Abstract
We investigated 39 previously developed Betula, Alnus, and Corylus simple sequence repeat (SSR) markers for their utility in the cross-generic amplification of two European alder species, i.e., Alnus glutinosa and A. incana. Of these markers, ten loci had successful amplification within Alnus species. Finally, we designed two multiplexes composed of eight and nine loci for A. glutinosa and A. incana, respectively. Multiplexes were tested on 100 samples from five different populations of each species across Europe. The majority of loci had a relatively high genetic diversity, were in Hardy–Weinberg equilibrium, and showed low error rates and low occurrence of null alleles. By comparing sequences of source species and both Alnus species, we concluded that repeat motifs of five of these ten loci differed from those described for the source species. These differences represent mainly the modifications of the original motifs and affected compound or interrupted repeats as well as pure ones. The repeat motifs of three loci of the two alder species also differed. These mutations could lead to erroneous estimates of allele homology, because alleles with identical lengths will not have the same number of repeat units. Hence, before using microsatellite markers in studies comparing two or more species, they should be carefully examined and sequenced to ensure that allele homology is really stable and not affected by various inserts that change the sequence.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bonin A, Bellemain E, Bronken Eidesen P et al (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273. doi:10.1111/j.1365-294X.2004.02346.x
Brookfield J (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453–455. doi:10.1046/j.1365-294X.1996.00098.x
Chapuis M, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631. doi:10.1093/molbev/msl191
Claessens H, Oosterbaan A, Savill P, Rondeux J (2010) A review of the characteristics of black alder (Alnus glutinosa (L.) Gaertn.) and their implications for silvicultural practices. Forestry 83:163–175. doi:10.1093/forestry/cpp038
Cox K, Vanden Broeck A, Van Calster H, Mergeay J (2011) Temperature-related natural selection in a wind-pollinated tree across regional and continental scales. Mol Ecol 20:2724–2738. doi:10.1111/j.1365-294X.2011.05137.x
Doyle J, Morgante M, Scott V, Wayne P (1998) Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine). Mol Biol Evol 15:215–218
Duchesne P, Godbout M-H, Bernatchez L (2002) PAPA (package for the analysis of parental allocation): a computer program for simulated and real parental. Mol Ecol Notes 2:191–193. doi:10.1046/j.1471-8286.2002.00164.x
Ellegren H (2000) Microsatellite mutations in the germline. Trends Genet 16:551–558. doi:10.1093/mutage/ger028
Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445. doi:10.1038/nrg1348
Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486
Guichoux E, Lagache L, Wagner S et al (2011a) Current trends in microsatellite genotyping. Mol Ecol Resour 11:591–611. doi:10.1111/j.1755-0998.2011.03014.x
Guichoux E, Lagache L, Wagner S et al (2011b) Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.). Mol Ecol Resour 11:578–585. doi:10.1111/j.1755-0998.2011.02983.x
Gürcan K, Mehlenbacher S (2010) Transferability of microsatellite markers in the Betulaceae. J Am Soc Hortic Sci 135:159–173
Gürcan K, Mehlenbacher SA, Botta R, Boccacci P (2010) Development, characterization, segregation, and mapping of microsatellite markers for European hazelnut (Corylus avellana L.) from enriched genomic libraries and usefulness in genetic diversity studies. Tree Genet Genomes 6:513–531. doi:10.1007/s11295-010-0269-y
Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Hoffman JI, Amos W (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Mol Ecol 14:599–612. doi:10.1111/j.1365-294X.2004.02419.x
Huntley B, Birks H (1983) An atlas of past and present pollen maps for Europe: 0–13000 years ago. Cambridge University Press, Cambridge
King A, Ferris C (1998) Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Mol Ecol 7:1151–1161. doi:10.1046/j.1365-294x.1998.00432.x
Kulju KKM, Pekkinen M, Varvio S (2004) Twenty-three microsatellite primer pairs for Betula pendula (Betulaceae). Mol Ecol Notes 4:471–473. doi:10.1111/j.1471-8286.2004.00704.x
Lance SL, Jones KL, Hagen C et al (2009) Development and characterization of nineteen polymorphic microsatellite loci from seaside alder, Alnus maritima. Conserv Genet 10:1907–1910. doi:10.1007/s10592-009-9851-y
