Research article

Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.)

Sudhir Khodwekar, Margaret Staton, Mark V. Coggeshall, John E. Carlson, Oliver Gailing

Sudhir Khodwekar
School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931
Margaret Staton
Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN 37996
Mark V. Coggeshall
Department of Forestry, University of Missouri, Columbia, MO 65274
John E. Carlson
Department of Ecosystem Science and Management and Department of Plant Science, The Pennsylvania State University, University Park, PA 16802.
Oliver Gailing
School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931. Email:

Online First: April 15, 2015
Khodwekar, S., Staton, M., Coggeshall, M., Carlson, J., Gailing, O. 2015. Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.). Annals of Forest Research DOI:10.15287/afr.2015.360

A set of seven new nuclear microsatellite markers (nSSRs) was developed
for sugar maple (Acer saccharum Marsh.) using paired-end Illumina sequencing. Out of 96 primers screened in a panel of six unrelated individuals, seven markers amplified polymorphic products. The utility of these markers, in addition to six already published microsatellites, for genetic variation and gene flow studies was assessed. Out of the seven newly developed markers, three amplified multiple fragments and were interpreted as dominant (absence/presence) markers, while four markers amplified a maximum of two amplification products per sample. The six published microsatellites and three of the four newly developed markers showed regular segregation in an open-pollinated single tree progeny. Observed heterozygosity (Ho) and expected heterozygosity (He) in 48 individuals from one population ranged from 0.436 to 0.917 and from 0.726 to 0.894, respectively. Dominant markers revealed 64 variable positions and moderate genetic variation within the population (He = 0.102, Shannon’s I = 0.193). Paternity analyses in the program CERVUS at co-dominant markers showed effective dispersal of pollen in the sugar maple population both at 95% and 80% confidence levels. Dependent on the confidence level, the mean pollen dispersal distance within the population ranged from 33.25 m to 38.75 m and gene flow from utside the stand from 78% to 82%. The absence of fine-scale Spatial Genetic Structure (SGS) suggested effective dispersal of both seeds and pollen.

Bal, T. L., D. L. Richter, A. J. Storer, and M. F. Jurgensen. 2013. The relationship of the sapstreak fungus, Ceratocystis virescens, to sugar maple dieback and decay in Northern Michigan. American Journal of Plant Sciences 4: 436-443. DOI: 10.4236/ajps.2013.42A056

Brown, A. H. D., and B. S. Weir. 1983. Measuring genetic variability in plant populations. In: Tanksley SD, Orton TJ (eds). Isozymes in Plant Genetics and Breeding, Part A. Elsevier,Amsterdam, pp 219-239.

Cavers, S., B. Degen, H. Caron, M. R. Lemes, R. Margis, F. Salgueiro, and A. J. Lowe. 2005. Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity 95: 281-289. DOI: 10.1038/sj.hdy.6800709

Dohm, J. C., C. Lottaz, T. Borodina, and H. Himmelbauer. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research 36: E1005. DOI: 10.1093/nar/gkn425

Finkeldey, R., and M. Ziehe. 2004. Genetic implications of silvicultural regimes. ForestEcology and Management 197: 231-244. DOI: 10.1016/j.foreco.2004.05.036

Gabriel, W. J. 1968. Dichogamy in Acer saccharum. Botanical Gazzette 129: 334-338. DOI: 10.1086/336453

Gabriel, W. J., and P. W. Garrett. 1984. Pollen vectors in sugar maple (Acer saccharum). Canadian Journal of Botany 62: 2889-2890. DOI: 10.1139/b84-385

Geburek, T. 1993. Are genes randomly distributed over space in mature populations of sugar maple (Acer saccharum Marsh.)? Annals of Botany 71: 217-222. DOI: 10.1006/anbo. 1993.1027

Gibson, P. J., and N. T. Wheelwright. 1995. Genetic structure in a population of a tropical tree Ocotea tenera (Lauraceae): influence of avian seed dispersal. Oecologia 103: 49-54. DOI: 10.1007/BF00328424

Gillet, E., and H. H. Hattemer. 1989. Genetic analysis of isozyme phenotypes using single tree progenies. Heredity 63: 135-143. DOI: 10.1038/hdy.1989.84

Godman, R. M., H. W. Yawney, and C. H. Tubbs. 1990. Acer saccharum Marsh. Sugar maple. In: Burns, RM, Honkala BH (eds.) Silvics of North America, Agricultural handbook 654 volume 2.Hardwoods-USDAForestService 2: 78-91.

Graignic, N., F. Tremblay, and Y. Bergeron. 2013. Development of polymorphic nuclear microsatellite markers in sugar maple (Acer saccharum Marsh.) using cross-species transfer and SSR-enriched shotgun pyrosequencing. Conservation Genetic Resources 5: 845-848. DOI: 10.1007/s12686-013-9923-7

Graignic, N., F. Tremblay, Y. Bergeron, and J. Williams. 2014. Geographical variation in reproductive capacity of sugar maple (Acer saccharum Marshall) northern peripheral populations. Journal of Biogeography 41: 145-157. DOI: 10.1111/jbi.12187

Gunter, L., E., G. Tuskan, A., C. Gunderson, A., and R. J. Norby. 2000. Genetic variation and spatial structure in sugar maple (Acer saccharum Marsh.) and implications for predicted global-scale environmental change. Global Change Biology 6: 335-344. DOI: 10.1046/j.1365-2486.2000.00313.x

Guries, R. P., and E. V. Nordheim. 1984. Flight characteristics and dispersal potential of maple samaras.ForestScience 30: 434-440.

