RAPD Analysis Reveals Geographic Differentiations within Allium schoenoprasum L. (Alliaceae)

Abstract

Random amplified polymorphic DNA (RAPD) analysis was used to study the phylogenetic relationships between species in Allium section Schoenoprasum and for the investigation of the intraspecific differentiation of A. schoenoprasum. RAPD analysis of 39 samples representing eight species of sect. Schoenoprasum and one sample of A. atrosanguineum (sect. Annuloprasum) resulted in 233 interpretable RAPD bands. The analysis clearly distinguishes the species of section Schoenoprasum. The arrangement of the accessions of A. schoenoprasum in all dendrograms mirrors the geographical distribution, with a clear differentiation between an Asian and European subgroup. Within the European group, Scandinavian material is clearly distinct from S and E European material. Informally described morphological types of A. schoenoprasum could not be confirmed by RAPD analysis but represent recurrent ecological adaptations. A combination of phenetic (UPGMA, neighbour-joining analysis), cladistic (parsimony analysis), and statistical (PCA) methods of data analysis resulted in clearer phylogenetic interpretations than each of the methods facilitates when used separately.

Abbreviations

RAPD: random amplified polymorphic DNA

UPGMA: unweighted pair group method using arithmetic averages

NJ: neighbour-joining analysis

MP: maximum parsimony

PCA: principal coordinate analysis

Allium sect. Schoenoprasum - Alliaceae - biogeography - ecology - evolution - RAPD

