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Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae)

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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, sunflower, and safflower as well as dozens of locally important crop and weed species. Using alignments of a conserved orthologous set (COS) of ESTs from lettuce and sunflower and genomic sequences of Arabidopsis, we designed a suite of primer pairs that are conserved across species, but which are predicted to flank 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 amplified in at least half of the taxa surveyed. Thirty-nine amplified in all 8 species. Comparisons amongst sequences within the lettuce and sunflower EST databases indicate that the vast majority of these loci will be polymorphic. As a direct test of the utility of these markers outside the lettuce and sunflower subfamilies, we sequenced a subset of ten loci from a panel of cultivated safflower 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.

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Acknowledgments

EST sequence data were obtained from the Compositae Genome Project website. This work was supported by grants from the National Science Foundation (DBI-0421630 to RVK and DBI-0332411 to JMB), the NSF Research Experience for Undergraduates Program (DBI-0354125 to UMass Boston) and the United States Department of Agriculture (03-35300-13104 to JMB). Comments from members of our lab groups improved an earlier version of this manuscript.

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  1. Department of Plant Biology, Miller Plant Sciences Building, University of Georgia, Athens, GA, 30602, USA

    Mark A. Chapman & John M. Burke

  2. Department of Biology, University of Massachusetts, Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA

    JianCheng Chang, David Weisman & Rick V. Kesseli

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  1. Mark A. Chapman
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Correspondence to Mark A. Chapman.

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Communicated by M. Xu.

Mark A. Chapman and JianCheng Chang have contributed equally to this work.

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Chapman, M.A., Chang, J., Weisman, D. et al. Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae). Theor Appl Genet 115, 747–755 (2007). https://doi.org/10.1007/s00122-007-0605-2

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