1. bookVolume 61 (2012): Issue 1-6 (December 2012)
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
access type Open Access

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

Published Online: 01 Aug 2017
Volume & Issue: Volume 61 (2012) - Issue 1-6 (December 2012)
Page range: 142 - 148
Received: 11 Oct 2011
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
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.

Keywords

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: 10-14.10.1111/j.1471-8286.2006.01560.xSearch in Google Scholar

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.Search in Google Scholar

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.Search in Google Scholar

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: 315-331.10.1016/0378-1127(92)90108-LSearch in Google Scholar

BROOKFIELD, J. F. Y. (1996): A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology 5: 453-455.10.1111/j.1365-294X.1996.tb00336.xSearch in Google Scholar

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: 17-24.10.1007/BF02507146Search in Google Scholar

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. 10.1016/j.foreco.2008.05.049Search in Google Scholar

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. 10.1007/BF0022093724170054Search in Google Scholar

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: 353-367.10.1007/s10709-011-9554-4305980921279823Search in Google Scholar

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: 293-297.10.1007/BF0022363524186009Search in Google Scholar

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: 591-611.10.1111/j.1755-0998.2011.03014.x21565126Search in Google Scholar

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. Search in Google Scholar

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: 101-110.10.1007/s10310-008-0109-1Search in Google Scholar

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: 1099-1106.10.1111/j.1365-294X.2007.03089.xSearch in Google Scholar

KERESZTESI, B. (1983): Breeding and cultivation of black locust, Robinia pseudoacacia, in Hungary. Forest Ecology and Management 9: 217-244.10.1016/S0378-1127(83)80004-8Search in Google Scholar

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: 31-41.10.1007/s11258-010-9735-8Search in Google Scholar

LEFÈVRE, S., S. WAGNER, R. J. PETIT and G. DE LAFONTAINE (2011): Multiplexed microsatellite markers for genetic studies of beech. Molecular Ecology Resources doi: 10.1111/j.1755-0998.2011.03094.x.Search in Google Scholar

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. Search in Google Scholar

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. 10.1007/s00122-003-1500-014625672Search in Google Scholar

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.Search in Google Scholar

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.Search in Google Scholar

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: 259-269.10.1007/s11295-009-0246-5Search in Google Scholar

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: 639-655.10.1046/j.1365-294x.1998.00374.x9633105Search in Google Scholar

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.Search in Google Scholar

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

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: 850-852.10.1111/j.1755-0998.2008.02306.x21564766Search in Google Scholar

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: 597-605.10.1111/j.1600-0633.2006.00201.xSearch in Google Scholar

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

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: 573-583.10.1007/s00468-008-0302-zSearch in Google Scholar

RÉDEI, K., Z. OSVÁTH-BUJTÁS and I. BALLA (2002): Clonal approaches to growing black locust (Robinia pseudoacacia) in Hungary: a review. Forestry 75: 547-552.10.1093/forestry/75.5.547Search in Google Scholar

SCHRÖCK, O. (1953): Beitrag zur Züchtung der Robinie (Robinia pseudoacacia). Der Züchter 23: 266-272.10.1007/BF00775682Search in Google Scholar

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: 873-880.10.1007/s00122-003-1490-y14625671Search in Google Scholar

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.Search in Google Scholar

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: 535-538.10.1111/j.1471-8286.2004.00684.xSearch in Google Scholar

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 546.10.17660/ActaHortic.2001.546.38Search in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo