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Articles containing the keyword 'microsatellites'.

Category: Research article

article id 7001, category Research article
Fei-Fei Zhai, Jun-Xiang Liu, Zhen-Jian Li, Jin-Mei Mao, Yong-Qiang Qian, Lei Han, Zhen-Yuan Sun. (2017). Assessing genetic diversity and population structure of Salix viminalis across Ergun and West Liao basin. Silva Fennica vol. 51 no. 3 article id 7001. https://doi.org/10.14214/sf.7001
Highlights: High genetic diversity and moderate population differentiation were detected in twelve Salix viminalis populations; Populations from Ergun basin presented higher genetic diversity than populations from West Liao basin; Populations with short distances presented low differentiation.

Salix viminalis L. is an important shrub that has potential for use as a bioenergy crop, for phytoremediation of heavy metal contaminated soil and sewage sludge treatment. It is mainly distributed in the northeast of China, but the species has not yet been used a resource here. We examined the genetic diversity and population structure of populations from the Ergun basin and West Liao basin using 20 microsatellite markers. A high level of genetic diversity (Na = 16.45, He = 0.742) was detected for S. viminalis, and populations from the Ergun basin exhibited higher genetic diversity and private alleles numbers than the West Liao basin. The 12 populations could be divided into two clusters by both Bayesian analysis and UPGMA clustering which were consistent with the populations derived from the two basins. Moderate population differentiation (FST = 0.076) was shown in S. viminalis, and AMOVA analysis confirmed that most of the genetic variation (86.13%) was attributed to individual differences within populations, while 11.49% was attributed to differences between basins and 2.38% to differences within each basin. Significant correlations of FST/(1–FST) with log (geographic distance) among 12 populations (r = 0.634, p < 0.00) and 10 populations within the Ergun basin (r = 0.482, p = 0.0002) indicated that geographical distance was the principal factor influencing genetic structure. As most of genetic variation exist within populations, so protection measures should be focused on populations with higher genetic diversity and unique alleles, such as Tuli, Mordaga downstream, Zhadun1 and Genhe.

  • Zhai, State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Haidian District, Beijing, 10091, PR China; School of Architectural and Artistic Design, Henan Polytechnic University, Century Avenue, Jiaozuo, Henan, 454000, PR China ORCID ID:E-mail: lkyzff@163.com
  • Liu, State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Haidian District, Beijing, 10091, PR China ORCID ID:E-mail: liu-jx295@163.com
  • Li, State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Haidian District, Beijing, 10091, PR China ORCID ID:E-mail: zhenjianli@163.com
  • Mao, State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Haidian District, Beijing, 10091, PR China; Research Institute of Economic Forest, Xinjiang Academy of Forestry, Anjunanlu, Urumqi, Xinjiang, PR China ORCID ID:E-mail: 350512173@qq.com
  • Qian, State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Haidian District, Beijing, 10091, PR China ORCID ID:E-mail: qianyq@caf.ac.cn
  • Han, State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Haidian District, Beijing, 10091, PR China ORCID ID:E-mail: hdd@caf.ac.cn
  • Sun, State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Haidian District, Beijing, 10091, PR China ORCID ID:E-mail: lkyszy@126.com (email)
article id 1510, category Research article
Tähti Pohjanmies, Sakina Elshibli, Pertti Pulkkinen, Mari Rusanen, Pekka Vakkari, Helena Korpelainen, Tomas Roslin. (2016). Fragmentation-related patterns of genetic differentiation in pedunculate oak (Quercus robur) at two hierarchical scales. Silva Fennica vol. 50 no. 2 article id 1510. https://doi.org/10.14214/sf.1510
Highlights: While long-lived, widespread tree species should be resistant to genetic impoverishment, we detected high differentiation among populations and pronounced genetic structure within populations of Quercus robur in Finland; These patterns seem indicative of population processes active at range margins, and of disequilibrium following historic habitat change; Preservation of remaining genetic variation is thus important in the conservation of Q. robur.

