Theor Appl Genet DOI 10.1007/s00122-007-0605-2 123 ORIGINAL PAPER Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae) Mark A. Chapman · JianCheng Chang · David Weisman · Rick V. Kesseli · John M. Burke Received: 3 April 2007 / Accepted: 30 June 2007 © Springer-Verlag 2007 Abstract The development of universal markers that can be assayed across taxa, but which are polymorphic within taxa, can facilitate both comparative map-based studies and phylogenetic analyses. Here we describe the development of such markers for use in the Asteraceae, which includes the crops lettuce, sunXower, and saZower as well as dozens of locally important crop and weed species. Using align- ments of a conserved orthologous set (COS) of ESTs from lettuce and sunXower and genomic sequences of Arabidop- sis, we designed a suite of primer pairs that are conserved across species, but which are predicted to Xank introns. We then tested 192 such primer pairs in 8 species from across the family. Of these, 163 produced an amplicon in at least 1 taxon, and 125 ampliWed in at least half of the taxa sur- veyed. Thirty-nine ampliWed in all 8 species. Comparisons amongst sequences within the lettuce and sunXower EST databases indicate that the vast majority of these loci will be polymorphic. As a direct test of the utility of these mark- ers outside the lettuce and sunXower subfamilies, we sequenced a subset of ten loci from a panel of cultivated saZower individuals. All 10 loci proved to be single-locus, and nine of the 10 loci were polymorphic with an average of 12.8 SNPs per kb. Taken together, these loci will provide an initial backbone for comparative genetic analyses within the Asteraceae. Moreover, our results indicate that these loci are phylogenetically informative, and hence can be used to resolve evolutionary relationships between taxa within the family as well as within species. Introduction The Weld of comparative genomics relies upon the identiW- cation of orthologous genes and genomic regions between the species of interest. Mapping of these orthologous regions in diVerent species provides insight into the extent of synteny, and can facilitate the map-based cloning of genes of interest (Gale and Devos 1998b; Paterson et al. 2000). Comparative genetic maps have been produced for a number of plant species; the majority of these are for crops with extensive linkage maps often containing thousands of mapped loci. Thus far, the largest eVorts have focused on the Solanaceae (Bonierbale et al. 1988; Livingstone et al. 1999; Doganlar et al. 2002), Brassicaceae (Kowalski et al. 1994; Lagercrantz and Lydiate 1996; Lagercrantz et al. 1996; Lagercrantz 1998; Lan and Paterson 2000), Fabaceae (Choi et al. 2006; Kalo et al. 2004), Rosaceae (Dirlewanger et al. 2004), and Poaceae (Lin et al. 1995; Paterson et al. 1995; Maroof et al. 1996; Gale and Devos 1998a; Ming et al. 1998; Wu et al. 2003; Bowers et al. 2005). Recent studies have revealed the potential of extending these anal- yses to comparisons of taxa from diVerent families; how- ever, such studies are generally restricted to localized regions and/or microsyntenic analyses based on the full Communicated by M. Xu. Mark A. Chapman and JianCheng Chang have contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s00122-007-0605-2) contains supplementary material, which is available to authorized users. M. A. Chapman (&) · J. M. Burke Department of Plant Biology, Miller Plant Sciences Building, University of Georgia, Athens, GA 30602, USA e-mail: mchapman@plantbio.uga.edu J. Chang · D. Weisman · R. V. Kesseli Department of Biology, University of Massachusetts, Boston, 100 Morrissey Blvd, Boston, MA 02125, USA