Browsing by Subject "POTATO"

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  • Haapalainen, Minna; Latvala, Satu; Wickstrom, Annika; Wang, Jinhui; Pirhonen, Minna; Nissinen, Anne I. (2020)
    A previously unknown haplotype of the plant pathogen 'Candidatus Liberibacter solanacearum' (Lso) was found in cultivated carrots and parsnips in eastern Finland. That same haplotype was found in western Finland, over 300 km away, in the family Polygonaceae, the species Fallopia convolvulus (wild buckwheat) and Persicaria lapathifolia (pale persicaria) growing as weeds within carrot and parsnip fields. The infected plants, both apiaceous and polygonaceous, showed symptoms of foliar discolouration. This is the first report of Lso bacteria in plants of the family Polygonaceae. The finding that the polygonaceous plants infected with a previously unknown haplotype of Lso were growing among the apiaceous plants infected with Lso haplotype C suggests that these two haplotypes might be transmitted by different vectors. Phylogenetic analyses showed that the new haplotype, called haplotype H, is distinct from the previously characterized haplotypes and appears to have diverged early from their common ancestor. Multi-locus sequence analysis revealed four different sequence types (strains) within the haplotype H. These findings suggest that the haplotype H is likely to be endemic in northern Europe and that the genetic diversity within the Lso species is higher than previously assumed.
  • Wang, Linping; Saarela, Jani; Poque, Sylvain; Valkonen, Jari P. T. (2020)
    The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.
  • Ebrahimi, Nashmin; Hartikainen, Helina; Simojoki, Asko; Hajiboland, Roghieh; Seppanen, Mervi (2015)
    The uptake by and subsequent translocation of selenium (Se) within the plant is dependent on its chemical form and soil properties that dictate this trace element's bioavailability. Plant species differ in their tendency to accumulate Se. Se taken-up by plants is returned to soil in plant residues, but the bioavailability of organic Se in those residues is poorly known. We investigated the impact of inorganic (Na2SeO4), organic (Se-enriched stem and leaf residues) Se applications and also soil microbial respiration on the growth and Se concentrations of various plant organs of oilseed rape (Brassica napus L.) during its development from the rosette to the seed filling stage. Both inorganic and organic Se slightly improved plant growth and enhanced plant development. Inorganic Se was more bioavailable than the organic forms and resulted in 3-fold to 6-fold higher Se concentrations in the siliques. Inorganic Se in autoclaved soil tended to elevate the Se concentration in all plant parts and at all growth stages. The organic Se raised Se concentrations in plants much less effectively than the inorganic selenate. Therefore, the use of inorganic Se is still recommended for biofortification.
  • Neset, Tina-Simone; Wiréhn, Lotten; Klein , Natacha; Käyhkö, Sara Janina; Juhola, Sirkku Kaarina (2019)
    Climatic changes are expected to pose challenges to Nordic agriculture. While some changes may provide opportunities for higher productivity, others may severely increase agricultural vulnerability. Farmers attempt to adapt or cope with these changes by taking measures to decrease vulnerability or to take advantage of potential benefits, but little is known what outcomes these adaptation measures might have. This study identifies unintended negative impacts of adaptation measures, drawing on a literature review and interviews with farmers and agricultural officials and experts in Sweden and Finland. Based on the conceptual framework of maladaptation, this study identifies outcomes that either increase the vulnerability of the implementing actor, shift the vulnerability to other actors or sectors or affect common pool resources. While a large number of adaptation measures rebound vulnerability to the implementing actor, several potential maladaptive outcomes may shift vulnerability or affect common pool resources. The findings point to the large number of trade-offs that are involved in adaptation decision-making and lead to the conclusion that raising awareness of these aspects can support future adaptation strategies.
  • Pasanen, Miia; Waleron, Malgorzata; Schott, Thomas; Cleenwerck, Ilse; Misztak, Agnieszka; Waleron, Krzysztof; Pritchard, Leighton; Bakr, Ramadan; Degefu, Yeshitila; van der Wolf, Jan; Vandamme, Peter; Pirhonen, Minna (2020)
    Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second Glade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421(T) (CFBP 8630(T)=LMG 30828(T)) is suggested as a type strain.
  • Hakala, Kati P.; Yli-Halla, Markku J.; Tuomainen, Paivi M.; Hartikainen, Helina (2020)
    Fluazinam, a widely used pesticide in conventional potato cultivation, is effective against epidemics of the fungal disease late blight. To assess fluazinam persistence in soil, laboratory experiments were conducted with fluazinam added to soil as a pure chemical or contained in the commercial product Shirlan (R). In a follow-up experiment, the persistence was monitored under constant temperature and water content conditions during a maximum period of 1 year. In an annual climatic rotation experiment, fluazinam added to soil was exposed to the year-round temperature and water content conditions occurring in the boreal zone. A third experiment was undertaken to clarify the effect of soil organic matter (SOM) on the recovery of fluazinam. In the follow-up and annual climatic rotation experiments, more than half of the added fluazinam was recovered after 1 year of incubation. The estimated half-life of fluazinam ranged between 355 and 833 days. The degradation of fluazinam was enhanced by an abundance of SOM, a warm temperature, and wetness. Additionally, in over half of soil samples collected from fields where potato had been intensively cultivated for many years, varying concentrations of fluazinam were detected. Fluazinam can carry over to the next growing season in professional potato production.
  • Santala, Johanna; Valkonen, Jari P. T. (2018)
    Plants recognize unrelated viruses by the antiviral defense system called RNA interference (RNAi). RNAi processes double-stranded viral RNA into small RNAs (sRNAs) of 21-24 nucleotides, the reassembly of which into longer strands in silico allows virus identification by comparison with the sequences available in databases. The aim of this study was to compare the virus detection sensitivity of sRNA-based virus diagnosis with the established virus species-specific polymerase chain reaction (PCR) approach. Viruses propagated in tobacco plants included three engineered, infectious clones of Potato virus A (PVA), each carrying a different marker gene, and an infectious clone of Potato virus Y (PVY). Total RNA (containing sRNA) was isolated and subjected to reverse-transcription real-time PCR (RT-RT-PCR) and sRNA deep-sequencing at different concentrations. RNA extracted from various crop plants was included in the reactions to normalize RNA concentrations. Targeted detection of selected viruses showed a similar threshold for the sRNA and reverse-transcription quantitative PCR (RT-qPCR) analyses. The detection limit for PVY and PVA by RT-qPCR in this study was 3 and 1.5 fg of viral RNA, respectively, in 50 ng of total RNA per PCR reaction. When knowledge was available about the viruses likely present in the samples, sRNA-based virus detection was 10 times more sensitive than RT-RT-PCR. The advantage of sRNA analysis is the detection of all tested viruses without the need for virus-specific primers or probes.
  • Abdullah; Faraji, Sahar; Mehmood, Furrukh; Malik, Hafiz Muhammad Talha; Ahmed, Ibrar; Heidari, Parviz; Poczai, Péter (2021)
    The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.