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Articles containing the keyword 'PCR'

Category : Research article

article id 169, category Research article

Susanne von Bargen, Elise Grubits, Risto Jalkanen, Carmen Büttner. (2009). Cherry leaf roll virus – an emerging virus in Finland? Silva Fennica vol. 43 no. 5 article id 169. https://doi.org/10.14214/sf.169

Keywords: Betula pendula; Betula pubescens; Betula nana; IC-RT-PCR; 3' non-coding region; CLRV; phylogenetic relationship

Abstract | View details | Full text in PDF | Author Info

Cherry leaf roll virus, CLRV, is a plant pathogen that infects a variety of deciduous trees and shrubs in temperate regions. Little is known about its occurrence at high latitudes and especially in Finnish birch species. Still, symptoms that seemed to be associated with CLRV such as vein banding, leaf roll and decline have been observed in birch trees throughout the country since the summer of 2002. Six different birch species, subspecies or varieties, i.e. Betula pubescens subsp. pubescens (downy birch), B. pendula (silver birch), B. nana (dwarf birch), B. pubescens var. appressa (Kiilopää birch), B. pubescens subsp. czerepanovii (mountain birch) and B. pendula var. carelica (curly birch) originating from all over Finland were assessed by immunocapture-reverse transcription-polymerase chain reaction (IC-RT-PCR) for CLRV infection. It was shown that CLRV is widely distributed in B. pendula and B. pubescens throughout the country. Furthermore, dwarf birch, mountain birch, Kiilopää birch and curly birch were confirmed to be previously unkown hosts of CLRV. Genetic analysis of virus sequence variants originating from Finnish birch trees revealed atypical phylogenetic relationships. In contrast to CLRV isolates from birches growing in the United Kingdom and Germany which clustered exclusively within group A, Finnish CLRV isolates belonged either to group B, D or E. Thus, virus population structure in Finnish birches seems to be more variable and host plant dependency seems not to apply for Finnish CLRV isolates.

Bargen, Humboldt-Universität zu Berlin, Department für Nutzpflanzen- und Tierwissenschaften, Fachgebiet Phytomedizin, Lentzeallee 55/57, 14195 Berlin, Germany E-mail: susanne.von.bargen@agrar.hu-berlin.de
Grubits, Humboldt-Universität zu Berlin, Department für Nutzpflanzen- und Tierwissenschaften, Fachgebiet Phytomedizin, Lentzeallee 55/57, 14195 Berlin, Germany E-mail: eg@nn.de
Jalkanen, Finnish Forest Research Institute, Rovaniemi Research Unit, P.O. Box 16, FI-96301 Rovaniemi, Finland E-mail: risto.jalkanen@metla.fi
Büttner, Humboldt-Universität zu Berlin, Department für Nutzpflanzen- und Tierwissenschaften, Fachgebiet Phytomedizin, Lentzeallee 55/57, 14195 Berlin, Germany E-mail: cb@nn.de

article id 301, category Research article

Sanni Raiskila, Minna Pulkkinen, Tapio Laakso, Kurt Fagerstedt, Mia Löija, Riitta Mahlberg, Leena Paajanen, Anne-Christine Ritschkoff, Pekka Saranpää. (2007). FTIR spectroscopic prediction of Klason and acid soluble lignin variation in Norway spruce cutting clones. Silva Fennica vol. 41 no. 2 article id 301. https://doi.org/10.14214/sf.301

Keywords: Norway spruce; FTIR; lignin; PCR; principal component regression

Abstract | View details | Full text in PDF | Author Info

Our purpose was to develop a FTIR spectroscopic method to be used to determine the lignin content in a large number of samples and to apply this method studying variation in sapwood and heartwood lignin content between three fast-growing cutting clones grown in three sites. Models were estimated with 18 samples and tested with 6 samples for which the Klason lignin + acid soluble lignin content had been determined. Altogether 272 candidate models were built with all-subset regressions from the principal components estimated from differently treated transmission spectra of the samples; the spectra were recorded on KBr pellets of sieved and unsieved unextracted wood powder and subjected to four different preprocessings and two different wavenumber selection schemes. The final model showed an adequate fit in the estimation data (R² = 0.74) as well as a good prediction performance in the test data (R²_P = 0.90). This model was based on the wavenumber range of 1850–500 cm^–1 of the line-subtraction-normalised spectra recorded from sieved samples. The model was used to predict lignin content in 64 samples of the same material. One of the clones had a slightly lower sapwood lignin content than the two other clones. The fertile growing site with fast growing trees showed slightly higher sapwood lignin content compared with the other two sites. The model was also used to predict the lignin content in the earlywood of 45 individual annual rings. Variation between individual stems and between annual rings was found to be large. No correlation was found between the lignin content and density of earlywood.