Hardy, O. J., and X. Vekemens. 2002. SPAGeDi: A versatile computer program to analyse spatial genetic structure at individual or population levels. Molecular Ecology Notes 2: 618-620. DOI: 10.1046/j.1471-8286.2002.00305.x

Huang, X. 1999. CAP3: A DNA sequence assembly program. Genome Research 9: 868-877. DOI: 10.1101/gr.9.9.868

Iverson, L. R., A. M. Prasad, S. N. Matthews, and M. Peters. 2008. Estimating potential habitat for 134 eastern US tree species under six climate scenarios. ForestEcology and Management 254: 390-406. DOI: 10.1016/j.foreco.2007.07.023

Krustovsky, K. V., and D. B. Neale. 2005. Forest genomics and new molecular approaches to measuring and conserving adaptive genetic diversity in forest trees, In: Conservation and Management of Forest Genetic Resources inEurope, T. Geburek and J. Turok (eds.), Arbora Publishers, Zvolen, pp 369-390.

Loiselle, B. A., V. L. Sork, G. Nason, and C. Graham. 1995. Spatial genetic structure of a tropical understory shrub. American Journal of Botany 82: 1420-1425. DOI: 10.2307/ 2445869

Marshall, T. C., J. Slate, L. E. B. Kruuk, and J. M. Pemberton. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: 639-655. DOI: 10.1046/j.1365-294x.1998.00374.x

Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of SciencesUSA70: 3321-3323. DOI: 10.1073/pnas.70.12.3321

Nei, M. 1987. Molecular Evolutionary Genetics.ColumbiaUniversityPress,New York.

Nesom, G. 2006. Plant Guide, sugar maple. United States Department Department of Agriculture Natural Resources Conservation Service (

Owusu, S. A., M. Staton, T. N. Jennings, S. Schlarbaum, M. V. Coggeshall, J. Romero-Severson, J. E. Carlson, and O. Gailing. 2013. Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina sequencing. Applications in Plant Sciences 1 (12): 1300050. DOI: 10.3732/apps.1300050

Pakkad, G., S. Ueno, and H. Yoshimaru. 2008. Gene flow pattern and mating system in a small population of Quercus semiserrata Roxb. (Fagaceae). ForestEcology and Management 255: 3819-3826. DOI: 10.1016/j.foreco.2008.03.017

Pandey, M., O. Gailing, D. Fischer, H. H. Hattemer, and R. Finkeldey. 2004. Characterization of microsatellite markers in sycamore (Acer pseudoplatanus L.). Molecular Ecology Notes 4: 253-255. DOI: 10.1111/j.1471-8286.2004.00633.x

Pandey, M., O. Gailing, H. H. Hattemer, and R. Finkeldey. 2012. Fine-scale spatial genetic structure of sycamore maple (Acer pseudoplatanus L.). European Journal of ForestResearch 131: 739-746. DOI: 10.1007/s10342-011-0546-9

Peakall, R., and P. E. Smouse. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28: 2537-2539. DOI: 10.1093/bioinformatics/bts460

Peakall, R. O. D., and P. E. Smouse. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295. DOI: 10. 1111/j.1471-8286.2005.01155.x

Perry, D. J., and P. Knowels. 1991. Spatial genetic structure within three sugar maple (Acer saccharum Marsh) stands. Heredity 66: 137-142. DOI: 10.1038/hdy.1991.17

Pluess, A. R., V. L. Sork, B. Dolan, F. W. Davis, D. Grivet, K. Merg, J. Papp, and P. E. Smouse. 2009. Short distance pollen movement in a wind-pollinated tree, Quercus lobata (Fagaceae). ForestEcology and Management 258: 735-744. DOI: 10.1016/j.foreco.2009. 05.014

Raymond, M., and F. Rousset. 1995. GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Eucemenicism. Journal of Heredity 86: 248 - 249.

Rousset, F. 2008. genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources 8: 103-106. DOI: 10.1111/j.1471-8286. 2007.01931.x

Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and biologist programmers. Methods in Molecular Biology 132: 365-386.

Selkoe, K. A., and R. J. Toonen. 2006. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters 9:615-629. DOI: 10.1111/j.1461-0248.2006.00889.x

Stefenon, V. M., O. Gailing, and R. Finkeldey. 2008. The role of gene flow in shaping genetic structures of the subtropical conifer species Araucaria angustifolia. Plant Biology 10:356-364. DOI: 10.1111/j.1438-8677.2008.00048.x

Stephens, H. A. 1973. Woody plants of the North Central plains.Lawrence,KS: The University Press ofKansas. 530 p.

Whitham, T. G., S. P. Difazio, J. A. Schweitzer, S. M. Shuster, G. J. Allan, J. K. Bailey, and S. A. Woolbright. 2008. Extending genomics to natural communities and ecosystems. Science 320: 492-495. DOI: 10.1126/science.1153918

Whitham, T. G., C. A. Gehring, L. J. Lamit, T. Wojtowicz, L. M. Evans, A. R. Keith, and D. S. Smith. 2012. Community specificity: life and afterlife effects of genes. Trends in Plant Science 17: 271-281. DOI: 10.1016/j.tplants.2012.01.005

Young, A. G., and H. G. Merrium. 1994. Effects of forest fragmentation on the spatial genetic structure in Acer saccharum Marsh. (sugar maple) populations. Heredity 72: 201-208. DOI: 10.1038/hdy.1994.27

Supplementary Data
No metrics available for this article.