Genetic Resources and Crop Evolution

, Volume 66, Issue 6, pp 1295–1309 | Cite as

Exploring genetic diversity of tomato (Solanum lycopersicum L.) germplasm of genebank collection employing SSR and SCAR markers

  • Evangelos D. Gonias
  • Ioannis Ganopoulos
  • Ifigeneia Mellidou
  • Androniki C. Bibi
  • Apostolos Kalivas
  • Photini V. Mylona
  • Maslin Osanthanunkul
  • Athanasios Tsaftaris
  • Panagiotis MadesisEmail author
  • Andreas G. DoulisEmail author
Research Article


Α wide selection of tomato (Solanum lycopersicum L.) genotypes with diverse origin and breeding history (14 modern varieties, 71 landraces and 22 commercial hybrids) has been initially genotyped with a selection of highly informative simple sequence repeat (SSR) markers and two SCAR markers originally developed for resistance against two main fungal tomato diseases. Our data revealed a high level of genetic diversity across the selection, with an average number of alleles per locus (NA) equal to 9.6, and the average polymorphism information content (PIC) equal to 0.74. Further, the selected SSRs have been verified as highly polymorphic and able to discriminate different patterns within our collection, amplifying a total of 56 alleles. Cluster analysis indicated that the collection could be grouped into three clades, with most of landraces and modern varieties being clearly distinguished from hybrids, but also with each other. Breeding involve the selection of specific phenotypes, limiting the genetic variation of the population. Herein, a notable genetic loss due to breeding was detected in the modern tomato gene pool.


Landraces SCAR marker Loss of diversity SSR markers Modern varieties 



This project was funded in part through AgroETAK to EDG (No. 3497/146) administered by HAO—DEMETER (responsible scientist, AGD) under the “Research, Technological Development & Innovation Projects”—in the framework of the Operational Program “Human Resources Development” MIS 453350. This was in turn co-financed by the European Union Social Fund and by Greece through the National Strategic Reference Framework (ESPA, Research Funding Program 2007–2013). This work was supported by Chiang Mai University.

Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest.


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Evangelos D. Gonias
    • 1
  • Ioannis Ganopoulos
    • 2
  • Ifigeneia Mellidou
    • 2
  • Androniki C. Bibi
    • 1
  • Apostolos Kalivas
    • 2
  • Photini V. Mylona
    • 2
  • Maslin Osanthanunkul
    • 3
    • 4
  • Athanasios Tsaftaris
    • 5
  • Panagiotis Madesis
    • 6
    Email author
  • Andreas G. Doulis
    • 1
    Email author
  1. 1.Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (HAO)-DEMETERHeraklion, CreteGreece
  2. 2.Institute of Plant Breeding and Genetic Resources, HAO-DEMETER. ThermiThessalonikiGreece
  3. 3.Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
  4. 4.Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai UniversityChiang MaiThailand
  5. 5.Perrotis College, American Farm SchoolThessalonikiGreece
  6. 6.Institute of Applied Biosciences, CERTHThessalonikiGreece

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