Plant Systematics and Evolution

, Volume 302, Issue 8, pp 1083–1091 | Cite as

Evolutionary relationships in the genus Secale revealed by DArTseq DNA polymorphism

  • Maja Al-Beyroutiová
  • Miroslav Sabo
  • Patrik Sleziak
  • Roman Dušinský
  • Erik Birčák
  • Pavol Hauptvogel
  • Andrzej Kilian
  • Miroslav ŠvecEmail author
Original Article


Till this day, there is not much known about the phylogeny of the Secale genus; therefore, in our research, we tried to shed some lights on the issue of rye (Secale genus) taxonomy. The genetic diversity and phylogenetic relationships were evaluated using 13,842 DArTseq™ polymorphic markers. The model-based clustering (STRUCTURE software) separated our 84 samples into three main clusters: perennial cluster, annual cluster, and S. sylvestre cluster. The same result was obtained using Neighbour Joining tree and self-organizing maps. Secale sylvestre, S. strictum, and S. cereale are the three main species of the Secale genus. Three samples of rye are in basal positions in phylogenetic trees. These accessions share ancient morphological characters and are probably the ancestors of different lineages within Secale. Annual Secale taxa, with the exception of S. sylvestre, create one mutual taxon. We have found out that the semi-perennial taxa of S. cereale var. multicaule and S. strictum subsp. ciliatoglume are genetically closest to the annual species of S. cereale. Phylogenetic signals for semi-perennial and annual taxa are also present in S. strictum subsp. africanum. SNP-based analysis revealed that evolution of annual S. cereale has already begun in S. strictum subsp. africanum. The results showed that S. vavilovii cannot be considered as a separate species but a subspecies of S. cereale Secale cereale subsp. dighoricum is a hybrid. It is still not clear whether we can consider S. strictum subsp. strictum and S. strictum subsp. kuprijanovii as two separate species.


DArTseq™ DNA polymorphism Genetic diversity Phylogenetic relationship Secale 



This paper was supported by the Slovak Research and Development Agency under the Contracts No. APVV-0197-10 and No. APVV-0661-10.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

606_2016_1318_MOESM1_ESM.pdf (63 kb)
Online Resource 1. List of used accessions with place of origin and gene bank name (PDF 62 kb)
606_2016_1318_MOESM2_ESM.pdf (87 kb)
Online Resource 2. Estimating Maximum Likelihood (lnL) and hybrid index (h) for the hybrid accessions, their presumed and potential parents, using FAMD program (PDF 86 kb)
606_2016_1318_MOESM3_ESM.pdf (179 kb)
Online Resource 3. Super network phylogram of Secale genus accessions generated using Splits Tree software (PDF 178 kb)
606_2016_1318_MOESM4_ESM.pdf (68 kb)
Online Resource 4. The U matrix for the variables (i.e., 59 Secale accessions) (PDF 67 kb)
606_2016_1318_MOESM5_ESM.pdf (562 kb)
Online Resource 5. Photo of tillering plants of MON1, and MON3 accessions (PDF 561 kb)
606_2016_1318_MOESM6_ESM.pdf (43 kb)
Online Resource 6. Maximum likelihood phylogram of Secale genus accessions generated using SNPhylo software from SNPs data with 500 bootstraps (PDF 42 kb)


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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  • Maja Al-Beyroutiová
    • 1
  • Miroslav Sabo
    • 2
  • Patrik Sleziak
    • 3
  • Roman Dušinský
    • 1
  • Erik Birčák
    • 1
  • Pavol Hauptvogel
    • 4
  • Andrzej Kilian
    • 5
  • Miroslav Švec
    • 1
    Email author
  1. 1.Department of Genetics, Faculty of Natural SciencesComenius University in BratislavaMlynská Dolina, BratislavaSlovakia
  2. 2.Faculty of Social and Economic SciencesComenius UniversityBratislavaSlovakia
  3. 3.Faculty of Civil EngineeringSlovak University of Technology in BratislavaBratislavaSlovakia
  4. 4.National Agricultural and Food CentreResearch Institute of Plant ProductionPiešťanySlovakia
  5. 5.Diversity Array Technology Pty Ltd.University of CanberraBruceAustralia

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