Defining the QTL for chill requirement during dormancy and dormancy release in apple (Malus x domestica Borkh.).
| dc.contributor.advisor | Burger, Johan T. | en_ZA |
| dc.contributor.advisor | Rees, Jasper | en_ZA |
| dc.contributor.author | Cornelissen, Stephanie | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. | en_ZA |
| dc.date.accessioned | 2021-12-03T12:04:54Z | |
| dc.date.accessioned | 2021-12-22T14:27:40Z | |
| dc.date.available | 2021-12-03T12:04:54Z | |
| dc.date.available | 2021-12-22T14:27:40Z | |
| dc.date.issued | 2021-12 | |
| dc.description | Thesis (PhDAgric)--Stellenbosch University, 2021. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: Dormancy is a physiological stage that all deciduous fruit trees experience during winter. It consists of three sub stages, para-, endo- and ecodormancy. During the endodormic stage, apple trees need to be exposed to cold temperatures for their chill requirement to be fulfilled. Most apple varieties have a unique chill requirement, for instance ‘Anna’ requires less than 300 hours. After this requirement is fulfilled, the plant will break dormancy if the environmental conditions are optimal, i.e. the less the chill requirement the earlier the plant will bud. This study looks at the genetic component of chill requirement by firstly determining the region of the apple genome that is primarily associated with budbreak and thereafter the genes within this region and their expression patterns. A mapping population was created by crossing ‘Lady Williams’ with ‘Anna’. ‘Lady Williams’ is a medium to high chill variety and ‘Anna’ is a low chill variety that requires less than 300 chill units. This population was used to generate a genetic map and subsequent QTL analysis, as well as association mapping, were used to determine the region of the apple genome that is associated with budbreak. A major QTL in the first 10Mb distal region of Linkage Group/chromosome 9 was discovered. This region consists of 741 genes, of which 27 were differentially expressed over time when exposed to cold. An RNA time series analysis was performed by periodically extracting RNA from the meristems of cuttings from ‘Anna’, incubated at 4°C for up to 800 hours. The expression patterns of the 27 genes grouped into seven distinct clusters. The major observation that could be made is that there is a difference between the expression patterns before and after the theoretical time of budbreak (300 hours) in ‘Anna’. The 27 genes were differentially expressed before budbreak but there was little to no differential expression after budbreak. Another observation that was made, is that the biggest differences in gene expression were between 0-hours and a 100-hours. This indicated that the plant could have experienced cold shock by transferring it to low temperature incubation and subsequently the onset of endodormancy. Known dormancy-associated DAM genes, were not differentially expressed over time. However, an ortholog of the predicted transcription factor ICE1-like, bHLH, and the gene RING domain ligase 2, that have been shown to be associated with the regulation of ICE1-like, was differentially expressed over time when first introduced to cold. Furthermore, genes regulating the expression of the plant hormones ethylene and auxin were differentially expressed. Other notable genes include ones that encode Tubulin alpha-2 chain and xyloglucan endotransglucosylase/hydrolase 9 proteins, both known to regulate transport through cell wall/membrane, and 5'-adenylyl phosphosulfate reductase 2 that is associated with oxidation-reduction homeostasis. This study serves as a starting point for further investigations of the complex nature of the onset of dormancy, chill accumulation during dormancy and the eventual budbreak, by identifying genes that are associated with dormancy. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Dormansie is ‘n fisiologiese fase wat alle bladwisselende bome ervaar gedurende winter. Dit bestaan uit drie sub-fases para-, endo- en ekodormansie. Gedurende endodormansie moet appelbome aan koue temperature bloodgestel word om hulle koue-vereistes te behaal. Die meeste appelbome het unieke koue-vereistes, byvoorbeeld die kultivar ‘Anna’ benodig minder as 300 uur. Wanneer aan hierdie koue -vereiste voldoen word, sal die plant dormansie breek, met ander woorde hoe laer die boom se koue-vereiste is, hoe vroeër sal die boom bot. Die studie kyk na die genetiese komponent van koue-vereiste, deur om eers die lokus wat geassosieer is met bot te identifideer, en daarna die gene en hulle uitdrukkingspatrone in hierdie lokus, te bestudeer. ‘n Populasie is gemaak deur om ‘Lady Williams’ met ‘Anna’ te kruis. ‘Lady Williams’ beskik oor ‘n medium tot ‘n hoë koue- vereiste en ‘Anna’ ‘n lae koue-vereiste van minder as 300 koue eenhede. Die populasie is gebruik om ‘n genetiese kaart en daaropvolgende QTL te bepaal, asook vir assosiasie- kartering, om die lokus op die appel-genoom te bepaal wat met bot geassosieer is. ‘n QTL is gevind op die eerste 10Mb distale streek van chromosoom 9. Die QTL bestaan uit 741 gene, waarvan 27 differensieel uitgedruk word wanneer die plante oor tyd aan koue blootgestel was. ‘n RNS tydreeks-studie was gedoen deur RNS periodiek uit die meristeem van ‘Anna’, wat by 4°C vir 800 uur geïnkubeer is, te isoleer. Die uitdrukkingspatrone van die 27 gene het in sewe unieke geengroeperings geval. Die belangrikste waarneming wat gemaak is, is dat daar ‘n duidelike verskil was tussen die uitdrukkingspatrone van die gene voor en na die teoretiese bot-tyd (300 ure). Al 27 gene toon differensiële uitdrukking voor bot-tyd, maar geen of min differensiële uitdrukking na bot-tyd. Nog ‘n waarneming wat gemaak is, is dat die grootste verskil in uitdrukking van gene tussen 0-uur en 100-uur was. Laasgenoemde toon dat die plant moontlik koue-skok ervaar het as gevolg van die lae temperatuur inkubasie daarvan en dat dit derhalwe die begin van dormansie geïnisieer het. Die bekende dormansie-geassosieerde gene (DAM) was nie differensieël uitgedruik oor tyd nie. Hoewel, ‘n soortgelyke transkripsie faktor aan “ICE1-like”, bHLH, en die geen “RING domain ligase 2”, wat ICE1-like reguleer, is differesieël uitgedruk in die teenwoordigheid van koue oor tyd. Gene wat die produksie van plant hormone (etileen en ouksien) reguleer was ook teenwoordig. Ander gene wat teenwoordig was, was díe wat kodeer vir “Tubulin alpha-2 chain” en “xyloglucan endotransglucosylase/hydrolase 9” proteïene, wat beide betrokke is by transport deur die selwand/membraan, asook “5'-adenylyl phosphosulfate reductase 2” wat geassosieer is met oksidasie-reduksie homeostase. Hierdie studie verskaf ’n beginpunt vir verdere studies om die kompleksiteit van die begin van dormansie, koue akkumulering en bot-tyd te verstaan, deurdat dit gene identifiseer het wat met dormansie geassosieer is. | af_ZA |
| dc.description.version | Doctoral | en_ZA |
| dc.format.extent | xii, 131 pages : illustrations (some color) | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/123895 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | Quantitative trait loci (QTL) | en_ZA |
| dc.subject | Apples -- Breeding | en_ZA |
| dc.subject | Apples -- Effect of cold on | en_ZA |
| dc.subject | Dormancy in apples | en_ZA |
| dc.subject | Apples --Dormancy | en_ZA |
| dc.subject | UCTD | en_ZA |
| dc.title | Defining the QTL for chill requirement during dormancy and dormancy release in apple (Malus x domestica Borkh.). | en_ZA |
| dc.type | Thesis | en_ZA |