Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplasm

Katharina Kempf, Marina Mora-Ortiz, Lydia Smith, Roland Koelliker, Leif Skot

Research output: Contribution to journalArticlepeer-review

30 Citations (Scopus)
191 Downloads (Pure)


Background: Sainfoin is a perennial forage legume with beneficial properties for animal husbandry due to the presence of secondary metabolites. However, worldwide cultivation of sainfoin is marginal due to the lack of varieties with good agronomic performance, adapted to a broad range of environmental conditions. Little is known about the genetics of sainfoin and only few genetic markers are available to assist breeding and genetic investigations. The objective of this study was to develop a set of SSR markers useful for genetic studies in sainfoin and their characterization in diverse germplasm.
Methods: A set of 400 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 32 sainfoin individuals, representing distinct varieties or landraces. Alleles were scored for presence or absence and polymorphism information content of each SSR locus was calculated with an adapted formula taking into account the tetraploid character of sainfoin. Relationships among individuals were visualized using cluster and principle components analysis
Results: Of the 400 primer combinations tested, 101 reliably detected polymorphisms among the 32 sainfoin individuals. Among the 1154 alleles amplified 250 private alleles were observed. The number of alleles per locus ranged from 2 to 24 with an average of 11.4 alleles. The average polymorphism information content reached values of 0.14 to 0.36. The clustering of the 32 individuals suggested a separation into two groups depending on the origin of the accessions.
Concluions: The SSR markers characterized and tested in this study provide a valuable tool to detect polymorphisms in sainfoin for future genetic studies and breeding programs. As a proof of concept, we showed that these markers can be used to separate sainfoin individuals based on their origin.
Original languageEnglish
Article number124
Number of pages14
JournalBMC Genetics
Publication statusPublished - 30 Aug 2016


  • Onobrychis viciifolia
  • sainfoin
  • microsatellite
  • SSR
  • Genetic diversity
  • molecular markers
  • fingerprinting


Dive into the research topics of 'Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplasm'. Together they form a unique fingerprint.

Cite this