Characterization of 20 new EST-SSR markers for northern red oak (Quercus rubra L.) and their transferability to Fagus sylvatica L. and six oak species of section Lobatae and Quercus

Authors

  • Martin Müller University of Goettingen, Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, Center for Integrated Breeding Research, Büsgenweg 2, 37077 Göttingen, Germany
  • Oliver Gailing University of Goettingen, Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, Center for Integrated Breeding Research, Büsgenweg 2, 37077 Göttingen, Germany

DOI:

https://doi.org/10.15287/afr.2018.1191

Keywords:

microsatellites, Fagaceae, genetic diversity

Abstract

Northern red oak (Quercus rubra L.) is widely distributed in the eastern United States and southeastern Canada. It has also been introduced to Europe, where it has become an economically important plantation species now. Despite growing genomic resources, the number of available EST-SSR (expressed sequence tag – simple sequence repeat) markers for Q. rubra is still limited. Here, we used existing sequence information to provide a new set of EST-SSRs for northern red oak. In total, we report 20 polymorphic EST-SSRs, for which performance was evaluated in three Q. rubra populations from different regions in Michigan. We further tested the transferability of these markers to six additional oak species of section Lobatae (Quercus ellipsoidalis E.J. Hill, and Quercus georgiana M.A. Curtis) and Quercus (Quercus robur L., Quercus alba L., Quercus pedunculiflora K. Koch, and Quercus petraea (Matt.) Liebl.), as well as to European beech (Fagus sylvatica L.). The reported markers can be used in future population genetic studies.

References

Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25 (17): 3389-3402. DOI: 10.1093/nar/25.17.3389 Antao T., Lopes A., Lopes R.J., Beja-Pereira A., Luikart G. 2008. LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9: 323. DOI: 10.1186/1471-2105-9-323 Barreneche T, Casasoli M, Russell K, Akkak A, Meddour H, Plomion C, Villani F, Kremer A (2004) Comparative mapping between Quercus and Castanea using simple-sequence repeats (SSRs). Theor Appl Genet 108 (3):558-566 DOI: 10.1007/s00122-003-1462-2 Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. BioTechniques 20 6:1004-1006, 1008-1010 DOI: 10.2144/96206st01 Burger K, Müller M, Gailing O (submitted) Characterization of EST-SSRs for European beech (Fagus sylvatica L.) and their transferability to Fagus orientalis Lipsky, Castanea dentata Bork., and Quercus rubra L. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4 (2):359-361 DOI: 10.1007/s12686-011-9548-7 Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125. DOI: 10.1038/sj.hdy.6801001 Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14 (8):2611-2620. DOI: 10.1111/j.1365-294X.2005.02553.x Giraudoux P (2017) pgirmess: data analysis in ecology. R package version 1.6.7. [online]. To be found in <https://CRAN.R-roject.org/package=pgirmess> Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F-statistics. J Hered 86 (6):485-486. DOI: 10.1093/oxfordjournals.jhered.a111627 Konar A, Choudhury O, Bullis R, Fiedler L, Kruser JM, Stephens MT, Gailing O, Schlarbaum S, Coggeshall MV, Staton ME, Carlson JE, Emrich S, Romero-Severson J (2017) High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra. BMC Genomics 18 (1):417. DOI: 10.1186/s12864-017-3765-8 Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 15 (5):1179-1191 DOI: 10.1111/1755-0998.12387 Kubisiak TL, Nelson CD, Staton ME, Zhebentyayeva T, Smith C, Olukolu BA, Fang GC, Hebard FV, Anagnostakis S, Wheeler N, Sisco PH, Abbott AG, Sederoff RR (2013) A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica). Tree Genet Genomes 9 (2):557-571. DOI: 10.1007/s11295-012-0579-3 Lalagüe H, Csilléry K, Oddou-Muratorio S, Safrana J, de Quattro C, Fady B, González-Martínez SC, Vendramin GG (2014) Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France. Tree Genet Genomes 10 (1):15. DOI: 10.1007/s11295-013-0658-0 Lind JF, Gailing O (2013) Genetic structure of Quercus rubra L. and Quercus ellipsoidalis E. J. Hill populations at gene-based EST-SSR and nuclear SSR markers. Tree Genet Genomes 9 (3):707-722. DOI: 10.1007/s11295-012-0586-4 Magni CR, Ducousso A, Caron H, Petit RJ, Kremer A (2005) Chloroplast DNA variation of Quercus rubra L. in North America and comparison with other Fagaceae. Molecular Ecology 14 (2):513-524. DOI: 10.1111/j.1365-294X.2005.02400.x Müller M, Finkeldey R (2016) Genetic and adaptive trait variation in seedlings of European beech provenances from Northern Germany. Silvae Genet 65 (2):65-73. DOI: 10.1515/sg-2016-0018 Peakall R, Smouse PE (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6 (1):288-295. DOI: 10.1111/j.1471-8286.2005.01155.x Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28 (19):2537-2539. DOI: 10.1093/bioinformatics/bts460 Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155 (2):945-959 Rice WR (1989) Analyzing Tables of Statistical Tests. Evolution 43 (1):223-225. DOI: 10.1111/j.1558-5646.1989.tb04220.x Rousset F (2008) genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8 (1):103-106. DOI: 10.1111/j.1471-8286.2007.01931.x Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18 (2):233-234. DOI: 10.1038/72708 Steinkellner H, Lexer C, Turetschek E, Glössl J (1997) Conservation of (GA)n microsatellite loci between Quercus species. Molecular Ecology 6 (12):1189-1194. DOI: 10.1046/j.1365-294X.1997.00288.x Sullivan AR, Lind JF, McCleary TS, Romero-Severson J, Gailing O (2013) Development and characterization of genomic and gene-based microsatellite markers in north American red oak species. Plant Molecular Biology Reporter 31 (1):231-239. DOI: 10.1007/s11105-012-0495-6 The Hardwood Genomics Project To be found in <https://hardwoodgenomics.org/> USDA NRCS (2002) Plant guide, northern red oak (Quercus rubra L.) [online]. To be found in <https://plants.usda.gov/plantguide/pdf/cs_quru.pdf> Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38 (6):1358-1370

Downloads

Published

2018-12-31

Issue

Section

Research article