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A genome-enabled, high-throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.)

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Abstract

Strawberry (Fragaria L.) genotypes bear remarkable phenotypic similarity, even across ploidy levels. Additionally, breeding programs seek to introgress alleles from wild germplasm, so objective molecular description of genetic variation has great value. In this report, a high-throughput, robust protocol for generating highly-informative simple sequence repeat (SSR) patterns is presented to address these issues. The methods are comparable to SSR use in DNA typing in humans and are based on identification of high-number repeats composed of tetra- through nona-nucleotide repeat units found in the Fragaria vesca genome sequence. Individual SSR-containing regions were examined for variability over a range of 219 strawberry genotypes. A single-fluorophore secondary labeling strategy was devised that allows simultaneous amplification of eight SSR regions in a single PCR reaction. The approach yields reproducible, highly-variable, complex patterns (Shannon-Weaver Index 7.09–13.88). The technique may be applied to detect closely-related individuals across ploidy levels, including full sibling progeny in an inter-related octoploid pedigree. Genetic diversity among various cultivars and progenitor wild species in the United States Department of Agriculture-Agricultural Research Service Fragaria Supercore collection was also evaluated. The results build on known relationships, and also raise questions about accepted relationships between several genotypes.

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Acknowledgments

This work was funded by the University of Florida Plant Molecular Breeding Initiative (VMW & KMF).

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Authors and Affiliations

  1. Horticultural Sciences Department, University of Florida, 1301 Fifield Hall, Gainesville, FL, 32611, USA

    Alan Chambers, Scott Carle & Kevin M. Folta

  2. Eurofins Lancaster Laboratories, 2425 New Holland Pike, Lancaster, PA, 17605, USA

    Wambui Njuguna

  3. Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA

    Srikar Chamala & W. Brad Barbazuk

  4. National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Rd, Corvallis, OR, 97333, USA

    Nahla Bassil

  5. Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL, 33598, USA

    Vance M. Whitaker

  6. Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA

    Kevin M. Folta

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  1. Alan Chambers
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  2. Scott Carle
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Correspondence to Kevin M. Folta.

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Chambers, A., Carle, S., Njuguna, W. et al. A genome-enabled, high-throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.). Mol Breeding 31, 615–629 (2013). https://doi.org/10.1007/s11032-012-9819-3

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  • DOI: https://doi.org/10.1007/s11032-012-9819-3

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