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Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.)

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Abstract

The American cranberry (Vaccinium macrocarpon Ait.) is a major commercial fruit crop in North America, but limited genetic resources have been developed for the species. Furthermore, the paucity of codominant DNA markers has hampered the advance of genetic research in cranberry and the Ericaceae family in general. Therefore, we used Roche 454 sequencing technology to perform low-coverage whole genome shotgun sequencing of the cranberry cultivar ‘HyRed’. After de novo assembly, the obtained sequence covered 266.3 Mb of the estimated 540–590 Mb in cranberry genome. A total of 107,244 SSR loci were detected with an overall density across the genome of 403 SSR/Mb. The AG repeat was the most frequent motif in cranberry accounting for 35% of all SSRs and together with AAG and AAAT accounted for 46% of all loci discovered. To validate the SSR loci, we designed 96 primer-pairs using contig sequence data containing perfect SSR repeats, and studied the genetic diversity of 25 cranberry genotypes. We identified 48 polymorphic SSR loci with 2–15 alleles per locus for a total of 323 alleles in the 25 cranberry genotypes. Genetic clustering by principal coordinates and genetic structure analyzes confirmed the heterogeneous nature of cranberries. The parentage composition of several hybrid cultivars was evident from the structure analyzes. Whole genome shotgun 454 sequencing was a cost-effective and efficient way to identify numerous SSR repeats in the cranberry sequence for marker development.

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Acknowledgments

The authors thank PS100, Eric Wiesman, Lisa Wasko, Beth Workmaster, Rebecca Harbut, Shawn Steffan, Jim Polashock, Nick Vorsa, and Rod Serres for their help with different aspects of this work. This research was supported by USDA-ARS (Project # 3655-21220-001-00) funding provided to J.E.Z.

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Authors and Affiliations

  1. Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, USDA-ARS, Madison, WI, USA

    D. Senalik, P. W. Simon & J. E. Zalapa

  2. Department of Horticulture, University of Wisconsin, Madison, WI, USA

    H. Zhu, B. H. McCown & E. L. Zeldin

  3. Biotechnology Center, DNA Sequencing Facility, University of Wisconsin, Madison, WI, USA

    J. Speers & J. Hyman

  4. National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, USA

    N. Bassil & K. Hummer

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  1. H. Zhu
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  2. D. Senalik
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  3. B. H. McCown
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  4. E. L. Zeldin
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  5. J. Speers
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  6. J. Hyman
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  7. N. Bassil
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  8. K. Hummer
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  9. P. W. Simon
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  10. J. E. Zalapa
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Corresponding author

Correspondence to J. E. Zalapa.

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Communicated by A. Schulman.

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Zhu, H., Senalik, D., McCown, B.H. et al. Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.). Theor Appl Genet 124, 87–96 (2012). https://doi.org/10.1007/s00122-011-1689-2

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  • DOI: https://doi.org/10.1007/s00122-011-1689-2

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