Populations at species’ range margins are expected to show lower genetic diversity than populations at the core of the range. Yet, long-lived, widespread tree species are expected to be resistant to genetic impoverishment, thus showing comparatively high genetic diversity within populations and low differentiation among populations. Here, we study the distribution of genetic variation in the pedunculate oak (Quercus robur L.) at its range margin in Finland at two hierarchical scales using 15 microsatellite loci. At a regional scale, we compared variation within versus among three oak populations. At a landscape scale, we examined genetic structuring within one of these populations, growing on an island of ca 5 km2. As expected, we found the majority of genetic variation in Q. robur to occur within populations. Nonetheless, differentiation among populations was markedly high (FST = 0.12) compared with values reported for populations of Q. robur closer to the core of its range. At the landscape level, some spatial and temporal sub-structuring was observed, likely explained by the history of land-use on the island. Overall, Q. robur fulfils the expectation of the central-marginal hypothesis of high differentiation among marginal populations, but the notable population differentiation has most likely been influenced also by the long, ongoing fragmentation of populations. Finnish oak populations may still be adjusting to the drastic habitat changes of the past centuries. Preservation of genetic variation within the remaining stands is thus an important factor in the conservation of Q. robur at its range margin.

  • Pohjanmies, University of Helsinki, Department of Agricultural Sciences, Spatial Foodweb Ecology Group, P.O. Box 27, FI-00014 University of Helsinki, Finland; University of Jyväskylä, Department of Biological and Environmental Sciences, P.O. Box 35, FI-40014 University of Jyväskylä, Finland ORCID ID:E-mail: tahti.t.pohjanmies@jyu.fi (email)
  • Elshibli, Natural Resources Institute Finland (Luke), Green technology, P.O. Box 18, FI-01301 Vantaa, Finland; University of Helsinki, Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Finland ORCID ID:E-mail: sakina.elshibli@helsinki.fi
  • Pulkkinen, Natural Resources Institute Finland (Luke), Green technology, Haapastensyrjäntie 34, FI-12600 Läyliäinen, Finland ORCID ID:E-mail: pertti.pulkkinen@luke.fi
  • Rusanen, Natural Resources Institute Finland (Luke), Green technology, P.O. Box 18, FI-01301 Vantaa, Finland ORCID ID:E-mail: mari.rusanen@luke.fi
  • Vakkari, Natural Resources Institute Finland (Luke), Green technology, P.O. Box 18, FI-01301 Vantaa, Finland ORCID ID:E-mail: pekka.vakkari@luke.fi
  • Korpelainen, University of Helsinki, Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Finland ORCID ID:E-mail: helena.korpelainen@helsinki.fi
  • Roslin, University of Helsinki, Department of Agricultural Sciences, Spatial Foodweb Ecology Group, P.O. Box 27, FI-00014 University of Helsinki, Finland; Swedish University of Agricultural Sciences, Department of Ecology, P.O. Box 7044, SE-750 07 Uppsala, Sweden ORCID ID:E-mail: tomas.roslin@helsinki.fi
article id 905, category Research article
Katarzyna A. Jadwiszczak, Danuta Drzymulska, Agata Banaszek, Piotr Jadwiszczak. (2012). Population history, genetic variation and conservation status of the endangered birch species Betula nana L. in Poland. Silva Fennica vol. 46 no. 4 article id 905. https://doi.org/10.14214/sf.905
The effective conservation of species requires data on the levels and distribution of genetic diversity within and among populations. In this study, we estimated the genetic variation in three isolated populations of Betula nana in Poland. An analysis of 11 nuclear microsatellites revealed moderate mean heterozygosities (HO=0.556, HE=0.562), low mean number of alleles per locus (A=4.57) and no inbreeding in the total sample. An M-ratio test indicated that each population had experienced a severe bottleneck in the past. Tests for heterozygosity excess revealed that a significant decrease in the numbers of individuals in two populations had occurred quite recently. The large number of private alleles and very restricted number of migrants between populations (Nm=0.35) strongly suggest that genetic drift and geographic isolation are the primary factors responsible for the reduction of genetic variation in the Polish populations of B. nana. We detected two cpDNA haplotypes in the study populations, which can be explained in terms of either the genetic drift acting on the relict localities or a postglacial recolonisation from distinct refugia. Palynological data indicated that one refugium could be located in the Carpathians and their northern foreland. The primary threat to B. nana in Poland is the overgrowth of its habitats by competing species, which has likely resulted in a lack of generative reproduction in the mountain populations.
  • Jadwiszczak, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland ORCID ID:E-mail: kszalaj@uwb.edu.pl (email)
  • Drzymulska, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland ORCID ID:E-mail:
  • Banaszek, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland ORCID ID:E-mail:
  • Jadwiszczak, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland ORCID ID:E-mail:
article id 326, category Research article
Xuejiang Zhang, Helena Korpelainen, Chunyang Li. (2006). Microsatellite variation of Quercus aquifolioides populations at varying altitudes in the Wolong Natural Reserve of China. Silva Fennica vol. 40 no. 3 article id 326. https://doi.org/10.14214/sf.326
Genetic variation and differentiation were investigated among five natural populations of Quercus aquifolioides occurring along an altitudinal gradient that varied from 2000 to 3600 m above sea level in the Wolong Natural Reserve of China, by analyzing variation at six microsatellite loci. The results showed that the populations were characterized by relatively high intra-population variation with the average number of alleles equaling 11.33 per locus and the average expected heterozygosity (HE) being 0.779. The amount of genetic variation varied only little among populations, which suggests that the influence of altitude factors on microsatellite variation is limited. However, there is a significantly positive correlation between altitude and the number of low-frequency alleles (R2 = 0.97, P < 0.01), which indicates that Q. aquifolioides from high altitudes has more unique variation, possibly enabling adaptation to severe conditions. F statistics showed the presence of a slight deficiency of heterozygosity (FIS = 0.136) and a low level of differentiation among populations (FST = 0.066). The result of the cluster analysis demonstrated that the grouping of populations does not correspond to the altitude of the populations. Based on the available data, it is likely that the selective forces related to altitude are not strong enough to significantly differentiate the populations of Q. aquifolioides in terms of microsatellite variation.
  • Zhang, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, P. R. China; Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China ORCID ID:E-mail:
  • Korpelainen, Department of Applied Biology, P.O. Box 27, FI-00014 University of Helsinki, Finland ORCID ID:E-mail:
  • Li, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, P. R. China ORCID ID:E-mail: licy@cib.ac.cn