Raiskila, Finnish Forest Research Institute, Vantaa Research Unit, P.O. Box 18, FI-01301 Vantaa, Finland E-mail: sr@nn.fi
Pulkkinen, Department of Forest Ecology, P.O. Box 27, FI-00014 University of Helsinki, Finland E-mail: mp@nn.fi
Laakso, Finnish Forest Research Institute, Vantaa Research Unit, P.O. Box 18, FI-01301 Vantaa, Finland E-mail: tl@nn.fi
Fagerstedt, Department of Biological and Environmental Sciences, Plant Biology, P.O. Box 65, FI-00014 University of Helsinki, Finland E-mail: kf@nn.fi
Löija, VTT Building and Transport, P.O. Box 1806, FI-02044 VTT, Finland E-mail: ml@nn.fi
Mahlberg, VTT Building and Transport, P.O. Box 1806, FI-02044 VTT, Finland E-mail: rm@nn.fi
Paajanen, VTT Building and Transport, P.O. Box 1806, FI-02044 VTT, Finland E-mail: lp@nn.fi
Ritschkoff, VTT Building and Transport, P.O. Box 1806, FI-02044 VTT, Finland E-mail: acr@nn.fi
Saranpää, Finnish Forest Research Institute, Vantaa Research Unit, P.O. Box 18, FI-01301 Vantaa, Finland E-mail: pekka.saranpaa@metla.fi

article id 291, category Research article

Yildiray Lise, Zeki Kaya, Fikret Isik, Rumi Sabuncu, Irfan Kandemir, Sertaç Önde. (2007). The impact of over-exploitation on the genetic structure of Turkish red pine (Pinus brutia Ten.) populations determined by RAPD markers. Silva Fennica vol. 41 no. 2 article id 291. https://doi.org/10.14214/sf.291

Keywords: Pinus brutia Ten.; RAPD-PCR; human over-exploitation; genetic structure; inbreeding

Abstract | View details | Full text in PDF | Author Info

To determine the possible impact of over-exploitation on the genetic structure of Turkish red pine (Pinus brutia Ten.) populations, three natural and three over-exploited (human degraded) populations of the species in the Mediterranean region of Turkey were investigated with Randomly Amplified Polymorphic DNA (RAPD). With the 80 RAPD primers tested, 12 of them yielded 137 polymorphic RAPD fragments. Four of the studied populations maintained unique fragments. The mean proportion of polymorphic fragments for all populations ranged from 89.8 to 98.9% and there were no significant differences between natural (94.8%) vs. over-exploited populations (92.7%). The estimated heterozygosity values suggested that Turkish red pine maintains high levels of genetic diversity (range 0.24–0.28) though studied populations and grouped ones as natural (H_e = 0.28) vs. over-exploited (0.27) did not differ significantly. The mean F_ST value indicated that the large portion of the total genetic diversity was within populations (93%), but this value was lower in the natural populations (92%) than in the over-exploited ones (94%). In over-exploited populations, excess of homozygosity was observed (about 6% higher) as compared to natural populations, indicating impacts of inbreeding in P. brutia.

Lise, Department of Biological Sciences, Middle East Technical University, 06531, Ankara, Turkey E-mail: yl@nn.tr
Kaya, Department of Biological Sciences, Middle East Technical University, 06531, Ankara, Turkey E-mail: kayaz@metu.edu.tr
Isik, North Carolina State University, Raleigh, USA E-mail: fi@nn.us
Sabuncu, Southwest Anatolia Forest Research Institute, Antalya, Turkey E-mail: rs@nn.tr
Kandemir, Department of Biology, Zonguldak Karaelmas University, 67100, Zonguldak, Turkey E-mail: ik@nn.tr
Önde, Department of Biological Sciences, Middle East Technical University, 06531, Ankara, Turkey E-mail: so@nn.tr

Category : Research note

article id 7749, category Research note

Eeva J. Vainio, Sannakajsa M. Velmala, Pertti Salo, Seppo Huhtinen, Michael M. Müller. (2017). Defoliation of Tilia cordata trees associated with Apiognomonia errabunda infection in Finland. Silva Fennica vol. 51 no. 4 article id 7749. https://doi.org/10.14214/sf.7749

Keywords: small-leaved lime; fungal disease; anthracnose; ITS rDNA; direct PCR; Tiliaceae

Highlights: Defoliation of Tilia cordata was investigated by fungal isolation from symptomatic leaf petioles and ITS sequence determination; The disease symptoms were associated with the presence of Apiognomonia errabunda; We report the first nucleotide sequences of A. errabunda from the Nordic countries.

