Molecular diversity and genetic relationships in Secale

J Genet. 2016 Jun;95(2):273-81. doi: 10.1007/s12041-016-0632-3.


The objective of this study was to quantify the molecular diversity and to determine the genetic relationships among Secale spp. and among cultivars of Secale cereale using RAPDs, ISSRs and sequence analysis of six exons of ScMATE1 gene. Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDs and 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primers generated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further, 69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of the ScMATE1 gene also demonstrated a high genetic variability that subsists in Secale genus. One difference observed in exon 1 sequences from S. vavilovii seems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs, ISSRs and exons of ScMATE1 gene were similar. S. ancestrale, S. kuprijanovii and S. cereale were grouped in the same cluster and S. segetale was in another cluster. S. vavilovii showed evidences of not being clearly an isolate species and having great intraspecific differences.

MeSH terms

  • Carrier Proteins / genetics*
  • DNA Primers
  • DNA, Intergenic / genetics
  • DNA, Plant / genetics*
  • Genotype
  • Microsatellite Repeats
  • Phylogeny*
  • Plant Breeding
  • Plant Proteins / genetics*
  • Polymorphism, Genetic*
  • Random Amplified Polymorphic DNA Technique
  • Repetitive Sequences, Nucleic Acid
  • Secale / classification
  • Secale / genetics*


  • Carrier Proteins
  • DNA Primers
  • DNA, Intergenic
  • DNA, Plant
  • Plant Proteins
  • citrate-binding transport protein