Articles containing the keyword 'microsatellite'

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 (N_a = 16.45, H_e = 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 (F_ST = 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 F_ST/(1–F_ST) 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 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 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 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 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 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 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 E-mail: lkyszy@126.com

Polymorphisms at a set of eighteen nuclear (nSSR) and chloroplast (cpSSR) microsatellite loci were investigated in sixteen populations of Scots pine (Pinus sylvestris L.) derived from the provenance trial experiment and representative of the species distribution range and climatic zones in Poland. The patterns of genetic variation were compared to the reference samples from the species distribution in Europe and Asia. A similar level of genetic variation and no evidence of population structure was found among the Polish stands. They showed genetic similarity and homogenous patterns of allelic frequency spectra compared to the Northern European populations. Those populations were genetically divergent compared to the marginal populations from Turkey, Spain and Scotland. The population structure patterns reflect the phylogeography of the species and the divergence of populations that most likely do not share recent history. As the analysed provenance trial populations from Poland are diverged in phenotypic traits but are genetically similar, they could be used to test for selection at genomic regions that influence variation in quantitative traits.

• Hebda, University of Agriculture in Krakow, Faculty of Forestry, Institute of Forest Ecology and Silviculture, Department of Genetics and Forest Tree Breeding, 29 Listopada 46, 31-425 Kraków, Poland http://orcid.org/0000-0002-3149-8644 E-mail: ana.hebda@gmail.com
• Wójkiewicz, Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland E-mail: bwojkiew@man.poznan.pl
• Wachowiak, Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland; Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland E-mail: witoldw@man.poznan.pl

Castanea sativa Mill. is one of the most endangered tree species in Iran where it is represented by small fragmented populations in the north of the country. 18 simple sequence repeat (SSR) loci (10 nuclear and 8 chloroplastic) were used to evaluate the genetic diversity and population structure of C. sativa from the Hyrcanian forest. For nuclear SSR, the number of alleles detected per locus ranged from 1 to 5 and observed heterozygosity (H_O) was between 0.125 and 1.000. Analysis of molecular variance (AMOVA) indicated a high level of variation within populations (84%) and low levels between populations (16%). Based on structure analysis, the four studied populations were divided into two main clusters that have genetic distance F_st = 0.3. The Shafaroud population was separated in the first cluster, Siyahmazgi, Qalehroudkhan and Veysroud were placed in the second cluster. The UPGMA analysis confirmed the results of Structure analysis, separating the Shafaroud population from the others. The 8 chloroplast SSR loci used to screen the populations showed no polymorphism. In General, low nuclear genetic diversity, no polymorphism in cpDNA and considerable genetic differentiation among populations in short geographical distance represent a serious genetic erosion threat for C. sativa in the Hyrcanian forest, even hinting at an ongoing extinction vortex. Therefore, due to significant decline in genetic diversity, it is essential to introduce constraints protection upon the areas of distribution of all four populations of this species in Iran.

• Janfaza, Department of Forestry, Sari University of Agriculture Sciences and Natural Resources, Km 9 Darya Road, P.O. Box 578, Mazandaran, Iran E-mail: aristocratka_b@yahoo.com
• Yousefzadeh, Department of Environment, Faculty of Natural Resources and Marine Science ,Tarbiat Modares University, Noor, Mazandaran, Iran E-mail: h.yousefzadeh@modares.ac.ir
• Hosseini Nasr, Department of Forestry, Sari University of Agriculture Sciences and Natural Resources, Km 9 Darya Road, P.O. Box 578, Mazandaran, Iran E-mail: s.hosseini@sanru.ac.ir
• Botta, Dipartimento di Scienze Agrarie Forestali e Alimentari, DISAFA, Università di Torino, Via Verdi 8, 10124 Torino, Italy E-mail: roberto.botta@unito.it
• Asadi Abkenar, Agricultural Research, Education and Extension Organization (AREEO) of IRAN, Agricultural Biotechnology Research Institute of Iran (RBRII), Branch of North Region, Guilan, Rasht, Iran E-mail: asadiabkenarasad@gmail.com
• Marinoni, Dipartimento di Scienze Agrarie Forestali e Alimentari, DISAFA, Università di Torino, Via Verdi 8, 10124 Torino, Italy E-mail: daniela.marinoni@unito.it

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 (F_ST = 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 E-mail: tahti.t.pohjanmies@jyu.fi
• 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 E-mail: sakina.elshibli@helsinki.fi
• Pulkkinen, Natural Resources Institute Finland (Luke), Green technology, Haapastensyrjäntie 34, FI-12600 Läyliäinen, Finland E-mail: pertti.pulkkinen@luke.fi
• Rusanen, Natural Resources Institute Finland (Luke), Green technology, P.O. Box 18, FI-01301 Vantaa, Finland E-mail: mari.rusanen@luke.fi
• Vakkari, Natural Resources Institute Finland (Luke), Green technology, P.O. Box 18, FI-01301 Vantaa, Finland E-mail: pekka.vakkari@luke.fi
• Korpelainen, University of Helsinki, Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Finland 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 E-mail: tomas.roslin@helsinki.fi

• Jadwiszczak, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland E-mail: kszalaj@uwb.edu.pl
• Drzymulska, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland E-mail: dd@nn.pl
• Banaszek, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland E-mail: ab@nn.pl
• Jadwiszczak, Institute of Biology, University of Białystok, wierkowa 20B, 15-950 Białystok, Poland E-mail: pj@nn.pl

• Wang, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China; Graduate School of the Chinese Academy of Sciences, Beijing 100039, China E-mail: yw@nn.cn
• Korpelainen, Department of Applied Biology, P.O. Box 27, FI-00014 University of Helsinki, Finland E-mail: hk@nn.fi
• Li, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China E-mail: licy@cib.ac.cn

• 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 E-mail: xz@nn.cn
• Korpelainen, Department of Applied Biology, P.O. Box 27, FI-00014 University of Helsinki, Finland E-mail: hk@nn.fi
• Li, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, P. R. China E-mail: licy@cib.ac.cn

• Jadwiszczak, Institute of Biology, University of Bialystok, wierkowa 20B, 15-950 Bialystok, Poland E-mail: kszalaj@uwb.edu.pl

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 http://orcid.org/0000-0001-7859-1750 E-mail: korecky@fld.czu.cz
• Bílý, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21, Prague, Czech Republic 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 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 http://orcid.org/0000-0002-6304-6669 E-mail: lstiburek@fld.czu.cz

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

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 (H_T = 0.949) and low genetic differentiation (G_ST = 0.024) at the cpDNA level, and moderate levels of genetic diversity (H_T = 0.357) and genetic differentiation (G_ST = 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 E-mail: saraczorica@gmail.com
• Dodoš, University of Belgrade, Faculty of Biology, Institute of Botany and Botanical Garden “Jevremovac”, Studentski trg 16, 11000 Belgrade, Serbia 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 E-mail: nemanja@bio.bg.ac.rs
• Bojović, University of Belgrade, Institute for Biological Research “Siniša Stanković”, Boulevard Despota Stefana 142, 11060 Belgrade, Serbia 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 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 E-mail: aleksic_jelena@yahoo.com.au