References

• 01 Antzupova,  T. P.. (1989);  New species of the genus Allium (Alliaceae) from Buryatia.  Novosti Systematiki Vysshich rastenii, Leningrad. 26 38-39 (in Russian)
• 02 Bachmann,  K.. (1997);  Nuclear DNA markers in plant biosystematic research.  Opera Botanica. 132 137-148
• 03 Bachmann,  K., and Hombergen,  E.-J.. (1996) Mapping genes for phenotypic variation in Microseris (Lactuceae) with molecular markers. Compositae: Biology and Utilization, Vol. 2. Caligari, P. D. S. and Hind, D. J. N., eds. London; Kew Gardens pp. 23-43
• 04 Backeljau,  T.,, De Bruyn,  L.,, De Wolf,  H.,, Jordaens,  K.,, van Dongen,  S.,, and Winnepenninckx,  B.. (1995);  Random amplified polymorphic DNA (RAPD) and parsimony methods.  Cladistics. 11 119-130
• 05 Bennett,  K. D.,, Tzedakis,  P. C.,, and Willis,  K. J.. (1991);  Quartenary refugia of north European trees.  Journal of Biogeography. 18 103-115
• 06 Blattner,  F. R., and Kadereit,  J. W.. (1999);  Morphological evolution and ecological diversification of the forest-dwelling poppies (Papaveraceae: Chelidonioideae) as deduced from a molecular phylogeny of the ITS region.  Plant Systematics and Evolution. 219 181-197
• 07 Colosi,  J. C., and Schaal,  B. A.. (1997);  Wild proso millet (Panicum miliaceum) is genetically variable and distinct from crop varieties of proso millet.  Weed Science. 45 509-518
• 08 Felsenstein,  J.. (1978);  Cases in which parsimony and compatibility methods will be positively misleading.  Systematic Zoology. 27 401-410
• 09 Felsenstein,  J.. (1985);  Confidence limits on phylogenies: an approach using the bootstrap.  Evolution. 39 783-791
• 10 Friesen,  N.. (1996);  A taxonomic and chorological revision of the genus Allium L. sect. Schoenoprasum Dumort.  Candollea. 51 461-473
• 11 Friesen,  N.,, Borisjuk,  N.,, Klaas,  M.,, Mes,  T. H. M.,, and Hanelt,  P.. (1997 a);  Allotetraploid origin of Allium altyncolicum (sect. Schoenoprasum) as investigated by karyological and molecular markers.  Plant Systematics and Evolution. 206 317-335
• 12 Friesen,  N.,, Fritsch,  R. M.,, and Bachmann,  K.. (1997 b);  Hybrid origin of some ornamental Alliums of subgenus Melanocrommyum verified with GISH and RAPD.  Theoretical and Applied Genetics. 95 1229-1238
• 13 Friesen,  N., and Herrmann,  N.. (1998);  Taxonomy, chorology and evolution of Allium lusitanicum - the European “A. senescens”. .  Linzer Biologische Beiträge. 30 815-830
• 14 Friesen,  N., and Klaas,  M.. (1998);  Origin of some minor vegetatively propagated Allium crops studied with RAPD and GISH.  Genetic Resources and Crop Evolution. 45 510-523
• 15 Friesen,  N.,, Pollner,  S.,, Bachmann,  K.,, and Blattner,  F. R.. (1999);  RAPDs and non-coding chloroplast DNA reveal a single origin of the cultivated Allium fistulosum from A. altaicum. .  American Journal of Botany. 86 554-562
• 16 Gabrielsen,  T. M.,, Bachmann,  K.,, Jakobsen,  K. S.,, and Brochmann,  C.. (1997);  Glacial survival does not matter: RAPD phylogeography of Nordic Saxifraga oppositifolia. .  Molecular Ecology. 6 831-842
• 17 Gabrielsen,  T. M., and Brochmann,  C.. (1998);  Sex after all: high levels of diversity detected in the Arctic clonal plant Saxifraga cernua using RAPD markers.  Molecular Ecology. 7 1701-1708
• 18 Hanelt,  P.,, Schultze-Motel,  J.,, Fritsch,  R.,, Kruse,  J.,, Maaß,  H. I.,, Ohle,  H.,, and Pistrick,  K.. (1992) Infragenetic grouping of Allium - the Gaterslebenen approach. The Genus Allium - Taxonomic Problems and Genetic Resources. Hanelt, P., Hammer, K., and Knüpffer, H., eds. Gatersleben; IPK pp. 107-123
• 19 Harris,  S. A.. (1995);  Systematics and randomly amplified polymorphic DNA in the genus Leucaea (Leguminosae, Mimosoideae).  Plant Systematics and Evolution. 197 195-208
• 20 Le Corre,  V.,, Dumolin-Lapègue,  S.,, and Kremer,  A.. (1997);  Genetic variation at allozyme and RAPD loci in sessile oak Quercus petraea (Matt.) Liebl.: the role of history and geography.  Molecular Ecology. 6 519-529
• 21 Maddison,  W. P., and Maddison,  D. R.. (1992) MacClade: interactive analysis of phylogeny and character evolution, version 3.05. Sunderland; Sinauer
• 22 Mes,  T. H. M.,, Friesen,  N.,, Fritsch,  R. M., Klaas,  M.,, and Bachmann,  K.. (1997);  Criteria for sampling in Allium based on chloroplast DNA PCR-RFLP's.  Systematic Botany. 22 701-712
• 23 Morell,  M. K.,, Peakall,  R.,, Appels,  R.,, Preston,  L. R.,, and Lloyd,  H. L.. (1995);  DNA profiling techniques for plant variety identification.  Australian Journal of Experimental Agriculture. 35 807-819
• 24 Nimis,  P. L.,, Malyshev,  L. I.,, Bolognini,  G.,, and Friesen,  N.. (1998);  A multivariate phytogeographic analysis of plant diversity in the Putorana Plateau (N Siberia).  Opera Botanica. 136 1-72
• 25 Pillay,  M., and Kenny,  S. T.. (1995);  Anomalies in direct pairwise comparisons of RAPD fragments for genetic analysis.  BioTechniques. 19 694-698
• 26 Purps,  D. M. L., and Kadereit,  J. W.. (1998);  RAPD evidence for a sister group relationship of the presumed progenitor-derivate species pair Senecio nebrodensis and S. viscosus (Asteraceae).  Plant Systematics and Evolution. 211 57-70
• 27 Rieseberg,  L. H.. (1996);  Homology among RAPD fragments in interspecific comparisons.  Molecular Ecology. 5 99-105
• 28 Rieseberg,  L. H.,, Choi,  H.,, Chan,  R.,, and Spore,  C.. (1993);  Genomic map of a diploid hybrid species.  Heredity. 70 285-293
• 29 Roelofs,  D., and Bachmann,  K.. (1997);  Comparison of chloroplast and nuclear phylogeny in the autogamous annual Microseris douglasii (Asteraceae, Lactuceae).  Plant Systematics and Evolution. 204 49-63
• 30 Saitou,  N., and Nei,  M.. (1987);  The neighbor-joining method: a new method for reconstructing phylogenetic trees.  Journal of Molecular Evolution. 4 406-425
• 31 Sambrook,  J.,, Fritsch,  E. F.,, and Maniatis,  T.. (1989) Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor; Cold Spring Harbor Laboratory Press
• 32 Serquen,  F. C.,, Bacher,  J.,, and Straub,  J. E.. (1997);  Mapping and QTL analysis of horticultural traits in a narrow cross in cucumber (Cucumis sativus L.) using random-amplified polymorphic DNA markers.  Molecular Breeding. 3 257-268
• 33 Stearn,  W. T.. (1978);  European species of Allium and allied genera of Alliaceae - a synonymic enumeration.  Annales Musei Goulandris. 4 83-198
• 34 Swofford,  D. L.,, Olsen,  G. J.,, Waddell,  P. J.,, and Hillis,  D. M.. (1996) Phylogenetic inference. Molecular Systematics, 2nd ed. Hillis, D. M., Moritz, C., and Mable, B. K., eds. Sunderland; Sinauer pp. 407-514
• 35 Tollefsrud,  M. M.,, Bachmann,  K.,, Jakobsen,  K. S.,, and Brochmann,  C.. (1998);  Glacial survival does not matter - II: RAPD phylogeography of Nordic Saxifraga cespitosa. .  Molecular Ecology. 7 1217-1232
• 36 van der Zande,  L., and Bijlsma,  R.. (1994);  Limitation of the RAPD technique in phylogeny reconstruction in Drosophila. .  Journal of Evolutionary Biology. 8 645-656
• 37 Vellekoop,  P.,, Buntjer,  J. B.,, Maas,  J. W.,, and van Brederode,  J.. (1996);  Can the spread of agriculture in Europe be followed by tracing the spread of the weed Silene latifolia. A RAPD study.  Theoretical and Applied Genetics. 92 1085-1090
• 38 Welsh,  J., and McClelland,  M.. (1990);  Fingerprinting genomes using PCR with arbitrary primers.  Nucleic Acids Research. 18 7213-7218
• 39 Williams,  J. G.,, Kubelik,  A. R.,, Livak,  K. J.,, Rafalski,  J. A.,, and Tingey,  S. V.. (1990);  DNA polymorphisms amplified by arbitrary primers are useful as genetic markers.  Nucleic Acids Research. 18 6531-6535
• 40 Wolfe,  A. D., and Liston,  A.. (1998) Contributions of PCR-based methods to plant systematics and evolutionary biology. Molecular Systematics of Plants II: DNA Sequencing. Soltis, D. E., Soltis, P. S., and Doyle, J. J., eds. Dordrecht; Kluwer pp. 43-86

Section Editor: M. Hasebe