SSR and SNP Markers for the Identification of Clones, Hybrids and Species Within the Genus Populus

Open access

Abstract

Several poplar species within a section, but also between sections, are cross-compatible, thus a high number of interspecies-hybrids occur naturally or have been artificially produced during the last 100 years. Very often, systematically kept records on the production or vegetative propagation of poplar hybrids and/or clones have not been available to date. Hence the origin of the poplar plant material used for the generation of hybrids or clones is not quite clear in many cases, thus making the differentiation between the clones a difficult task. Therefore, genetic markers are needed to clearly identify and differentiate the species and hybrids in the genus Populus, including both identification of existing clones and the breeding of new ones. One aspect of this study is therefore to develop molecular markers for the identification and differentiation of species, hybrids, and clones of the genus Populus.

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • BEKKAOUI F. B. MANN and B. SCHROEDER (2003): Application of for the identification and management of hybrid poplar accessions. Agroforestry Systems 59: 53-59.

  • CHAMBERS G. K. and E. S. MACAVOY (2000): Microsatellites: consensus and controversy. Comp Biochem Physiol B 126: 455-476.

  • CHASE M. W. N. SALAMIN M. WILKINSON J. M. DUNWELL R. P. KESANAKURTHI N. HAIDAR and V. SAVOLAINEN (2005): Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci 360: 1889-1895.

  • CHO R. J. M. MINDRINOS D. R. RICHARDS R. J. SAPOLSKY et al. (1999): Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23: 203-207.

  • CONSTABEL C. P. L. YIP J. J. PATTON and M. E. CHRISTOPHER (2000): Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol 124: 285-295.

  • DAYANANDAN S. O. P. RAJORA and K. S. BAWA (1998): Isolation and characterization of microsatellites in trembling aspen (Populus tremuloides). Theor Appl Genet 96: 950-956.

  • DEGEN B. and M. FLADUNG (2008): Use of DNA-markers for tracing illegal logging. Landbauforschung - vTI Agriculture and Forestry Research 321: 6-14.

  • ECKENWALDER J. E. (1996): Systematics and evolution of Populus pp 7-32. In: Biology of Populus and its Implications for Management and Conservation Part I Chapter 1 edited by R. F. STETTLER H. D. BRADSHAW JR P. E. HEILMAN and T. M. HINCKLEY NRC Research Press National Research Council of Canada Ottawa ON Canada.

  • FLADUNG M. and J. BUSCHBOM (2009): Identification of Single Nucleotide Polymorphisms (SNPs) in different Populus species. Trees 23: 1199-1212.

  • GARCIA-GIL M. R. M. MIKKONEN and O. SAVOLAINEN (2003): Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol Ecol 12: 1195-1206.

  • GILCHRIST E. J. G. W. HAUGHN C. C. YING S. P. OTTO J. ZHUANG D. CHEUNG B. HAMBERGER F. ABOUTORABI T. KALYNYAK L. JOHNSON J. BOHLMANN B. E. ELLIS C. J. DOUGLAS and Q. C. B. CRONK (2006): Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol Ecol 15: 1367-1378.

  • HOLLINGSWORTH M. L. A. A. CLARK L. L. FORREST J. RICHARDSON R. T. PENNINGTON D. G. LONG R. COWAN M. W. CHASE M. GAUDEUL and P. M. HOLLINGSWORTH (2009): Selecting barcoding loci for plants: evaluation of seven candidate loci with specieslevel sampling in three divergent groups of land plants. Mol Ecol Resources 9: 439-457.

  • INGVARSSON P. K. (2005): Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L. Salicaceae). Genetics 169: 945-953.

  • JONES N. H. OUGHAM H. THOMAS and I. PASAKINSKIENE (2009): Markers and mapping revisited: finding your gene. New Phytol 183: 935-966.

  • LEVINSON G. and G. A. GUTMAN (1987): Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-221.

  • LICHT L. A. and J. G. ISEBRANDS (2005): Linking phytoremediated pollutant removal to biomass economic opportunities. Biomass & Bioenergy 28: 203-218.

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

  • PAKULL B. K. GROPPE M. MEYER T. MARKUSSSEN and M. FLADUNG (2009): Genetic linkage mapping in aspen (Populus tremula L. and P. tremuloides Michx.). Tree Genet Genom 5: 505-515.

