Genetic variation of Clivia caulescens
| dc.contributor.advisor | Spies, J. J. | |
| dc.contributor.author | Stegmann, Suzanne | |
| dc.date.accessioned | 2015-11-24T08:07:27Z | |
| dc.date.available | 2015-11-24T08:07:27Z | |
| dc.date.copyright | 2011-06 | |
| dc.date.issued | 2011-06 | |
| dc.date.submitted | 2011-06 | |
| dc.description.abstract | English: At present, the genus Clivia consists of six species, including Clivia nobilis Lindl., C. miniata (Lindl.) Regel, C. gardenii Hook., C. caulescens RA Dyer, C. mirabilis Rourke and C. robusta Murray, Ran, De Lange, Hemmet, Truter & Swanevelder. Many of the species and cultivars are extensively grown worldwide, making this group of considerable horticultural importance. This study mostly focused on Clivia caulescens with a natural habitat on the escarpment from Limpopo to Swaziland through Mpumalanga. The overlapping distribution between C. miniata and C. caulescens resulted in the formation of a natural hybrid between these species at the Bearded Man Mountain. The occurrences of natural hybrids between the various species are rarely recorded. In an attempt to find out if genetic erosion is currently a threat to the various C. caulescens populations and Bearded Man Mountain clivias, this study was conducted to establish if genetic variation is present. Genetic variation refers to the variation in the genetic material of a population, and includes the nuclear, mitochondrial, ribosomal DNA as well as the DNA of other organelles. The relative genetic diversity among individuals or populations can be determined using morphological and molecular markers. Five chloroplast DNA regions, i.e. atpH-I, matK, rpoB, rpoC and trnL-F, were used in an attempt to study the molecular diversity of C. caulecsens. This study concentrated on Single Nucleotide Polymorphisms (SNPs) from these regions and microsatellites to study genetic variation. The aim of this study was to determine the genetic variation between and within the different populations of C. caulescens, to determine whether gene flow occur between the different populations and to determine which of the DNA regions included in the study can contribute to the identification of plants from a specific geographical area. Regarding the study of Clivias situated at the Bearded Man Mountain, the main objectives were to estimate genetic diversity and determine the genetic relationship among the different species of Clivia (C. miniata, C. caulescens and C. xnimbicola) from this area. Of the initial five regions that were sequenced, trnL-F amplification failed repeatedly, and this region was therefore excluded from all analyses. The other four regions showed variation between the different populations of C. caulescens and for the Bearded Man Mountain clivias, except the rpoC1 region. When the results of the phylogenetics and statistical analysis (genetic distances) were combined, it was detected that most Bearded Man Mountain specimens and God‟s Window specimens clustered together in the cladograms and in the mean distances tables. Intraspecific variation was present in all the regions and combined dataset. All attempts during this study to amplify STRs and test allelic diversity in 13 microsatellite loci for 20 specimens failed. Cross-species amplification was not as effective as hoped. Microsatellites‟ species-specific nature could have a negative effect on obtaining results, although other researchers (as mentioned in the introduction of Chapter 4) could employ cross species markers successfully. Glen & Schabble (2005) reported that a given pair of microsatellite primers rarely works across broad taxonomic groups, so primers are usually developed anew for each species. The next step would therefore be to attempt the designing of specific primers for C. caulescens. | en_ZA |