Category: Research note

article id 5644, category Research note
Jiří Korecký, Jan Bílý, Petr Sedlák, Milan Lstibůrek. (2017). Innovative multiplex and its evaluation for effective genotyping of wild cherry. Silva Fennica vol. 51 no. 3 article id 5644. https://doi.org/10.14214/sf.5644
Highlights: We present simple and cost-efficient method of SSR genotyping in cherry species; Seven of fifteen previously published primer sequences have been altered in order to produce complementary amplicons in pseudo 15-plex; The effectiveness and discriminatory power of established multiplex were verified by SSRs analysis of 48 wild cherry trees.

Trees from the family Rosaceae play an important role in forest and agricultural ecosystems. Therefore, they are often an object of interest for both forest and horticultural tree breeders. Here, we present the utilization of an effective microsatellite (SSRs) genotyping method for wild cherry (Prunus avium L.) and verified the discriminatory power of the presented multiplex by genotyping 48 genetically distinctive individuals (plus-trees). Concerned loci were previously proven to be cross-compatible among various cultivars of cherry, hence, the method could have a broader utilization beyond to the field of forestry.
Our technique is based on post-PCR processing of 15 polymorphic SSRs loci amplified in three multiplex reactions with fluorescently labeled primers (6-FAM, VIC, PET and NED). All PCR products could be pooled and analyzed simultaneously (pseudo 15-plex). In order to make this approach feasible, we redefined sequences of several primers. Thus, utilizing modified primers provides non-overlapping amplicons of each fluorescent dye.

  • Korecký, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21, Prague, Czech Republic ORCID ID: http://orcid.org/0000-0001-7859-1750 E-mail: korecky@fld.czu.cz (email)
  • Bílý, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21, Prague, Czech Republic ORCID ID: http://orcid.org/0000-0001-5794-0907 E-mail: bily@fld.czu.cz
  • Sedlák, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 21, Prague, Czech Republic ORCID ID: http://orcid.org/0000-0001-8016-8900 E-mail: sedlak@af.czu.cz
  • Lstibůrek, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21, Prague, Czech Republic ORCID ID: http://orcid.org/0000-0002-6304-6669 E-mail: lstiburek@fld.czu.cz
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
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.

