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AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae)¹

² Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA Wageningen, The Netherlands ³ Institut fuer Allgemeine Botanik und Pflanzenphysiologie AG Spezielle Botanik, Justus-Liebig-Universitaet Giessen, Senckenbergstr. 17 35390 Giessen, Germany ⁴ Unit Plant, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research, Caritasstraat 21, 9090 Melle, Belgium ⁵ Department of Systematic Botany, Friedrich Schiller Universität Jena, Philosophenweg 16 07743 Jena, Germany ⁶ Ecologisch Adviesbureau Maes, Achter Clarenburg 2, 3511 JJ Utrecht, The Netherlands ⁷ Balsgård-Department of Plant Breeding and Biotechnology, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 291 94 Kristianstad, Sweden ⁸ Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuserstrasse 2 30419 Hannover, Germany

ABSTRACT

The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.

Key Words: amplified fragment length polymorphism (AFLP) • Bayesian inference • parsimony • phylogeny • Rosa • Rosaceae • roses • UPGMA

Received for publication 29 June 2007. Accepted for publication 31 January 2008.

FOOTNOTES

¹ The authors thank Prof. Dr. M.S.M. Sosef (Nationaal Herbarium Nederland-Wageningen branch, Biosystematics Group, Wageningen University, The Netherlands) for discussing the merits of paraphyletic groups, Mrs. M. Lemmens-Pott and Mr. H. de Leeuw (Nationaal Herbarium Nederland-Wageningen branch, Biosystematics Group, Wageningen University, The Netherlands) for information and discussion on Rosa provenances from botanical gardens De Dreijen and Belmonte, and Dr. L. Leus (Unit Plant, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research, Melle, Belgium) for collecting herbarium material at Rozentuin Mechelen. This study has been carried out with financial support from the Netherlands Ministry of Agriculture, Nature and Food Safety, and from the Commission of the European Community (QLRT-2001-01278, Genetic evaluation of European rose resources for conservation and horticultural use [Generose]). This study does not necessarily reflect the Commission's views and in no way anticipates the Commission's future policy in this area.

⁹ Current address: Koopman Scientific Services, P.O. Box 404, 1600 AK Enkhuizen, The Netherlands

¹⁰ Author for correspondence (e-mail: koopman{at}koopmanscientific.com)

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