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Genomic investigation for markers linked to fruit and bunch quality traits in grapevine
Thesis (MScAgric)--Stellenbosch University, 2022.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867613980015460352 |
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| access_status_str | Open Access |
| author | Govender, Varootsha |
| author2 | Lashbrook, Justin G. |
| author_browse | Govender, Varootsha Lashbrook, Justin G. |
| author_facet | Lashbrook, Justin G. Govender, Varootsha |
| author_sort | Govender, Varootsha |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125153 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:44:45.702Z |
| 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:10019.1/125153 Genomic investigation for markers linked to fruit and bunch quality traits in grapevine Govender, Varootsha Lashbrook, Justin G. Vivier, Melane Stellenbosch University. Faculty of Agrisciences. Dept. of Viticulture and Oenology. Grapes -- Breeding Genetic markers Grapes -- Genome mapping Genomics -- Data processing Grapes -- Effect of environment on Fruit -- Quality Arabidopsis thaliana Grapes -- Effect of temperature on Grapes -- Climatic factors UCTD Thesis (MScAgric)--Stellenbosch University, 2022. ENGLISH ABSTRACT: Grape production faces several challenges such as climate change, pests, diseases, and new demands from consumers and growers. Breeding programmes offer a solution by creating new cultivars that can maintain yield and quality in changing environmental conditions while providing fruit that appeals to the wine and table grape global market. Modern breeding methods now integrate genomic tools with traditional practices to increase the selection efficiency and precision of cultivar improvement. Genomic tools such as molecular markers are developed using knowledge of the underlying genetics and inheritance of a trait. In grapevine, very few markers exist for fruit quality due to the lack of information on the genetic basis of important agricultural traits. Compactness is a key grapevine breeding target and refers to the arrangement of berries within a bunch. This trait impacts both disease resistance and fruit quality as highly dense bunches tend to be more susceptible to fungal infections and uneven berry ripening. Compactness is strongly influenced by cluster architecture traits that includes several bunch, berry, and rachis characteristics. Quantitative Traits Loci (QTL) mapping has previously been used to elucidate the genetic determinants of cluster architecture however, no stable QTLs that are consistent across different genetic and environmental backgrounds have been identified. To detect robust QTLs, a meta-analysis was performed for grapevine fruit and bunch morphology traits. Using the BioMercartor program, a consensus map was built by integrating genetic maps from 26 previously published grapevine studies, onto which a total of 258 QTLs from 15 previous QTL studies distributed on 18 chromosomes were projected. Twenty-four meta-QTLs were identified for fruit and cluster architecture traits and further genomic investigation of these new regions revealed 16 putative candidate genes. These genes were classified as regulatory, growth and development genes in Arabidopsis thaliana and could potentially be involved in the genetic architecture of grapevine fruit traits. To develop accurate markers to predict a phenotype, identifying genetic variation within candidate genes linked to a trait is important. A bioinformatics pipeline was created to analyse variation within genomic regions associated with a trait of interest using publicly available whole-genome sequencing datasets for grapevine cultivars. This pipeline was validated by analysing variation at the well- studied colour locus containing VvMYBA1 and VvMYBA2 genes. Alleles for both genes were detected for 100 Vitis accessions and compared to the current genotype-phenotype model for berry colour. Among the accessions analysed, 81 cultivars conformed to the model and results indicate that alternative genotypes could exist for red, white, and intermediate cultivars. Further study of sequence variation at the colour locus is needed to update the current model for berry colour. A table grape mapping population that segregates for berry colour and compactness was prepared to further validate the meta-QTL regions and study the berry colour genotype-phenotype model. Eighty-one individuals that showed trueness-to-parentage were phenotyped for fruit and bunch quality traits during the 2020 and 2021 harvest seasons. Using this population and trait data, associations between the genotype and phenotype for fruit traits can be studied using biparental QTL mapping to detect QTLs associated with berry colour, compactness, and cluster architecture traits. The genomic information generated in this project contributes to our understanding of the genetic complexity of fruit morphology traits and can aid molecular enhanced breeding. A thorough understanding of the genetic architecture can be used to predict phenotype variation for the development of markers allowing breeders to create grapevine cultivars for a range of useful characteristics. AFRIKAANSE OPSOMMING: Druiweproduksie staar verskeie uitdagins soos klimaatsverandering, plae, siektes en nuwe eise van verbruikers en produsente in the gesig. Teelprogramme bied 'n oplossing, deur die skep van nuwe kultivars wat opbrengs en kwaliteit kan handhaaf in verandere omgewingstoestande, als terwyl