| dc.description.abstract | Afrikaans: Tans is daar ses spesies in die genus Clivia, naamlik C. nobilis Lindl., C. miniata (Lindl.) Regel, C. gardenii Hook., C. caulescens RA Dyer, C. mirabilis Rourke en C. robusta Murray, Ran, De Lange, Hemmet, Truter & Swanevelder. Al hierdie spesies en kultivars word wêreldwyd gekweek en is dus van groot tuinboukundige belang (Truter et al., 2007). Hierdie studie het gefokus op C. caulescens, met 'n geografiese verspreiding op die platorand van Limpopo na Swaziland, deur Mpumalanga. 'n Natuurlike baster tussen C. caulescens en C. miniata kom voor as gevolg van hulle simpatriese verspreidings op die “Bearded Man” berg. Die voorkoms van natuurlike basters tussen verskeie spesies is seldsaam en min voorbeelde is beskryf. 'n Poging is aangewend om te bepaal of genetiese erosie in die verskillende populasies van C. caulescens wat bestudeer is, voorkom. Genetiese variasie verwys na die variasie in genetiese materiaal van 'n populasie, en sluit kern, mitochondriale, ribosomale genome en genome van ander organelle in. Die relatiewe genetiese diversiteit onder individue of populasies kan bepaal word deur die gebruik van morfologiese of molekulêre merkers. Vyf chloroplas DNS gebiede naamlik atpH-I, matK, rpoB, rpoC en trnL-F, is gebruik in 'n poging om die molekulêre diversiteit van C. caulescens te bepaal. Die studie het gefokus op enkel nukleotied polimorfismes van die onderskeie gebiede en mikrosatelliete om genetiese variasie te ondersoek. Die doel van die studie was om die genetiese variasie tussen en binne die verskillende populasies van C. caulescens te bepaal, asook of geenvloei bestaan tussen die verskillende populasies en om te bepaal watter van hierdie DNS gebiede kan bydrae tot die identifisering van plante van 'n spesifieke geografiese gebied. Ten opsigte van die “Bearded Man” berg plante was die hoof mikpunte om genetiese variasie te bepaal en die genetiese verhouding van die verskillende spesies teenoor mekaar te ondersoek. Van die aanvanklike gebiede waarvan die nukleotiedvolgordes bepaal is, het trnL-F se amplifisering herhaaldelik misluk en hierdie gebied is uitgelaat by alle analises. Die ander vier gebiede het ge-amplifiseer en verskille tussen al die populasies van C. caulescens en die spesies van “Bearded Man” berg aangedui. Die uitsondering was die rpoC1 gebied wat geen verskille getoon het nie. Die gekombineerdie filogenetiese en statistiese resultate (genetiese afstande) dui daarop dat die eksemplare van “Bearded Man” berg met die van God's Window saam groepeer in die kladogramme en in die hoof afstandstabelle. Intraspesifieke variasie word deur al die gebiede en die gekombineerde datastel aangetoon. Alle pogings gedurende die studie om 13 mikrosatelliete vir 20 eksemplare te amplifiseer, het herhaaldelik misluk. Kruis-spesie amplifisering was nie so effektief soos vooraf gereken nie. Mikrosatelliete se spesie-spesifieke aard kon 'n negatiewe effek gehad het op die verkryging van resultate. Hoewel ander navorsers suksesvol was, is daar ook diegene wat nie sukses behaal het as gevolg van die moontlikheid dat sekere mikrosatellietmerkers nie oor groot taksonomiese groepe werksaam is nie en dat daar gewoonlik nuwe merkers spesifiek vir elke spesie ontwerp moet word. Die volgende stap sou dus wees om te poog om nuwe merkers, spesifiek vir C. caulescens, te ontwikkel indien navorsers verder deur mikrosatelliete genetiese variasie in Clivias wil bepaal. | af |
| dc.description.sponsorship | National Research Foundation (NRF) | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/11660/1783 | |
| dc.language.iso | en | en_ZA |
| dc.publisher | University of the Free State | en_ZA |
| dc.rights.holder | University of the Free State | en_ZA |
| dc.subject | Single Nucleotide Polymorphisms (SNPs) | en_ZA |
| dc.subject | rpoC1 | en_ZA |
| dc.subject | rpoB | en_ZA |
| dc.subject | Polymorphism | en_ZA |
| dc.subject | Microsatellite | en_ZA |
| dc.subject | matK | en_US |
| dc.subject | Introgression | en_ZA |
| dc.subject | Hybridization | en_ZA |
| dc.subject | Genetic variation | en_ZA |
| dc.subject | atpH-I | en_ZA |
| dc.subject | Amaryllidaceae | en_ZA |
| dc.subject | Clivia -- Classification | en_ZA |
| dc.subject | Clivia -- South Africa -- Genetics | en_ZA |
| dc.subject | Hybridization | en_ZA |
| dc.subject | Dissertation (M.Sc. (Genetics))--University of the Free State, 2011 | en_ZA |
| dc.title | Genetic variation of Clivia caulescens | en_ZA |
| dc.type | Dissertation | en_ZA |