Browsing by discipline "Växtproduktions biologi (växtpatologi)"
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(2011)Potato virus Y (PVY) is currently the most yield and quality limiting pathogen of the cultivated potato (Solanum tuberosum L.) globally. While yield losses specific to PVY are hard to measure in presence of other pathogens they are estimated as 20 to 80 %. The most important way by which the virus spreads are virus-infected seed potatoes. High quality seed potato is very important for food, food industry and starch potato production. Visual inspection of the potato plants underestimates usually the real percentage of PVY infection. Laboratory tests provide more accurate results about the incidence of infections. The problem with testing PVY is that the virus cannot be detected reliably from samples taken from dormant tubers. Different treatments have been used to break dormancy of tubers e.g. chemicals (Rindite, bromoethane), plant hormones (gibberellic acid) and adjusted storage temperatures (cold and heat treatment). The results have varied a lot. In this thesis an experiment with oxygen-carbon dioxide (O2 40 %-CO2 20 %) treatment with different periods of time was used to end dormancy of potato tubers. The aim was to test whether the treatment could end dormancy of tubers earlier than normally and to see if the treatment has an effect on detection of PVY. One aim was also to test how reliably PVY could be detected from tuber and sprout samples compared with potato leaf samples which are normally used for virus testing. Results from the sprouting treatment were variable and could not be readily generalized. The treatment had no effect on the detection of PVY incidence. When the different plant materials were compared with each other, tuber material showed the lowest PVY percentage when compared to sprouts and leaves. Testing sprouts also underestimated the incidence PVY. The best material for testing PVY in potatoes were the leaf samples.
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(2012)Plant is able to recognize dsRNA, and cleave the dsRNA into siRNA in the cell. This mechanism helps plant to against virus. A novel method of virus detection based on siRNA deep-sequencing has been developed. The method does not require any prior supposition, and it provides an unbiased view for detecting of all viruses. Thus it was used to detect viruses from a wild plant (Arctium tomentosum) with viral symptoms in Helsinki, Finland. Overlapping siRNA reads were used to build contigs using the program Velvet. Programs MAQ and Novoalign were used to align the siRNA reads to a reference sequence for the viral sequence recovery. In this study, two viruses, Alstroemeria virus X (AlsVX, genus Potexvirus, family Alphaflexiviridae) and Fig mosaic virus-Hel (FMV, unassigned genus Emaravirus) were identified. This is the first report for the occurrences of both viruses in Finland. The siRNA deep-sequencing detection results were confirmed by RT-PCR. The distributions of the viruses in Helsinki were also studied. Partial sequences of AlsVX-Hel and FMV-Hel were compared with related viruses in NCBI. The amino acid identity of the coat protein gene between AlsVX-Hel detected from Helsinki and AlsVX-Jap from Japan is 90%, and the amino acid identities of the putative nucleocapsid protein gene between FMV-Hel and other FMV strains were about 78%. The differences indicate that the AlsVX-Hel in Helsinki might be a new strain of AlsVX, and FMV-Hel might be a new strain of FMV, or a new virus.
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