Lepais O, Bacles CFE (2011) De novo discovery and multiplexed amplification of microsatellite markers for black alder (Alnus glutinosa) and related species using SSR-enriched shotgun pyrosequencing. J Hered 102:627–632. doi:10.1093/jhered/esr062
McVean D (1953) Account of Alnus glutinosa (L.) Gaertn. for the Biological Flora of the British Isles. J Ecol 41:447–466
Oddou-Muratorio S, Vendramin GG, Buiteveld J, Fady B (2009) Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci? Conserv Genet 10:1343–1347. doi:10.1007/s10592-008-9648-4
Ogyu K, Tsuda Y, Sugaya T et al (2003) Identification and characterization of microsatellite loci in Betula maximowicziana Regel. Mol Ecol Notes 3:268–269. doi:10.1046/j.1471-8286.2003.00419.x
Peakall R, Gilmore S, Keys W (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability. Mol Biol Evol 15:1275–1287
Pearse DE, Crandall KA (2004) Beyond FST: analysis of population genetic data for conservation. Conserv Genet 5:585–602. doi:10.1007/s10592-003-1863-4
Petit RJ, Deguilloux M, Chat J et al (2005) Standardizing for microsatellite length in comparisons of genetic diversity. Mol Ecol 14:885–890. doi:10.1111/j.1365-294X.2005.02446.x
Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6:847–859. doi:10.1038/nrg1707
Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629. doi:10.1111/j.1461-0248.2006.00889.x
Štorchová H, Hrdličková R, Chrtek J et al (2000) An improved method of DNA isolation from plants collected in the field and conserved in saturated NaCl/CTAB solution. Taxon 49:79–84. doi:10.2307/1223934
Tallantire (1974) The palaeohistory of the grey alder (Alnus incana (L.) Moench.) and black alder (A. glutinosa (L.) Gaertn.) in Fennoscandia. New Phytol 73:529–546. doi:10.1111/j.1469-8137.1974.tb02131.x
Truong C, Palme A, Felber F, Naciri-Graven Y (2005) Isolation and characterization of microsatellite markers in the tetraploid birch, Betula pubescens ssp. tortuosa. Mol Ecol Notes 5:96–98. doi:10.1111/j.1471-8286.2004.00848.x
Tsuda Y, Ueno S, Ide Y, Tsumura Y (2009a) Development of 14 EST-SSRs for Betula maximowicziana and their applicability to related species. Conserv Genet 10:661–664. doi:10.1007/s10592-008-9608-z
Tsuda Y, Ueno S, Ranta J et al (2009b) Development of 11 EST-SSRs for Japanese white birch, Betula platyphylla var. japonica and their transferability to related species. Conserv Genet 10:1385–1388. doi:10.1007/s10592-008-9701-3
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. doi:10.1111/j.1471-8286.2004.00684.x
Weir B, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370. doi:10.2307/2408641
Wilson G, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177–1191
Wu B, Lian C, Hogetsu T (2002) Development of microsatellite markers in white birch (Betula platyphylla var. japonica). Mol Ecol 3:413–415. doi:10.1046/j.1471-8278
Yatrik Y (1982) Betulaceae. In: Davis P (ed) Flora Turkey, vol 7. Edinburh University Press, Edinburgh, pp 688–694
Zhuk A, Veinberga I, Daugavietis M, Rungis D (2008) Cross-species amplification of Betula pendula Roth. simple sequence repeat markers in Alnus species. Balt For 14:116–121
Acknowledgments
We would like to thank Martina Hadincová and Eva Ničová for their help in the lab and John P. Bailey for language editing of the manuscript. We also would like to thank Phil Gibson for his help with microsatellite markers originally developed for Alnus maritima. This study was supported by grant no. P504/11/0402 from the Grant Agency of the Czech Republic and as a long-term research development project no. RVO 67985939.
Data Archiving Statement
The sequence data generated in this study have been deposited at GenBank under the accession numbers KF724864–KF724880.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by P. Ingvarsson
Electronic supplementary material
Below is the link to the electronic supplementary material.
Online Resource 1
Characteristics of 39 microsatellite loci from Betulaceae used for cross-amplification on A. glutinosa and A. incana sorted according to success or failure during optimization. (DOCX 33 kb)
Rights and permissions
About this article
Cite this article
Drašnarová, A., Krak, K., Vít, P. et al. Cross-amplification and multiplexing of SSR markers for Alnus glutinosa and A. incana . Tree Genetics & Genomes 10, 865–873 (2014). https://doi.org/10.1007/s11295-014-0727-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11295-014-0727-z