Thesis (Ph. D.)--University of Adelaide, Dept. of Crop Protection, 1999. / Copies of author's previously published articles inserted. Includes bibliographical references (leaves 128-143).

Thesis (M. Ag. Sci.) -- University of Adelaide, Dept. of Plant Pathology, 1966. / [Typescript]. Includes bibliography.

Thesis (M.Sc.)--York University, 2005. Graduate Programme in Biology. / Typescript. Includes bibliographical references. Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR11767

Thesis (Ph. D.)--University of Wisconsin--Madison, 1948. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 89-92).

Reciprocal transplant experiments have been made to investigate the .intra-specific variation in two clonal species, Primula vulgaris and RBDUDculus repens. Primula transplants performed best when returned to their native populations, indicating that they were differentia~ed in response to local conditions. There was marked variation in the degree of local specialisation of plants in different primrose populations and possible causes of this variation are discussed. Although buttercup transplants also showed great variability, there was no evidence that they were specialised, either between, or within, local populations. The lack of genetic specialisation in RBDUDculus repens may be due to its spreading growth form, widespread distribution and low level of seedling recruitment. In glasshouse experiments, the presence or absence of neighbours affected many parameters of buttercup growth. Within a genet the effect of edaphic and biotic heterogeneity was integrated, so that ramets in favourable conditions supported interconnected ramets in less favourable sites. Plants of R. repens vary phenotypically in different environments but appear to respond to heterogeneous local conditions by phenotypic plasticity of individual ramets rather than genetic specialisation. The assumption that differences between transplants are solely indicative of genetic specialisation has been questioned. Virus infection was detected in 7 of 14 primrose populations surveyed. Infected plants showed no symptoms of disease, yet they produced significantly fewer but larger leaves than uninfected plants. Differences between transplants which could easily be attributed to genetic variation may be due to differential virus infection. Furthermore, viruses may ultimately contribute to genetic differentiation and have a role as selective forces in the environment. Phenotypic differences between ramets of the same genet of R. repens were maintained and even increased after 26 week's growth in a cammon environment. It is clearly imPortant in transplant experiments to use comparable phenotypes and virus-free plants when determining the role of genotype in the match between organism and environment.

No description available.

No description available.

Cassava (Manihot esculenta Crantz) is affected by two major viral diseases, namely Cassava brown streak disease (CBSD) and Cassava mosaic disease (CMD). Two of the most widely distributed begomoviruses in East Africa associated with CMD, are East African cassava virus- Uganda2 (EACMV-UG2) and African cassava mosaic virus (ACMV). Despite efforts of generating improved Tropical Manihot Series (TMS) by traditional breeding and using highly resistant geminivirus cassava landraces such as Tropical Manihot Esculenta1 (TME1) and Tropical Manihot Esculenta3 (TME3), more recently two circular single stranded (ss) satellite-like DNA molecules (episomal DNA-II and DNA-III) have been found to be associated with CMD and are able to break resistance to EACMV-UG2 and enhance virus symptoms. The nature of these satellite-like DNA molecules is unknown, and furthermore, the discovery of integration of partial copies of DNA molecules (DNA-II and III fragments), and evidence for transcription from cassava Expressed Sequence Tag (EST) database screening, has led to an even more perplexing disease complex. In the present study, we attempted to further explore the interaction between the satellite-like DNAs and their associated cassava-infecting begomoviruses by investigating the impact of these DNA molecules on disease development in TME3 (tolerant) and cv. 60444 (susceptible) cassava cultivars, and to also gather biological evidence for transcription of integrated genomic and episomal (putative predicted ORFs) sequences in the ACMV and EACMV-UG2-associated DNA-II and DNA-III. Biolistic inoculation of EACMV-UG2, ACMV, and in co-bombardment with DNA-II, DNA-III, DNA-II + DNA-III was successfully performed. CMD symptoms were developed earlier on cassava plants inoculated with ACMV + DNA-II, ACMV + DNA-III, ACMV + DNA-II + DNA-III and EACMV-UG2 + DNA-II, EACMV-UG2 + DNA-III, EACMV-UG2 + DNA-II + DNA-III molecules compared with cassava plants inoculated with begomoviruses alone. Additionally, CMD symptoms were more severe in cv.60444 compared to TME3 when inoculated with begomoviruses alone, or in combination with DNA-II, DNA-III and DNA-II + DNA-III molecules. DNA-II and III were able to break resistance to the highly CMD-tolerant cassava landrace, TME3, and enhance virus symptoms. In order to confirm EST-generated evidence for transcription of DNA-II and III fragments, cDNA was subjected to RT-PCR. RT-PCR of transcripts was successful for only three putative ORFs: ORF C4 of the antisense DNA-II strand, ORF V1 on sense DNA-II strand, and ORF C2 on antisense strand for DNA-III. Primers for transcripts amplified 250 bp and 220 bp for ORF C4 of DNA-II and ORF V1 of DNA-III, respectively. Transcribed ORFs were confirmed by sequencing, and the sequences were similar to the published sequences of Begomovirus associated DNA-II satellite and Begomovirus associated DNA-III satellite, respectively. These results showed that at least two putative ORFs for DNA-II and one (the largest ORF VI) DNA-III can be transcribed. Furthermore, surveys were undertaken in order to ascertain the distribution of episomal and integrated DNA-II and III in cassava germplasm from several countries, namely Tanzania, Uganda, Kenya and Rwanda. Results from this research successfully established genetic diversity and wide geographical distribution of integrated DNA-II and DNA-III molecules. Two primer pairs were designed from a central conserved sequence found in all the integrated DNA-II or III fragments identified from the cDNA libraries (EST database). These primers also amplified integrated sequences of expected size in cassava accessions and wild Manihot species which were similar to satellite-like sequence occurrences in the ESTs. Using designed primers, PCR amplification yielded integrated DNA-II and DNA-III products of ~895 bp and ~306 bp, respectively. Analysis of 363 field leaf samples detected the presence of DNA-II or DNA-III from Kenya (3.3% or 8.3%), Uganda (18% or 2.5%), Rwanda (6.5% or 19.6%) and Tanzania (5.7% or 11.9%) , results which were confirmed by analysis of the sequenced PCR amplicons. Detection of both DNA-II and DNA-III molecules on the samples collected was also found from Kenya (73%), Uganda (69.1%), Rwanda (50%) and Tanzania (69.3%). Interestingly integrated DNA-II and II copies were amplified from healthy, symptomless and infected cassava samples. DNA-II sequences did not vary significantly (93.3% - 99.8%) and were highly similar to the sequences of Begomovirus associated sat DNA-II (AY836366) and 99% with mentha leaf deformity disease associated satellite DNA-II, while DNA-III sequences and Begomovirus associated DNA-II satellite (AY833667). In conclusion, this study has provided useful information that contributes to a further understanding of the biological function of integrated and episomal DNA-II and III molecules in begomoviruses infected cassava plant. However the relationship, if any between episomal and integrated forms needs to be established in future, and investigation into whether the transcribed ORFs can produce functional proteins, needs to be undertaken. How DNA-II and III interact with EACMV-UG2 and ACMV in disease modulation remains to be explored, and the replication of episomal DNA-II and III by these associated begomoviruses needs to be confirmed if these DNA molecules are to truly show a satellite-like relationship. Furthermore, the findings in this study that partial and varied-sized integrated DNA-II and III fragments occur widely in healthy and infected cassava germplasm will enable researchers (plant virologists and breeders) working on cassava in Sub Saharan Africa (SSA) to explore this complex more deeply in order to develop durable management strategies for CMD.

