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Development, polymorphism, and cross-taxon utility of EST–SSR markers from safflower (Carthamus tinctorius L.)

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Abstract

Due to their highly polymorphic and codominant nature, simple-sequence repeat (SSR) markers are a common choice for assaying genetic diversity and genetic mapping. In this paper, we describe the generation of an expressed-sequence tag (EST) collection for the oilseed crop safflower and the subsequent development of EST–SSR markers for the genetic analysis of safflower and related species. We assembled 40,874 reads into 19,395 unigenes, of which 4,416 (22.8%) contained at least one SSR. Primer pairs were developed and tested for 384 of these loci, resulting in a collection of 104 polymorphic markers that amplify reliably across 27 accessions (3 species) of the genus Carthamus. These markers exhibited a high level of polymorphism, with an average of 6.0 ± 0.4 alleles per locus and an average gene diversity of 0.54 ± 0.03 across Carthamus species. In terms of cross-taxon transferability, 50% of these primer pairs produced an amplicon in at least one other species in the Asteraceae, and 28% produced an amplicon in at least one species outside the safflower subfamily (i.e., lettuce, sunflower, and/or Gerbera). These markers represent a valuable resource for the genetic analysis of safflower and related species, and also have the potential to facilitate comparative map-based analyses across a broader array of taxa within the Asteraceae.

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Acknowledgments

We would like to thank the greenhouse staff at UGA for maintenance of the safflower plants, the JGI for sequencing, data processing and delivery of the EST data and Huaqin Xu for maintenance of the CGPDB website. This work was supported by grants to J.M.B. from the National Science Foundation Plant Genome Research Program (DBI-0332411) and the Plant Genome Program of the USDA Cooperative State Research, Education, and Extension Service-National Research Initiative (03-35300-13104), and to the Compositae Genome Project from the USDA Initiative for Future Agriculture and Food Systems (IFAFS 2000-04292) and the NSF Plant Genome Research Program (DBI-0421630).

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Authors and Affiliations

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

    Mark A. Chapman, John Hvala, Jason Strever & John M. Burke

  2. Department of Plant Sciences, The Genome Center, University of California, Davis, CA, 935616, USA

    Marta Matvienko, Alexander Kozik & Richard W. Michelmore

  3. Center for Applied Genomic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA

    Shunxue Tang & Steven J. Knapp

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  1. Mark A. Chapman
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  4. Marta Matvienko
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  7. Shunxue Tang
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  8. Steven J. Knapp
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  9. John M. Burke
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Correspondence to John M. Burke.

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Communicated by A. Bervillé.

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Chapman, M.A., Hvala, J., Strever, J. et al. Development, polymorphism, and cross-taxon utility of EST–SSR markers from safflower (Carthamus tinctorius L.). Theor Appl Genet 120, 85–91 (2009). https://doi.org/10.1007/s00122-009-1161-8

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