Optimisation of a multiplex PCR assay of nuclear microsatellite markers for population genetics and clone identification in Robinia pseudoacacia L.

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Abstract

Black locust (Robinia pseudoacacia L.) is a tree species native to North America. The multipurpose tree is cultivated worldwide, but causes problems due to its partially invasive character. The application of nuclear microsatellite loci has many aims in population genetic studies. Here we introduce a very cost-effective method for combining the information of 14 nuclear microsatellite loci into two multiplex PCR sets as a contribution to greater standardisation and more comparable results. Combined non-exclusion probabilities for clone identification using example populations are estimated at between 1.37*E-5 and 1.67*E-11, and for paternity analysis for 1.59*E-4. The detected weak linkage between some microsatellite loci is not considered to be a substantial restriction to the reliability of the set of markers in providing an appropriate method for fingerprinting and parentage analysis.

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  • AMOS W. J. I. HOFFMAN A. FRODSHAM L. ZHANG S. BEST and A. V. S. HILL (2007): Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes 7: 10-14.

  • BÖCKER R. and M. DIRK (1998): Distribution and Spreading of Alien Trees and Shrubs in South Western Germany and Contributions to Germination Biology. pp. 285-297. In: Plant Invasions: Ecological Mechanisms and Human Responses edited by U. STARFINGER K. EDWARDS I. KOWARIK and M. WILLIAMSON Backhuys Publishers Leiden The Netherlands.

  • BÖHMER H. J. T. HEGER and L. TREPL (2001): Robinia pseudoacacia L. Black locust. pp. 64-75. In: Fall - studien zu gebietsfremden Arten in Deutschland - Case Studies on Alien Species in Germany Umweltbundesamt (Federal Environment Agency) Berlin.

  • BONGARTEN B. C. D. A. HUBER and D. K. APSLEY (1992): Environmental and genetic influences on short-rotation biomass production of black locust (Robinia pseudoacacia L.) in the Georgia Piedmont. Forest Ecology and Management 55: 315-331.

  • BROOKFIELD J. F. Y. (1996): A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology 5: 453-455.

  • CHANG C.-S. B. BONGARTEN and J. HAMRICK (1998): Genetic Structure of Natural Populations of Black Locust (Robinia pseudoacacia L.) at Coweeta North Carolina. Journal of Plant Research 111: 17-24.

  • DINI-PAPANASTASI O. (2008): Effects of clonal selection on biomass production and quality in Robinia pseudoacacia var. monophylla Carr. Forest Ecology and Management 256: 849-854.

  • DUMOLIN S. B. DEMESURE and R. J. PETIT (1995): Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. TAG Theoretical and Applied Genetics 91: 1253-1256.

  • ELLIS J. S. J. GILBEY A. ARMSTRONG T. BALSTAD E. CAUWELIER C. CHERBONNEL S. CONSUEGRA J. COUGHLAN T. F. CROSS W. CROZIER E. DILLANE D. ENSING C. G. D. LEÁNIZ E. GARCÍA-VÁZQUEZ A. M. GRIFFITHS K. HINDAR S. HJORLEIFSDOTTIR D. KNOX G. MACHADOSCHIAFFINO P. MCGINNITY D. MELDRUP E. E. NIELSEN K. OLAFSSON C. R. PRIMMER P. PRODOHL L. STRAD - MEYER J.-P. VÄHÄ E. VERSPOOR V. WENNEVIK and J. R. STEVENS (2011): Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.). Genetica 139: 353-367.

  • GERBER S. and F. RODOLPHE (1994): Estimation and test for linkage between markers: a comparison of lod score and X2 test in a linkage study of maritime pine (Pinus pinaster Ait.). TAG Theoretical and Applied Genetics 88: 293-297.

  • GUICHOUX E. L. LAGACHE S. WAGNER P. CHAUMEIL P. LÉGER O. LEPAIS C. LEPOITTEVIN T. MALAUSA E. REVARDEL F. SALIN and R. J. PETIT (2011): Current trends in microsatellite genotyping. Molecular Ecology Resources 11: 591-611.

  • HERTEL H. and V. SCHNECK (2003): Untersuchungen zur genetischen Struktur eines Robinienbestandes (Robinia pseudoacacia L.) in Brandenburg. pp. 257-263. In: Bedrohung der biologischen Vielfalt durch invasive gebietsfremde Arten - Erfassung Monitoring und Risikoanalyse edited by M. Welling Landwirtschaftsverlag GmbH Münster.

  • JUNG S.-C. N. MATSUSHITA B.-Y. WU N. KONDO A. SHIRAISHI and T. HOGETSU (2009): Reproduction of a Robinia pseudoacacia population in a coastal Pinus thunbergii windbreak along the Kujukurihama Coast Japan Journal of Forest Research 14: 101-110.

  • KALINOWSKI S. T. M. L. TAPER and T. C. MARSHALL (2007): Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16: 1099-1106.

  • KERESZTESI B. (1983): Breeding and cultivation of black locust Robinia pseudoacacia in Hungary. Forest Ecology and Management 9: 217-244.