Abstract | Full text in HTML | Full text in PDF | Author Info

We investigated the causative agent of a disease outbreak affecting small-leaved limes (Tilia cordata Mill.) and resulting in darkening of the leaf petioles and excessive defoliation during summer 2016 in southern Finland. The fungal species composition of the symptomatic petioles was examined by culture isolation and molecular identification using ITS rDNA sequences, which revealed the most prevalent fungal species present in the petioles as Apiognomonia errabunda (Roberge) Höhn. Based on reviewing curated herbarium specimens deposited at the Universities of Helsinki and Turku, A. errabunda is native and widely distributed in small-leaved limes in Finland, and occasionally infects also other broadleaved trees, including Quercus robur L. and ornamental species of Tilia L. and Fagus L. The ITS sequence analysis conducted during this study revealed minor within-species polymorphisms similar to those observed earlier in the Central European and Russian populations of A. errabunda, and reports the first nucleotide sequences of this species from the Nordic countries.

Vainio, Natural Resources Institute Finland (Luke), Management and Production of Renewable Resources, P.O. Box 2, FI-00791 Helsinki, Finland http://orcid.org/0000-0002-6739-7968 E-mail: eeva.vainio@luke.fi
Velmala, Natural Resources Institute Finland (Luke), Management and Production of Renewable Resources, P.O. Box 2, FI-00791 Helsinki, Finland E-mail: sannakajsa.velmala@luke.fi
Salo, Finnish Museum of Natural History, Botanical Museum, P.O. Box 7, FI-00014 University of Helsinki, Finland E-mail: pertti.salo@helsinki.fi
Huhtinen, University of Turku, Herbarium, Biodiversity Unit, FI-20014 Turku, Finland E-mail: sephuh@utu.fi
Müller, Natural Resources Institute Finland (Luke), Management and Production of Renewable Resources, P.O. Box 2, FI-00791 Helsinki, Finland E-mail: micms.muller@gmail.com

article id 1674, category Research note

Nevenka Ćelepirović, Monika Karija Vlahović, Aikaterini Dounavi, Mladen Ivanković. (2016). Optimizations of high throughput multiplex polymerase chain reaction with simple sequence repeat markers for genotyping of common walnut populations (Juglans regia L.). Silva Fennica vol. 50 no. 5 article id 1674. https://doi.org/10.14214/sf.1674

Keywords: SSR markers; nuclear microsatellites; Juglans regia L.; multiplex PCR

Highlights: We combined eleven SSR markers in one multiplex PCR to make faster and cost effective amplification of the common walnut DNA from Croatia; Genetic variation of common walnut from Croatia was moderate at analyzed SSR loci; The resultant multiplex PCR could be used for genotyping of common walnut populations.

Abstract | Full text in HTML | Full text in PDF | Author Info

Multiplex polymerase chain reaction (PCR) allows amplification of two or more pair of primers in parallel for amplification of multiple target sequences in a single reaction tube. In this study, we combined existing simple sequence repeat (SSR) markers (nuclear microsatellites) in the novel combination of multiplex PCR to study the population genetics of common walnut from Croatia. From twenty one tested SSR markers, eleven produced satisfactory results in one multiplex PCR. Population genetic results achieved from 15 samples of Croatian common walnut showed moderate genetic variability (average value: He 0.473; Ho 0.568). Our multiplex PCR allowed cost effective work concerning chemicals, plastic ware, device, and working time producing optimal results. The optimized multiplex PCR represented the best combination of eleven SSR primers for genotyping common walnut in a single PCR reaction.

Ćelepirović, Division of Genetics, Forest Tree Breeding and Seed Science, Croatian Forest Research Institute, Jastrebarsko, Croatia E-mail: celepirovic.nevenka@gmail.com
Karija Vlahović, DNA Laboratory, Department of Forensic Medicine&Criminology, School of Medicine, University of Zagreb, Zagreb, Croatia E-mail: monika.karija.vlahovic@mef.hr
Dounavi, Department of Forest Protection, Forest Research Insitute of Baden-Württemberg, Wonnhaldesttr. 4, 79100 Freiburg, Germany E-mail: aikaterini.dounavi@forst.bwl.de
Ivanković, Division of Genetics, Forest Tree Breeding and Seed Science, Croatian Forest Research Institute, Jastrebarsko, Croatia E-mail: mladeni@sumins.hr

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