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

<i>Secale</i> is a small but very diverse genus from the tribe <i>Triticeae</i> (family <i>Poaceae</i>), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic im...

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Bibliographic Details
Main Authors: Lidia Skuza, Ewa Filip, Izabela Szućko, Jan Bocianowski
Format: Article
Language:English
Published: MDPI AG 2020-12-01
Series:International Journal of Molecular Sciences
Subjects:
Online Access:https://www.mdpi.com/1422-0067/21/24/9421
Description
Summary:<i>Secale</i> is a small but very diverse genus from the tribe <i>Triticeae</i> (family <i>Poaceae</i>), 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 <i>Secale</i>. 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 <i>Secale</i>, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: <i>atpB-rbcL</i> and <i>trnT</i>-<i>trnL</i> and non-coding regions of mitochondrial DNA: <i>nad1B</i>-<i>nad1C</i> and <i>rrn5/rrn18</i>. Our results demonstrate the utility of the SPInDel concept for the characterisation of <i>Secale</i> species.
ISSN:1661-6596
1422-0067