  • KUROKOCHI H. K. TOYAMA and T. HOGETSU (2010): Regeneration of Robinia pseudoacacia riparian forests after clear-cutting along the Chikumagawa River in Japan. Plant Ecology 210: 31-41.

  • LEFÈVRE S. S. WAGNER R. J. PETIT and G. DE LAFONTAINE (2011): Multiplexed microsatellite markers for genetic studies of beech. Molecular Ecology Resources doi:

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    • Export Citation
  • LIAN C. and T. HOGETSU (2002): Development of microsatellite markers in black locust (Robinia pseudoacacia) using a dual-supression-PCR technique. Molecular Ecology Notes 2: 211-213.

  • LIAN C. R. OISHI N. MIYASHITA and T. HOGETSU (2004): High somatic instability of a microsatellite locus in a clonal tree Robinia pseudoacacia TAG Theoretical and Applied Genetics 108: 836-841.

  • LIESEBACH H. (2012): Genetische Charakterisierung von Robinienbeständen (Robinia pseudoacacia L.) in Deutsch - land mit nuklearen Mikrosatelliten-Markern: Erkenntnisse zu ihrer Bestandesbegründung (Genetic characterisation of black locust stands (Robinia pseudoacacia L.) in Germany with nuclear microsatellite markers: background on population history). Beiträge aus der Nordwestdeutschen Forstlichen Versuchsanstalt in press.

  • LIESEBACH H. and G. NAUJOKS (2012): Klonidentifizierung bei Zuchtmaterial der Robinie (Robinia pseudoacacia L.) mit nuklearen Mikrosatellitenmarkern (Clone identification of breeding material from black locust (Robinia pseudoacacia L.) from nuclear microsatellite markers). Beiträge aus der Nordwestdeutschen Forstlichen Versuchsanstalt Volume 8 267-274.

  • LIESEBACH H. V. SCHNECK and E. EWALD (2010): Clonal fingerprinting in the genus Populus L. by nuclear microsatellite loci regarding differences between sections species and hybrids. Tree Genetics & Genomes 6: 259-269.

  • MARSHALL T. C. J. SLATE L. E. B. KRUUK and J. M. PEMBERTON (1998): Statistical confidence for likelihoodbased paternity inference in natural populations. Molecular Ecology 7: 639-655.

  • MCCAIG B. C. J. L. HAMRICK and B. L. HAINES (1993): Clonal structure of Robinia pseudoacacia (black locust) in the Southern Appalachians. Bulletin of the Ecological Society of America 74: 350.

  • MEBRAHTU T. and J. W. HANOVER (1989): Heritability and expected gain estimates for traits of Black locust in Michigan. Silvae Genetica 38: 125-130.

  • MISHIMA K. T. HIRAO S. URANO A. WATANABE and K. TAKATA (2009): Isolation and characterization of microsatellite markers from Robinia pseudoacacia L. Molecular Ecology Resources 9: 850-852.

  • MORAN P. D. J. TEEL E. S. LAHOOD J. DRAKE and S. KALINOWSKI (2006): Standardising multi-laboratory microsatellite data in Pacific salmon: an historical view of the future. Ecology of Freshwater Fish 15: 597-605.

  • NAUJOKS G. I. ZASPEL and U. BEHRENDT (1999): Microorganisms acting in tissue cultures of black locust (Robinia pseudoacacia L.). Acta Horticulturae 530: 129-135.

  • RATHMACHER G. M. NIGGEMANN H. WYPUKOL K. GEBHARDT B. ZIEGENHAGEN and R. BIALOZYT (2009): Allelic ladders and reference genotypes for a rigorous standardization of poplar microsatellite data. Trees - Structure and Function 23: 573-583.

  • RÉDEI K. Z. OSVÁTH-BUJTÁS and I. BALLA (2002): Clonal approaches to growing black locust (Robinia pseudoacacia) in Hungary: a review. Forestry 75: 547-552.

  • SCHRÖCK O. (1953): Beitrag zur Züchtung der Robinie (Robinia pseudoacacia). Der Züchter 23: 266-272.

  • SLAVOV G. T. G. T. HOWE I. A. YAKOVLEV K. J. EDWARDS K. V. KRUTOVSKY G. A. TUSKAN J. E. CARLSON S. H. STRAUSS and W. T. ADAMS (2004): Highly variable SSR markers in Douglas-fir: Mendelian inheritance and map locations. TAG Theoretical and Applied Genetics 108: 873-880.

  • SURLES S. E. J. L. HAMRICK and B. BONGARTEN (1990): Mating systems in open-pollinated families of black locust (Robinia pseudoacacia). Silvae Genetica 39: 35-40.

  • Van Oosterhout C. W. F. HUTCHINSON D. P. M. WILLS and P. SHIPLEY (2004): MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535-538.

  • VOSMAN B. R. COOKE M. GANAL R. PEETERS P. ISAAC and G. BREDEMEIJER (2001): Standardization and application of microsatellite markers for variety identification in tomato and wheat. Acta Horticulturae 546.

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