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 ORCID ID:E-mail: celepirovic.nevenka@gmail.com (email)
  • Karija Vlahović, DNA Laboratory, Department of Forensic Medicine&Criminology, School of Medicine, University of Zagreb, Zagreb, Croatia ORCID ID:E-mail: monika.karija.vlahovic@mef.hr
  • Dounavi, Department of Forest Protection, Forest Research Insitute of Baden-Württemberg, Wonnhaldesttr. 4, 79100 Freiburg, Germany ORCID ID:E-mail: aikaterini.dounavi@forst.bwl.de
  • Ivanković, Division of Genetics, Forest Tree Breeding and Seed Science, Croatian Forest Research Institute, Jastrebarsko, Croatia ORCID ID:E-mail: mladeni@sumins.hr
article id 1415, category Research note
Zorica Šarac, Tanja Dodoš, Nemanja Rajčević, Srdjan Bojović, Petar Marin, Jelena Aleksić. (2015). Genetic patterns in Pinus nigra from the central Balkans inferred from plastid and mitochondrial data. Silva Fennica vol. 49 no. 5 article id 1415. https://doi.org/10.14214/sf.1415
Highlights: Seven populations of Pinus nigra from the central Balkans, representing four infraspecific taxa, were analyzed with chloroplast microsatellites and a mitochondrial locus; Molecular data failed to support infraspecific circumscriptions; Levels of genetic diversities/differentiation at both genomes were in the range of those reported in western Mediterranean populations of P. nigra; Iberian/African and Balkans’ populations share one mtDNA polymorphism and differ in three mutations.

Pinus nigra J.F. Arnold, European black pine, is a typical component of Mediterranean and sub-Mediterranean coniferous forests with highly fragmentary distribution. Western Mediterranean populations of this species have been studied genetically to date, while eastern populations from the central Balkans, which are larger and more abundant, are still genetically understudied. We analyzed seven populations of P. nigra representing all infraspecific taxa recognized within the central Balkans (subspecies nigra with varieties nigra and gocensis Đorđević; and subspecies pallasiana (Lamb.) Holmboe with varieties pallasiana and banatica (Endl.) Georgescu et Ionescu), with three chloroplast microsatellites (cpDNA SSRs) and one mitochondrial (mtDNA) locus. Although our molecular data failed to support circumscription of studied infraspecific taxa, we found that genetic patterns at both genomes are in accordance with those found previously in westward populations of this species, that is – exceptionally high levels of genetic diversity (HT = 0.949) and low genetic differentiation (GST = 0.024) at the cpDNA level, and moderate levels of genetic diversity (HT = 0.357) and genetic differentiation (GST = 0.358) at the mtDNA level. Based on genealogical relations of mtDNA types currently present in Balkans’ and Iberian/African populations, we inferred that the ancestral gene pool of P. nigra already harbored polymorphism at position 328 prior to the divergence to two lineages currently present in westward and eastward parts of the species range distribution. Subsequent occurrence of three mutations, which distinguish these two lineages, suggests their long-term isolation.

  • Šarac, University of Niš, Faculty of Sciences and Mathematics, Department of Biology and Ecology, Višegradska 33, 18000 Niš, Serbia ORCID ID:E-mail: saraczorica@gmail.com (email)
  • Dodoš, University of Belgrade, Faculty of Biology, Institute of Botany and Botanical Garden “Jevremovac”, Studentski trg 16, 11000 Belgrade, Serbia ORCID ID:E-mail: tanjadodos@bio.bg.ac.rs
  • Rajčević, University of Belgrade, Faculty of Biology, Institute of Botany and Botanical Garden “Jevremovac”, Studentski trg 16, 11000 Belgrade, Serbia ORCID ID:E-mail: nemanja@bio.bg.ac.rs
  • Bojović, University of Belgrade, Institute for Biological Research “Siniša Stanković”, Boulevard Despota Stefana 142, 11060 Belgrade, Serbia ORCID ID:E-mail: bojovic@ibiss.bg.ac.rs
  • Marin, University of Belgrade, Faculty of Biology, Institute of Botany and Botanical Garden “Jevremovac”, Studentski trg 16, 11000 Belgrade, Serbia ORCID ID:E-mail: pdmarin@bio.bg.ac.rs
  • Aleksić, University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444a, P.O. Box 23, 11000 Belgrade, Serbia ORCID ID:E-mail: aleksic_jelena@yahoo.com.au

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