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12 October 2015 Characterization and Transferability of Microsatellite Markers Developed for Carpinus betulus (Betulaceae)
Kathleen Prinz, Reiner Finkeldey
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The European hornbeam, Carpinus betulus L. (Betulaceae), is a common, late-successional, shade-tolerant tree often forming bushes and hedges. These edge communities between forest and pasture are highly valued for conservation due to their biodiversity. In addition, they provide refugia for plants and animals and connect biotopes. Carpinus betulus is also often used as an ornamental planting in gardens and nonforested landscapes.

Genetic analyses in C. betulus are scarce; they were based on universal chloroplast markers (Grivet and Petit, 2003) or anonymous amplified fragment length polymorphisms (AFLPs; Coart et al., 2005). Microsatellite markers were established for several species within the family (e.g., Barbará et al., 2007; Gürcan and Mehlenbacher, 2010), but not for C. betulus.

The species is octoploid and thus complex fragment patterns are expected using codominant microsatellite markers. Recent advances in statistical methods and new software allow for analysis of genetic diversity even in polyploid species (e.g., Wiehle et al., 2014).

METHODS AND RESULTS

Genomic DNA was extracted from young leaves of an adult tree of C. betulus growing in Göttingen, Germany (Appendix 1), using the DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). A microsatellite-enriched library was generated based on the protocol of Fischer and Bachmann (1998) with some modifications (Prinz et al., 2009). We used biotinylated oligonucleotides with the motif of (GA)10 for hybridization at 60°C. All steps of the enrichment procedure were repeated once. Final PCR products were purified and ligated into the pCR 2.1-TOPO vector (Invitrogen, Carlsbad, California, USA). The vectors were transformed chemically to One Shot TOP10 Competent cells (Invitrogen). Ninety-six positive clones were sequenced forward and reverse in an ABI Prism 3100 automatic sequencer (Applied Biosystems, Foster City, California, USA), and 44 sequences were suitable for primer design. The remaining fragments showed low quality, short sizes of the flanking regions, or were identified as duplicates. A total of 35 primers were designed applying Primer3 version 2.2.3 (Rozen and Skaletsky, 1999) and tested for amplification. PCR assays were conducted in a final volume of 15 µL containing approximately 10 ng of genomic DNA, 1× Hot Start Buffer (0.8 M Tris-HCl [pH 9.0], 0.2 M (NH4)2SO4, 0.2% w/v Tween-20; Solis BioDyne, Tartu, Estonia), 2.5 mM MgCl2, 0.2 mM of each dNTP, 0.1 unit Hot Start DNA Polymerase (5 U/µL HOT FIREPol; Solis BioDyne), and 0.3 pmol of each primer. Forward primers of each pair were labeled with a fluorescent tag. PCR was performed applying a touchdown program adapted to the annealing temperatures (T a) of each primer provided by Primer3 version 2.2.3 (Rozen and Skaletsky, 1999) and producers. The general protocol contained cycles of 1 min at 94°C, 1 min at T a + 3−5°C to T a – 3−5°C reducing the temperature at 1°C in each cycle, 1 min at 72°C, followed by 25 cycles at the final annealing temperature without further touchdown. PCR products were checked for quality and approximate lengths of the fragments. Nineteen primer pairs revealed unambiguously observable fragments in an expected size range. A test for variability was performed in 25 individuals of C. betulus sampled in Germany and Romania as well as in 13 individuals of several species of the Betulaceae (Appendix 1). After amplification, fragments were separated in an ABI Prism 3100 automatic sequencer (Applied Biosystems), and fragment sizes were scored using GeneScan 3.7 analysis software based on the internal standard GeneScan 500 ROX (Applied Biosystems).

Eleven out of 19 loci revealed unambiguously scorable patterns that were polymorphic among samples of C. betulus (Table 1). Eight loci revealed ambiguous and nonvaluable patterns (Appendix 2). The 11 informative loci were resequenced for some samples to verify the specific amplification products. In total, 252 alleles were detected ranging from 15 to 30 per locus (Table 2). Three to six alleles per locus were most frequently observed in each individual polyploid plant. Lower average numbers of alleles for individual plants were observed only at locus Cb_33, but they were not fixed. Thus, genetic diversity is high, ranging from 0.199 to 0.320, calculated from a converted binary data matrix in which present alleles are represented by “1” and absent alleles by “0” (e.g., Sampson and Byrne, 2012).

Cross-amplification was successful for almost all loci (Table 3). Thus, six loci amplified in all Carpinus species, and one additional locus was successfully applied in seven out of eight Carpinus samples. The reduced number of transferred loci is likely caused by species-specific taxonomic relationships to the species of origin. Successful cross-amplification among species of different Betulaceae genera was observed for three loci amplified in all individuals and two additional loci amplified in four out of five species. Most alleles were shared with C. betulus, whereas two loci showed more than 50% additional alleles (Table 3). Reduced genetic diversity of transferred loci can be explained by low sample size, the general observation of reduced amplification success and genetic diversity after cross-amplification (e.g., Selkoe and Toonen, 2006; Barbará et al., 2007), and finally by differing ploidy levels, which are not known for all species.

Table 1.

Characterization of microsatellite loci developed for Carpinus betulus.

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CONCLUSIONS

In this study, we developed microsatellite markers for C. betulus despite complex fragment patterns resulting from the octoploid nature of the species. We also tested their transferability to other species within Carpinus and other genera of the Betulaceae with ploidy levels that differ and are not known for all species. Highly polymorphic and codominant microsatellite markers allow for detailed analyses of genetic diversity and structure, i.e., gene flow within and among species.

Table 2.

Species-specific genetic diversity of microsatellite loci among 25 Carpinus betulus individuals represented by number of alleles, number of rare alleles (<10%), and unbiased genetic diversity (GenAlEx version 6.4; Peakall and Smouse. 2006).

t02_01.gif

Table 3.

Number of alleles per microsatellite locus resulting from cross-amplification of loci developed for Carpinus betulus and observed in single plants of related species.

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LITERATURE CITED

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Appendices

Appendix 1.

Origin and voucher information for all samples included in the establishment of newly developed microsatellite markers for Carpinus betulus.

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Appendix 2.

Details for additional microsatellite loci developed for Carpinus betulus that revealed ambiguous and nonvaluable patterns.

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Kathleen Prinz and Reiner Finkeldey "Characterization and Transferability of Microsatellite Markers Developed for Carpinus betulus (Betulaceae)," Applications in Plant Sciences 3(10), (12 October 2015). https://doi.org/10.3732/apps.1500053
Received: 5 May 2015; Accepted: 1 July 2015; Published: 12 October 2015
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