1 3 Theor Appl Genet (2014) 127:1237–1249 DOI 10.1007/s00122-014-2294-y ORIGINAL PAPER New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin) Magdalena Kroc · Grzegorz Koczyk · Wojciech S ´ wie ˛cicki · Andrzej Kilian · Matthew N. Nelson Received: 23 August 2013 / Accepted: 21 February 2014 / Published online: 15 March 2014 © Springer-Verlag Berlin Heidelberg 2014 this most basal clade of Papilionoid legumes, L. angus- tifolius serves as a useful model for exploring legume genome evolution. Here, we report an improved refer- ence genetic map of L. angustifolius comprising 1207 loci, including 299 newly developed Diversity Arrays Technology markers and 54 new gene-based PCR mark- ers. A comparison between the L. angustifolius and Med- icago truncatula genomes was performed using 394 sequence-tagged site markers acting as bridging points between the two genomes. The improved L. angustifolius genetic map, the updated M. truncatula genome assem- bly and the increased number of bridging points between the genomes together substantially enhanced the resolu- tion of synteny and chromosomal colinearity between these genomes compared to previous reports. While a high degree of syntenic fragmentation was observed that was consistent with the large evolutionary distance between the L. angustifolius and M. truncatula genomes, there were striking examples of conserved colinearity of loci between these genomes. Compelling evidence was found of large-scale duplication and/or triplication in the L. angustifolius genome, consistent with one or more ancestral polyploidy events. Introduction Narrow-leafed lupin (Lupinus angustifolius L.) is one of four lupin grain crop species that together produce around 1.1 million tonnes of grain annually (FAO 2011). It was first cultivated as a green manure and forage crop in the late nineteenth century in Northern Europe and only became a significant grain crop as domestication traits including reduced seed alkaloids were incorporated through system- atic breeding efforts in Europe and Australia (Berger et al. Abstract Key message This is the first clear evidence of duplica- tion and/or triplication of large chromosomal regions in a genome of a Genistoid legume, the most basal clade of Papilionoid legumes. Abstract Lupinus angustifolius L. (narrow-leafed lupin) is the most widely cultivated species of Genistoid leg- ume, grown for its high-protein grain. As a member of Communicated by A. H. Paterson. Electronic supplementary material The online version of this article (doi:10.1007/s00122-014-2294-y) contains supplementary material, which is available to authorized users. M. Kroc · W. S ´ wie ˛cicki Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland G. Koczyk Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland A. Kilian Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, Canberra, ACT 2600, Australia M. N. Nelson School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia M. N. Nelson (*) The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia e-mail: matthew.nelson@uwa.edu.au