in services aimed at resolving cultivar uncertainties. Lastly, data demonstrated that NGS data for grapevine can be generated in South Africa to show sequence differences between cultivars. AFRIKAANSE OPSOMMING: Swampatogene, wat poeieragtige en donsige skimmelinfeksies veroorsaak, het 'n groot negatiewe impak op druiweproduksie wêreldwyd. Kwantitatiewe eienskap lokus (QTL) kartering projekte het verskeie lokusse geïdentifiseer wat gekoppel is aan die genetiese faktore wat verantwoordelik is vir weerstand teen hierdie patogene. Talle studies het gefokus op die kultivar 'Regent', wat die weerstandslokusse dra teen donsskimmel op chromosoom 18 (Rpv3), asook poeieragtige skimmel op chromosoom 15 (Ren3, Ren9). Hierdie studie het ten doel gehad om die effektiwiteit van die gerapporteerde weerstand in 'Regent' teen beide siektes in Suid-Afrika te bepaal en om die gepaardgaande QTL-effekte en chromosoomposisies te valideer. Eerstens is 'n mikrosatelliet-gebaseerde genetiese kaart geskep vir beide 'Regent' (weerstandig) en 'Red Globe' (vatbaar) deur die eerste generasie nageslag van 'n kruising tussen hierdie twee kultivars te gebruik. Deur 'n QTL-karteringsbenadering te gebruik, is die posisie van die lokusse wat weerstand verleen, bepaal. 'n Belangrike weerstandlokus is vir elk van die siektes op die verwagte kaartposisies geïdentifiseer. Nabygeleë merkers aan weerskante van die weerstandsgene is geïdentifiseer tesame met hul spesifieke allele wat aan die weerstandsallele gekoppel is om merker-ondersteunde seleksie te fasiliteer in verdere weerstandsteelpogings met behulp van 'Regent'. In 'n tweede fokus het volgende-generasie-volgordebepaling (NGS) van beide 'Regent' en 'Red Globe' inligting van die DNA-volgorde-diversiteit tussen hierdie twee genome verskaf. Die genoomdata het 'n hoër enkelnukleotied-polimorfisme (SNP) digtheid in 'Regent' as 'Red Globe' geopenbaar soos verwag, gebaseer op die nie-Vinifera afkoms van 'Regent'. 'n Per-geen analise van die SNP's tussen weerstandbiedende en vatbare kultivars in die teiken QTL streke het 'n beter insig verskaf van die diversiteit van die gene geleë by Rpv3, Ren3 en Ren9. Derdens is DNS-vingerafdrukke gebaseer op 20 mikrosatelliete gegenereer vir 'n seleksie van druifkultivars en teellyne wat dikwels in die tafelteelprogram gebruik word, asook 'n klein seleksie wynkultivars. Unieke vingerafdrukke is aan 98 van die 113 kultivars en teellyne wat getoets is, toegeken, terwyl sewe bykomende vingerafdrukke aan sewe groepe kultivars toegeken is. Hierdie vingerafdrukke bevestig die teelgeskiedenis van die meeste kultivars, maar openbaar ook 'n paar teenstrydighede. Ingesluit by die seleksie van mikrosatelliete was van die merkers wat aan die weerstandslokusse gekoppel is, wat bevestig het dat agt van die nege donsskimmel weerstandbiedende kultivars wat in hierdie datastel ingesluit is, dieselfde gekonserveerde Rpv3 haplotipe gehad het wat in 'Regent' gevind is, terwyl 'Ajvaz' slegs 'n deel van die haplotipe behou het, wat potensiële koppelingsweerstand by hierdie lokusweerstand kan verminder indien dit in toekomstige lokusweerstand gebruik word. Benewens die bevestiging van die doeltreffendheid van die weerstand lokus, het hierdie studie die resolusie van die QTL interval wat die Ren3 lokus bevat, verbeter. Dit het 'n grondslag gelê vir meer onlangse werk deur ander navorsers wat getoon het dat die Ren3 en Ren9 lokusse nou verbind is by die oorspronklik beskryfde groter Ren3 lokus. Die resultate van die vingerafdrukstudie is sedertdien in die tafelteelprogram geïnkorporeer sowel as in dienste wat daarop gemik is om kultivar-onsekerhede op te los. Laastens het data getoon dat NGS-data vir wingerd in Suid-Afrika gegenereer kan word om volgordeverskille tussen kultivars aan te toon. Doctoral 2025-06-04T10:27:48Z 2025-06-04T10:27:48Z 2025-03 Thesis https://scholar.sun.ac.za/handle/10019.1/132345 en Stellenbosch University 143 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Grapes -- Breeding -- South Africa Grape powdery mildew disease -- Genetics Grapes -- Genetics -- Variation Grapes -- Disease and pest resistance DNA fingerprinting -- Technique Fungal diseases of plants -- Genetic aspects Plant genomes UCTD Van Heerden, Carel Jacobus Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars |
| title | Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars |
| title_full | Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars |
| title_fullStr | Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars |
| title_full_unstemmed | Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars |
| title_short | Genetic analysis of downy and powdery mildew resistance in grapevine : a comparative study of 'Regent' and 'Red Globe' cultivars |
| title_sort | genetic analysis of downy and powdery mildew resistance in grapevine a comparative study of regent and red globe cultivars |
| topic | Grapes -- Breeding -- South Africa Grape powdery mildew disease -- Genetics Grapes -- Genetics -- Variation Grapes -- Disease and pest resistance DNA fingerprinting -- Technique Fungal diseases of plants -- Genetic aspects Plant genomes UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/132345 |
| work_keys_str_mv | AT vanheerdencareljacobus geneticanalysisofdownyandpowderymildewresistanceingrapevineacomparativestudyofregentandredglobecultivars |