Molecular Breeding

, Volume 31, Issue 3, pp 615–629 | Cite as

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

  • Alan Chambers
  • Scott Carle
  • Wambui Njuguna
  • Srikar Chamala
  • Nahla Bassil
  • Vance M. Whitaker
  • W. Brad Barbazuk
  • Kevin M. Folta
Article

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.

Keywords

Strawberry Fragaria Simple sequence repeat Genotyping Genetic diversity 

Supplementary material

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Supplementary material 1 (PDF 41 kb)
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Supplementary material 2 (PNG 17 kb)
11032_2012_9819_MOESM3_ESM.pdf (51 kb)
Supplementary material 3 (PDF 51 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Alan Chambers
    • 1
  • Scott Carle
    • 1
  • Wambui Njuguna
    • 2
  • Srikar Chamala
    • 3
  • Nahla Bassil
    • 4
  • Vance M. Whitaker
    • 5
  • W. Brad Barbazuk
    • 3
  • Kevin M. Folta
    • 1
    • 6
  1. 1.Horticultural Sciences DepartmentUniversity of FloridaGainesvilleUSA
  2. 2.Eurofins Lancaster LaboratoriesLancasterUSA
  3. 3.Department of BiologyUniversity of FloridaGainesvilleUSA
  4. 4.National Clonal Germplasm RepositoryUSDA-ARSCorvallisUSA
  5. 5.Gulf Coast Research and Education CenterUniversity of FloridaWimaumaUSA
  6. 6.Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleUSA

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