Plant viruses can cause many plant diseases, which result in substantial damage to crop production. To overcome viral infections, plants evolved RNA silencing which can recognise viral RNAs during their replications and slice them into small RNA (sRNA) using antiviral nucleases called DICER or Dicer-like (DCL). The resulting virus-derived small interfering RNA (vsiRNA, 21-24 nucleotides) then guides effector nucleases, namely ARGONAUTE (AGO), to cleave viral RNAs in the cytoplasm in a nucleotide-specific manner. However, the activity of vsiRNA is not restricted to the control of viral RNA accumulation. Virus-derived sRNAs can regulate host gene expression if host mRNAs share sequence complementarity with vsiRNAs. Interestingly, vsiRNAs are also able to target and methylate homologous DNA sequences in the nucleus indicating that vsiRNAs have potential to regulate endogenous genes at transcriptional level by modifying the epigenetic status of gene promoter sequences. This mechanism is referred to as transcriptional gene silencing (TGS). Thus, RNA silencing opens up new strategies to stably and heritably alter gene expression in plants. However, the mechanisms and efficacy of plant virus-induced TGS are largely unknown. The aim of my PhD was to investigate the molecular and environmental factors that are involved in virus-induced epigenetic modifications in the infected plants and in their progeny. First, I examined the required sequence complementary between sRNAs and their nuclear target sequence. I demonstrated for the first time that nuclear-imported vsiRNAs can induce RNA-directed DNA methylation (RdDM) and subsequently heritable virus-induced transcriptional gene silencing (ViTGS) even when they do not share 100% nucleotide sequence complementarity with the target DNA. This finding reveals a more dynamic interaction between viral RNAs and the host epigenome than previously thought. Secondly, I explored how environmental stimuli such as light and temperature can affect the efficacy of ViTGS. I found that ViTGS is greatly inhibited at high temperature. Using RNA-seq, I established that inefficient ViTGS at high temperature is due to the limited production of secondary sRNAs that may limit the initiation, amplification and spreading of virus-induced DNA methylation to neighbouring cells and down generations. Lastly, I studied the link between the viral suppressors of RNA silencing (VSRs): viral proteins that can interfere with plant RNA silencing and ViTGS. I established that VSRs of certain viruses can impair TGS in infected tissues, suggesting that viruses may alter the epigenome and consequently plant gene expression in the infected plants and their progeny. Collectively, my work reveals how viruses can re-program the epigenome of infected plants, and deepens our knowledge of how we can harness pathogens to modify the epigenome for plant breeding.

Includes bibliography.