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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MDPI AG
2020-12-01
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| Series: | International Journal of Molecular Sciences |
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| author | Lidia Skuza Ewa Filip Izabela Szućko Jan Bocianowski |
| author_facet | Lidia Skuza Ewa Filip Izabela Szućko Jan Bocianowski |
| author_sort | Lidia Skuza |
| collection | DOAJ |
| description | <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. |
| first_indexed | 2024-03-10T14:11:09Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T14:11:09Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-cf8d10e936124138a8aaf1903e470f192023-11-21T00:13:55ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-12-012124942110.3390/ijms21249421SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: <i>Secale</i>) SpeciesLidia Skuza0Ewa Filip1Izabela Szućko2Jan Bocianowski3Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, PolandInstitute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, PolandInstitute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, PolandDepartment of Mathematical and Statistical Methods, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 28 Wojska Polskiego, 60-637 Poznań, Poland<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.https://www.mdpi.com/1422-0067/21/24/9421<i>Secale</i>cpDNAmtDNASPInDelhypervariable regions |
| spellingShingle | Lidia Skuza Ewa Filip Izabela Szućko Jan Bocianowski SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: <i>Secale</i>) Species International Journal of Molecular Sciences <i>Secale</i> cpDNA mtDNA SPInDel hypervariable regions |
| title | SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: <i>Secale</i>) Species |
| title_full | SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: <i>Secale</i>) Species |
| title_fullStr | SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: <i>Secale</i>) Species |
| title_full_unstemmed | SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: <i>Secale</i>) Species |
| title_short | SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: <i>Secale</i>) Species |
| title_sort | spindel analysis of the non coding regions of cpdna as a more useful tool for the identification of rye poaceae i secale i species |
| topic | <i>Secale</i> cpDNA mtDNA SPInDel hypervariable regions |
| url | https://www.mdpi.com/1422-0067/21/24/9421 |
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