Development of  Genic SSR (Simple Sequence Repeat) Markers Based on an  Oregano (Origanum vulgare L.) Transcriptome Assembly

Ali Tevfik UNCU

doi:https://doi.org/10.54498/ETBD.2024.37

Ali Tevfik UNCU, Ayşe Özgür Uncu, Fatıma Ceylan

Year : 2025
Vol : 5
Issue : 1
Page : 1-10

DOI : https://doi.org/10.54498/ETBD.2024.37

Developments in next generation sequencing technologies and bioinformatic analyses enable the identification of sequence specific DNA markers at the whole genome/transcriptome level. During the last decade, diversification of the next generation sequencing platforms as well as the associated sequence analysis algorithms have made generic marker systems such as RAPD (random amplified polymorphic DNA) and ISSR (inter simple sequence repeat) almost obsolete and sequence specific markers constitute useful genomic tools for applications in plant molecular genetics. The aim of the present work was to develop genic SSR (simple sequence repeat) markers specific for the well-known medicinal and aromatic herb, oregano (Origanum vulgare L.). Although the Origanum genus hosts widely-recognized medicinal and aromatic species, only 33 genome-specific markers have been developed to date for the genus. In the course of the present work, the transcriptome sequence of O. vulgare L. ssp. vulgare, one of the most widely known members of the Origanum genus, was assembled via a de novo transcriptome assembly approach. The assembly was scanned for the identification of trinucleotide SSRs. GC rich loci were found to be the most abundant simple sequence repeats, which is indeed characteristic for coding sequences. While genic SSRs are more conserved compared to genomic SSRs, markers that represent transcribed loci are more likely to be useful for trait association studies. In the course of the present work, the loci identified in the transcriptome sequences were used in the high-throughput marker development process, yielding a total of 1731 sequence-specific genic SSR markers. Since SSR polymorphisms located in open reading frames and 5’/3’ UTR (untranslated region) carry the potential to affect the amino acid sequence or protein folding and the level of gene expression, the markers introduced in the present work constitute a genome-specific set of candidate functional markers.

Cite this Article As : Ceylan, F., & Uncu, A. T., & Özgür Uncu, A. (2025). Kekik (origanum vulgare l.) genik ssr (basit dizi tekrarı) markörlerinin transkriptoma dayalı geliştirilmesi. Ereğli Tarım Bilimleri Dergisi, 5(1), 1-10. https://doi.org/10.54498/ETBD.2025.37

Description : Yazarların hiçbiri, bu makalede bahsedilen herhangi bir ürün, aygıt veya ilaç ile ilgili maddi çıkar ilişkisine sahip değildir. Araştırma, herhangi bir dış organizasyon tarafından desteklenmedi.Yazarlar çalışmanın birincil verilerine tam erişim izni vermek ve derginin talep ettiği takdirde verileri incelemesine izin vermeyi kabul etmektedirler. None of the authors, any product mentioned in this article, does not have a material interest in the device or drug. Research, not supported by any external organization. grant full access to the primary data and, if requested by the magazine they agree to allow the examination of data.

Development of Genic SSR (Simple Sequence Repeat) Markers Based on an Oregano (Origanum vulgare L.) Transcriptome Assembly, Research Article,
2025, Vol. 5 (1)

Received : 10.12.2024, Accepted : 19.03.2025 , Published Online : 30.06.2025