vrugte verskaf word wat aanklank vind by die wyn- en tafeldruifwêreldmark. Moderne teelmetodes integreer nou genomiese hulpmiddels met tradisionele praktyke om die seleksiedoeltreffendheid en akkuraatheid van kultivarverbetering te verhoog. Genomiese instrumente soos molekulêre merkers word ontwikkel deur van die kennis van die onderliggende genetika en oorerwing van 'n eienskap gebruik te maak. In winger bestaan baie min merkers vir vrugkwaliteit weens die gebrek aan inligting oor die genetiese basis van belangrike landbou-eienskappe. Kompaktheid is 'n belangrike wingerdteelteiken en verwys na die rangskikking van bessies binne 'n tros. Hierdie eienskap beïnvloed beide siekteweerstand en vrugkwaliteit, aangesien hoogs digte trosse geneig is om meer vatbaar te wees vir swaminfeksies en ongelyke rypwording van bessies. Kompaktheid word sterk beïnvloed deur trosargitektuur-eienskappe wat verskeie bos-, bessie- en rachis-eienskappe insluit. Kwantitatiewe kenmerk lokuls (KKL) kartering is voorheen gebruik om die genetiese determinante van trosargitektuur toe te lig, maar geen stabiele KKLs wat konsekwent is oor verskillende genetiese en omgewingsagtergronde, is geïdentifiseer nie. Om robuuste KKL's op te spoor, is 'n meta-analise uitgevoer vir wingerdvrugte en tros morfologie eienskappe. Met die gebruik van die BioMercartor-sagteware program, is 'n konsensuskaart gebou deur genetiese kaarte van 26 voorheen gepubliseerde wingerdstudies te integreer, waarop 'n totaal van 258 KKL's van 15 vorige KKL-studies versprei is op 18 chromosome, geprojekteer is. Vier-en-twintig meta-KKL's is geïdentifiseer vir vrugte- en trosargitektuur- eienskappe en verdere genomiese ondersoek van hierdie nuwe streke het 16 vermeende kandidaatgene aan die lig gebring. Hierdie gene was geklassifiseer as regulatoriese, groei- en ontwikkelingsgene in Arabidopsis thaliana en kon potensieel betrokke wees in die genetiese argitektuur van wingerdvrug- eienskappe. Om akkurate merkers te ontwikkel om 'n fenotipe te voorspel, is die identifisering van genetiese variasie binne kandidaatgene wat aan 'n eienskap gekoppel is belangrik. ’n Bioinformatika-pyplyn is geskep om variasie binne genomiese streke te ontleed wat met ’n eienskap van belang geassosieer word deur die gebruik van publieke beskikbare heelgenoomvolgorde-datastelle vir wingerdkultivars. Hierdie pyplyn is bekragtig deur variasie te analiseer by die goed bestudeerde kleur lokus wat VvMYBA1 en VvMYBA2 gene bevat. Allele vir beide gene is opgespoor vir 100 Vitis-toetredings en is vergelyk met die huidige genotipe- fenotipe model vir bessiekleur. Onder die aksessies wat ontleed is, het 81 kultivars aan die model voldoen en resultate dui daarop dat alternatiewe genotipes vir rooi, wit en intermediêre kultivars kan bestaan. Verdere studie van volgordevariasie by die kleurlokus is wel nodig om die huidige model vir bessiekleur op te dateer. 'n Tafeldruif kartering populasie wat segregeer vir bessie kleur en kompaktheid is voorberei om die meta- KKL streke verder te bevestig en die bessie kleur genotipe-fenotipe model te bestudeer. Een-en-tagtig individue wat getrouheid tot ouerskap getoon het, is gedurende die 2020- en 2021-oesseisoene vir vrugte- en troskwaliteitseienskappe gefenotipeer. Deur hierdie populasie- en eienskapdata te gebruik, kan assosiasies tussen die genotipe en fenotipe vir vrugte-eienskappe bestudeer word deur gebruik te maak van biouerlike KKL-kartering om KKL's op te spoor wat geassosieer word met bessiekleur, kompaktheid en trosargitektuur-eienskappe. Die genomiese inligting wat gegenereer is in hierdie projek, dra by tot ons begrip van die genetiese kompleksiteit van vrugtemorfologie-eienskappe en kan bydra tot molekulêre verbeterde teling. n Deeglike begrip van die genetiese argitektuur kan gebruik word om fenotipise variasie te voorspel vir die ontwikkeling van merkers wat telers in staat stel om wingerdkultivars vir 'n reeks nuttige eienskappe te skep. Masters 2022-03-11T11:45:55Z 2022-04-29T12:56:18Z 2023-03-31T03:00:11Z 2022-03 Thesis http://hdl.handle.net/10019.1/125153 en_ZA Stellenbosch University ix, [17], 81 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Grapes -- Breeding Genetic markers Grapes -- Genome mapping Genomics -- Data processing Grapes -- Effect of environment on Fruit -- Quality Arabidopsis thaliana Grapes -- Effect of temperature on Grapes -- Climatic factors UCTD Govender, Varootsha Genomic investigation for markers linked to fruit and bunch quality traits in grapevine |
| title | Genomic investigation for markers linked to fruit and bunch quality traits in grapevine |
| title_full | Genomic investigation for markers linked to fruit and bunch quality traits in grapevine |
| title_fullStr | Genomic investigation for markers linked to fruit and bunch quality traits in grapevine |
| title_full_unstemmed | Genomic investigation for markers linked to fruit and bunch quality traits in grapevine |
| title_short | Genomic investigation for markers linked to fruit and bunch quality traits in grapevine |
| title_sort | genomic investigation for markers linked to fruit and bunch quality traits in grapevine |
| topic | Grapes -- Breeding Genetic markers Grapes -- Genome mapping Genomics -- Data processing Grapes -- Effect of environment on Fruit -- Quality Arabidopsis thaliana Grapes -- Effect of temperature on Grapes -- Climatic factors UCTD |
| url | http://hdl.handle.net/10019.1/125153 |
| work_keys_str_mv | AT govendervarootsha genomicinvestigationformarkerslinkedtofruitandbunchqualitytraitsingrapevine |