  • RAHMAN M. H. S. DAYANANDAN and O. P. RAJORA (2000): Microsatellite DNA markers in Populus tremuloides. Genome 43: 293-297.

  • RAHMAN H. M. and O. P. RAJORA (2002): Microsatellite DNA fingerprinting differentiation and genetic relationships of clones cultivars and varieties of six poplar species from three sections of the genus Populus. Genome 45: 1083-1094.

  • RAJORA O. P. and M. H. RAHMAN (2003): Microsatellite DNA and RAPD fingerprinting identification and genetic relationships of hybrid poplar (Populus x canadensis) cultivars. Theor Appl Genet 106: 470-477.

  • RATHMACHER G. M. NIGGEMANN M. KOHNEN B. ZIEGENHAGEN and R. BIALOZYT (2010): Short-distance gene flow in Populus nigra L. accounts for small-scale spatial genetic structures: implications for in situ conservation measures. Conserv Genet 11 (4): 1327-1338.

  • SELKOE K. A. and R. J. TOONEN (2006): Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Letters 9: 615-629.

  • SMULDERS M. J. M. R. BERINGEN R. VOLOSYANCHUK A. VANDEN BROECK J. VAN DER SCHOOT P. ARENS and B. VOSMAN (2008): Natural hybridisation between Populus nigra L. and P. x canadensis Moench. Hybrid off- spring competes for niches along the Rhine River in the Netherlands. Tree Genet Genom 4: 663-675.

  • TAUTZ D. M. TRICK and G. A. DOVER (1986): Cryptic simplicity in DNA is a major source of genetic variation. Nature 322: 652-656.

  • TUSKAN G. A. L. E. GUNTER Z. K. YANG T. M. YIN M. M. SEWELL and S. P. DIFAZIO (2004): Characterization of Microsatellites Revealed by Genomic Sequencing of Populus trichocarpa. Can J For Res 34: 85-93.

  • TUSKAN G. A. S. DIFAZIO S. JANSSON J. BOHLMANN et al (2006): The genome of black cottonwood Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.

  • VAN DER SCHOOT J. M. POSPÍSKOVÁ B. VOSMAN and M. J. M. SMULDERS (2000): Development and characterization of microsatellite markers in black poplar (Populus nigra L.). Theor Appl Genet 101: 317-322.

  • VANDE WALLE I. N. VAN CAMP L. VAN DE CASTEELE K. VERHEYEN and R. LEMEUR (2007): Short-rotation forestry of birch maple poplar and willow in Flanders (Belgium) II. Energy production and CO2 emission reduction potential. Biomass & Bioenergy 31: 276-283.

  • VANDEN BROECK A. M. VILLAR E. VAN BOCKSTAELE and J. VAN SLYCKEN (2005): Natural hybridization between cultivated poplars and their wild relatives: evidence and consequences for native poplar populations. Ann For Sci 62: 601-613.

  • XING C. F. R. SCHUMACHER G. XING Q. Lu T. WANG and R. C. ELSTON (2005): Comparison of microsatellites single- nucleotide polymorphisms (SNPs) and composite markers derived from SNPs in linkage analysis. BMC Genetics 6 (suppl. 1): S29.

  • ZHANG D. Q. and Z. Y. ZHANG (2005): Single nucleotide polymorphisms (SNPs) discovery and linkage disequilibrium (LD) in forest tress. For Stud China 7: 1-14.

  • ZIEGENHAGEN B. S. GNEUSS G. RATHMACHER I. LEYER R. BIALOZYT B. HEINZE and S. LIEPELT (2008): A fast andsimple genetic survey reveals the spread of poplar hybrids at a natural Elbe river site. Conserv Genet 9: 373-379.

Search
Journal information
Impact Factor


IMPACT FACTOR 2018: 0,741
5-year IMPACT FACTOR: 0,651

CiteScore 2018: 0.77

SCImago Journal Rank (SJR) 2018: 0.345
Source Normalized Impact per Paper (SNIP) 2018: 0.362

Cited By
Metrics
All Time Past Year Past 30 Days
Abstract Views 0 0 0
Full Text Views 345 267 9
PDF Downloads 140 110 4