Barley yellow dwarf virus (BYDV), an aphid transmitted luteovirus, is the most widespread and economically damaging virus of cereal crops. The work in this thesis aims to characterise the basis of the naturally occurring resistance to BYDV in cereals in three ways: Firstly, by facilitating the isolation of the Yd2 gene for BYDV resistance from barley by a map-based approach. Secondly, by determining if a BYDV resistance gene in rice is orthologous to Yd2. Thirdly, by establishing if other BYDV resistance genes in non- Ethiopian barleys are allelic to Yd2. It is hoped that the information generated in this study will ultimately assist in the production of BYDV resistant cereal cultivars. A detailed genetic map of the Yd2 region of barley chromosome 3 was constructed, containing 19 RFLP loci, the centromere and the Yd2 gene. Yd2 mapped on the long arm, 0.5 cM from the centromere, and in the mapping population of 106 F2 individuals, perfectly cosegregated with the RFLP loci XYlp, and Xwg889. This map represents the first stage in a project to isolate the Yd2 gene by a map-based approach. The isolation of Yd2 could help to elucidate the molecular mechanism of the Yd2-mediated BYDV resistance, and may allow the production of BYDV resistant cereals by genetic transformation. The RFLP markers mapped closest to Yd2 could also be useful in barley breeding, by enabling selection for both the presence of Yd2 and the absence of agronomically undesirable traits known to be closely linked to Yd2. Genetically Directed Representational Difference Analysis (GDRDA) is a technique based on subtractive hybridisation, which can be used to identify RFLP markers closely linked to a gene of interest. Two GDRDA experiments were performed with the intention of generating additional RFLP markers close to Yd2. However, the first experiment yielded RFLP probes that were not derived from the barley genome, while the second experiment yielded probes that detected repetitive sequences. It was concluded that GDRDA is of limited use in generating further markers close to Yd2. To isolate the Yd2 gene by a map-based approach, a much larger mapping population will need to be analysed to genetically resolve markers tightly linked to Yd2. If the two morphological markers uzu dwarf and white stripe,,j flank Yd2, then they could assist in this task by enabling the visual identification of F2 seedlings resulting from recombination close to Yd2. However, in this study, both morphological markers were found to be located distal to Yd2. Therefore, these two morphological markers can not be used together to facilitate high resolution genetic mapping of the Yd2 locus. It may be possible to use large-insert genomic DNA clones from the relatively small genome of rice to generate further RFLP markers close to the Yd2 gene in barley, provided that the order of orthologous sequences in barley and rice is conserved close to the Yd2 locus. To assess the feasibility of this approach, RFLP probes used to identify loci close to Yd2 were mapped in rice using a segregating rice F2 population. Five of the RFLP loci mapped together and in the same order as RFLP loci mapped close to Yd2 in barley using the same probes. By comparing the location of RFLPs mapped by other researchers in rice using probes mapped close to Yd2, the region of conserved linkage between rice and the Yd2 region was tentatively identified as the central portion of rice chromosome 1. The collinearity shown by orthologous sequences in barley and rice indicated that it may indeed be possible to use rice to assist in generating RFLP markers close to Yd2. Of all the cereals, rice is the most amenable to map-based gene isolation, due to its small genome, well developed physical and genetic maps, and its ability to be genetically transformed with high efficiency. If a BYDV resistance gene that is orthologous to Yd2 could be identified in rice, this gene could be isolated with relative ease, and then used to identify barley cDNA clones corresponding to Yd2 gene by virtue of the sequence homology expected between these genes. To test if a BYDV resistance gene from an Italian rice line is orthologous to Yd2, recombinant-inbred rice lines previously characterised for this gene were analysed using probes mapped close to Yd2 in barley. No genetic linkage was detected between the RFLP loci and the BYDV resistance gene, indicating that the gene is unlikely to be orthologous to Yd2. BYDV resistance alleles at the Yd2 locus which are of a non-Ethiopian origin may show interesting differences to Ethiopian Yd2 resistance alleles. To identify barleys which may contain resistance alleles of Yd2, ten BYDV resistant barleys not known to contain Yd2 were assessed for their resistance to the PAVadel isolate of BYDV in the glasshouse. CI 1179, Rojo, Perry, Hannchen, Post and CI 4228 were found to be the most resistant under these conditions, and were analysed further. If the resistance from these barleys is controlled by alleles of Yd2, RFLP markers close to Yd2 will be expected to cosegregate with the resistance in F2 families derived from crosses between these resistant barleys and the BYDV susceptible barleys Atlas and Proctor. RFLPs suitable for use in these allelism tests were identified using probes mapped close to Yd2. However, time did not permit the analysis of these F2 populations. / Thesis (Ph.D.) -- University of Adelaide, Dept. of Plant Science, 1996

Errata attached to inside front cover. / Bibliography: leaves [156-188] / vi, 155, [33] leaves, [48] leaves of plates : ill. (some col.) ; 30cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 2001

Includes bibliographical references. The thesis aims to characterise the basis of naturally occuring resistance to BYDV in cereals in three ways: i. A map-based approach to the isolation of the Yd2 gene for BYDV resistance from barley. -- ii. Determining if a BYDV resistance gene in rice is orthologous to Yd2. -- iii. Establishing if other BYDV resistance genes in non-Ethiopian barleys are allelic to Yd2.

Errata sheet pasted on front end-paper. / Includes bibliographical references. / v, 125, [99] leaves, [3] leaves of plates : ill. (chiefly col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, (1995?)

Master of Science / Department of Plant Pathology / William Bockus / Barley yellow dwarf (BYD) is one of the most important wheat diseases in the state of Kansas. Despite the development of cultivars with improved levels of resistance to BYD, little is known about the impact that this resistance has on yield loss from the disease. The intent of this research was to estimate yield loss in winter wheat cultivars in Kansas due to BYD and quantify the reduction in losses associated with resistant cultivars. During seven years, BYD disease incidence was visually assessed on numerous winter wheat cultivars in replicated field nurseries. Cultivars were planted about three weeks early to promote disease. When grain yields were regressed against BYD incidence scores, negative linear relationships significantly fit the data for each year and for the combined dataset covering all seven years. The models showed that, depending upon the year, 19-48% (average 33%) of the yields was explained by BYD incidence. For the combined dataset, 29% of the relative yield was explained by BYD incidence. The models predicted that cultivars showing high disease incidence had 25-86% (average 49%) less yield than a hypothetical cultivar that showed zero incidence. Using the models, the moderate level of resistance in the cultivar Everest was calculated to reduce yield loss from BYD by about 73%. Therefore, utilizing visual BYD symptom evaluations in Kansas, coupled with grain yields, is useful to estimate yield loss from the disease. Furthermore, linear models that incorporate those parameters can be used to calculate the impact of improving cultivar resistance to BYD on yield losses.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2006. / Härtill 4 uppsatser.

abstract: The increased number of novel pathogens that potentially threaten the human population has motivated the development of mathematical and computational modeling approaches for forecasting epidemic impact and understanding key environmental characteristics that influence the spread of diseases. Yet, in the case that substantial uncertainty surrounds the transmission process during a rapidly developing infectious disease outbreak, complex mechanistic models may be too difficult to be calibrated quick enough for policy makers to make informed decisions. Simple phenomenological models that rely on a small number of parameters can provide an initial platform for assessing the epidemic trajectory, estimating the reproduction number and quantifying the disease burden from the early epidemic phase. Chapter 1 provides background information and motivation for infectious disease forecasting and outlines the rest of the thesis. In chapter 2, logistic patch models are used to assess and forecast the 2013-2015 West Africa Zaire ebolavirus epidemic. In particular, this chapter is concerned with comparing and contrasting the effects that spatial heterogeneity has on the forecasting performance of the cumulative infected case counts reported during the epidemic. In chapter 3, two simple phenomenological models inspired from population biology are used to assess the Research and Policy for Infectious Disease Dynamics (RAPIDD) Ebola Challenge; a simulated epidemic that generated 4 infectious disease scenarios. Because of the nature of the synthetically generated data, model predictions are compared to exact epidemiological quantities used in the simulation. In chapter 4, these models are applied to the 1904 Plague epidemic that occurred in Bombay. This chapter provides evidence that these simple models may be applicable to infectious diseases no matter the disease transmission mechanism. Chapter 5, uses the patch models from chapter 2 to explore how migration in the 1904 Plague epidemic changes the final epidemic size. The final chapter is an interdisciplinary project concerning within-host dynamics of cereal yellow dwarf virus-RPV, a plant pathogen from a virus group that infects over 150 grass species. Motivated by environmental nutrient enrichment due to anthropological activities, mathematical models are employed to investigate the relevance of resource competition to pathogen and host dynamics. / Dissertation/Thesis / Doctoral Dissertation Applied Mathematics 2016

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