Molecular Genetics and Genomics

, Volume 292, Issue 4, pp 847–855 | Cite as

Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)

  • Şurhan Göl
  • Mehmet Göktay
  • Jens Allmer
  • Sami Doğanlar
  • Anne FraryEmail author
Original Article


Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.


Next generation sequencing Genomic SSRs Genetic diversity Microsatellites Population structure 



This research was supported by funding from an Izmir Institute of Technology Scientific Research Project, IYTE-BAP2012-2014.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards statement

This article does not contain any studies with human participants or animals performed by any of the authors.

Data availability

Sequence data are available at the SRA database of NCBI (SRX2266012).

Supplementary material

438_2017_1314_MOESM1_ESM.pdf (205 kb)
Supplementary material 1 (PDF 205 KB)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Şurhan Göl
    • 1
  • Mehmet Göktay
    • 1
  • Jens Allmer
    • 1
  • Sami Doğanlar
    • 1
  • Anne Frary
    • 1
    Email author
  1. 1.Department of Molecular Biology and GeneticsIzmir Institute of TechnologyUrla IzmirTurkey

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