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Secale  is a small but very diverse genus from the tribe  Triticeae  (family  Poaceae ), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus  Secale . Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus  Secale , however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA:  atpB-rbcL  and  trnT - trnL  and non-coding regions of mitochondrial DNA:  nad1B - nad1C  and  rrn5/rrn18 . Our results demonstrate the utility of the SPInDel concept for the characterisation of  Secale  species.

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species