Novel polymorphic nuclear microsatellite markers for Pinus sylvestris L.

Sebastiani, Federico; Pinzauti, F.; Kujala, Sonja; González‐Martínez, Santiago C.; Vendramin, G. G.

doi:10.1007/s12686-011-9513-5

Cited by 39 publications

(25 citation statements)

References 14 publications

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“…To date, the low number of nSSR loci developed for Scots pine is the main limiting factor for multiplex development. Recently, a few more nSSR loci have been published (Sebastiani et al 2012) and the number is expected to increase substantially with the emergence of next-generation sequencing technologies. Typically, multiplexing involves three to twelve loci (Frey et al 2004;Guichoux et al 2011); however, higher levels of multiplexing are still possible (e.g., Hill et al 2009;Campoy et al 2010), while the identification of SSR loci of a larger size range is still the main limiting factor.…”

Section: Resultsmentioning

confidence: 99%

Development and transferability of two multiplexes nSSR in Scots pine (Pinus sylvestris L.)

et al. 2015

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Single sequence repeat (SSR) multiplexing is a semi high-throughput PCR methodology for the analysis of multiple SSRs. We developed two SSR multiplexes selected from SSR loci previously reported in the pine literature and tested the transferability of both SSR multiplexes in nine other pine species. We tested 234 nuclear SSR loci (nSSRs) previously described in the pine literature and selected ten nSSRs following the simple criteria of interpretability and reproducibility. Selected nuclear loci were divided into two nSSRs multiplex sets and their amplification was optimized for three different multiplex PCR methods based on: (a) a custom PCR protocol, (b) a custom protocol with hotstart taq polymerase, and (c) a commercially available kit for SSR multiplexing. To validate their performance, the level of genetic diversity was assessed in three Scots pine natural populations (Hungary, northern Sweden and southern Sweden). In addition, we also tested the transferability of these multiplexes in nine other pine species. We have developed two nSSRs multiplexes of five loci each that will contribute to reduce the costs of nSSR scoring, while increasing the capacity of nSSR loci analysis. Amplification was successful in all three populations (94 % success) and the level of polymorphism (7.1 alleles/marker) was similar to that previously reported for other Scots pine natural populations. Transferability of both multiplexes was successful for those pine species closely related to Scots pine.

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Section: Resultsmentioning

confidence: 99%

Development and transferability of two multiplexes nSSR in Scots pine (Pinus sylvestris L.)

et al. 2015

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“…The high genetic diversity has been reported in isolated populations from Italy (H e = 0.847 and 0.81; Belletti et al 2012;Scalfi et al 2009, respectively) and in populations from the broad pine distribution from Romania and Sweden (H e ranged from 0.50 to 0.80; Floran et al 2010), determined by the nuclear microsatellites. On the other hand low values of heterozygosity (H e = 0.338, H e = 0.376, H e = 0.325, respectively) for some Scots pine populations from continuous species distribution, from Finland and two populations from Russia, have been showed (Sebastiani et al 2012). Additionally, the high level of the genetic diversity for chloroplast microsatellites loci was observed in populations of Scots pine from Scotland, Spain, Western and Central Europe (H ranged from 0.950 to 0.987, Provan et al 1998), in Italian (H = 0.92, Scalfi et al 2009) and Spanish P. sylvestris (H = 0.978, Robledo-Arnucio et al 2004).…”

Section: Discussionmentioning

confidence: 98%

“…All trees were genotyped using eighteen microsatellite loci, including the following nuclear SSRs: psyl42, psyl25, psyl18, psyl44, psyl57, psyl36 (Sebastiani et al 2012), PtTX3025 (Elsik et al 2000), PtTX4011, PtTX4001 (Zhou et al 2002), Spac11.4 , and the following chloroplast SSR loci: PCP36567, PCP30277, PCP102652, PCP26106, PCP87314, PCP45071, PCP1289, and PCP41131 . PCR (Polymerase Chain Reaction) amplifications were performed with a final volume of 10 μl containing 10 mM of each dNTP, 5 μM each of forward and reverse primers, 0.15 U Taq DNA polymerase, 1x BSA, 1.5 μM MgCl 2 and 1x PCR buffer.…”

Section: Microsatellite Genotyping and Analysismentioning

confidence: 99%

Genetic characteristics of Scots pine in Poland and reference populations based on nuclear and chloroplast microsatellite markers

Hebda¹,

Wójkiewicz²,

Wachowiak³

2017

Silva Fenn.

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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.

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Section: Methodsmentioning

confidence: 99%

“…Primers for the genetic analysis of Norway spruce samples were adopted from Fluch et al [51], and for the analysis of Scots pine samples from Soranzo et al [39] (Spac12.5, Spac11.4 and Spac7.14), Sebastiani et al [52] (Psyl16, Psyl57 and Psyl18) and Elsik et al [53] (PtTX4001 and PtTX4011) ( Table 1). Amplification of Norway spruce DNA was performed separately for each sample, while Scots pine DNA was amplified in three multiplex reactions (multiplex A-primer Spac7.14, multiplex B-primers psyl18 and psyl57, and multiplex C-primers psyl16, Spac11.4, Spac12.5, PtTX4001 and PtTX4011).…”

Section: Methodsmentioning

confidence: 99%

Genetic Diversity and Its Spatial Distribution in Self-Regenerating Norway Spruce and Scots Pine Stands

Verbylaitė

Pliūra

Lygis

et al. 2017

Forests

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Abstract:Tree genetic diversity is among the most important factors determining the sustainability of forest ecosystems. The main aim of the present study was to track possible changes in genetic diversity of regenerating populations of Norway spruce (Picea abies (L.) H. Karst) and Scots pine (Pinus sylvestris L.) in areas subjected either to a natural disturbance (windthrows and subsequent clear-cutting of the affected spruce stand) or to a changed land-use legacy (pine regeneration on abandoned agricultural land) with the aim of testing whether the new forest generation retains the genetic diversity of the putative maternal stand. Eight highly polymorphic microsatellite loci were used to reveal the genetic diversity and its spatial distribution in the studied tree populations. Self-regenerating juveniles of Norway spruce and Scots pine were spatially random and as genetically diverse as in the putative maternal populations. Genetic differentiation between putatively maternal trees and regenerating juveniles was low for both species. A high genetic diversity and random spatial genetic structure revealed in the regenerating populations provides a basis for the formation of evolutionary and ecologically sound stands able to adapt to ever-changing climatic conditions. Information on the genetic dynamics of the studied natural populations of long-lived coniferous tree species may be important for evaluating possible changes in genetic diversity at a local scale following forest ecosystem disturbances and changes in land-use legacies.

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Novel polymorphic nuclear microsatellite markers for Pinus sylvestris L.

Cited by 39 publications

References 14 publications

Development and transferability of two multiplexes nSSR in Scots pine (Pinus sylvestris L.)

Development and transferability of two multiplexes nSSR in Scots pine (Pinus sylvestris L.)

Genetic characteristics of Scots pine in Poland and reference populations based on nuclear and chloroplast microsatellite markers

Genetic Diversity and Its Spatial Distribution in Self-Regenerating Norway Spruce and Scots Pine Stands

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