Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications

Tuğba Ünsal Sapan; Nur Gizem Tanrıverdi

doi:10.30616/ajb.2006304

TR EN

Taze ve kurutulmuş Pinus brutia iğne yapraklarından DNA ekstraksiyonunun farklı homojenizasyon yöntemleriyle optimizasyonu: Adli botanik uygulamaları için bir yaklaşım

Abstract

Bitki dokularından yeterli miktarda DNA elde edilmesi; moleküler taksonomi, popülasyon genetiği, koruma biyolojisi ve adli botanik uygulamaları açısından önem taşımaktadır. Ancak iğne yapraklı türlerden DNA izolasyonu, dokuların yüksek miktarda polisakkarit, polifenol, terpenoid ve reçine bileşikleri içermesi nedeniyle güçleşmekte; bu bileşikler DNA izolasyonunu ve sonraki moleküler analizleri olumsuz etkileyebilmektedir. Bu çalışmada, Türkiye’de yaygın olarak bulunan Pinus brutia iğne yapraklarında örnek durumu ve homojenizasyon yönteminin elde edilen DNA konsantrasyonu üzerindeki etkilerinin değerlendirilmesi amaçlanmıştır. Bu kapsamda Çanakkale ilinde bulunan 24 farklı P. brutia ağacından iğne yaprak örnekleri toplanmıştır. On iki ağaçtan alınan örnekler taze olarak işlenirken, diğer 12 ağaçtan alınan örnekler laboratuvar koşullarında 20 gün süreyle kurutulmuştur. Her bir örnek durumu içerisinde örnekler, havanda öğütme sonrasında TissueLyser ile homojenizasyon ve blender ile homojenizasyon olmak üzere iki farklı yöntemle işlenmiştir. Genomik DNA, i-genomic Plant DNA Extraction Mini Kit kullanılarak izole edilmiş ve DNA konsantrasyonu Qubit™ 4 Florometre ile dsDNA High Sensitivity Assay kiti kullanılarak belirlenmiştir. Elde edilen veriler iki yönlü varyans analizi (ANOVA) ile değerlendirilmiştir. Taze örneklerde kurutulmuş örneklere göre daha yüksek DNA konsantrasyonları elde edilirken, havanda öğütme sonrasında TissueLyser ile homojenizasyon uygulanan örneklerde blender ile homojenize edilen örneklere göre daha yüksek DNA konsantrasyonları belirlenmiştir. İki yönlü ANOVA, örnek durumu ve homojenizasyon yönteminin DNA konsantrasyonu üzerinde anlamlı ana etkilerinin yanı sıra iki faktör arasında anlamlı bir etkileşim bulunduğunu göstermiştir. Bu bulgular hem örnek durumunun hem de homojenizasyon yönteminin P. brutia iğne yapraklarından elde edilen DNA konsantrasyonunu etkilediğini göstermekte ve moleküler bitki araştırmaları ile adli botanik uygulamalarında DNA ekstraksiyon prosedürlerinin örnek özelliklerine göre optimize edilmesinin önemini ortaya koymaktadır.

Keywords

Supporting Institution

Üsküdar Üniversitesi Bağımlılık ve Adli Bilimler Enstitüsü

Ethical Statement

Bu çalışma yalnızca bitki materyali üzerinden gerçekleştirilmiş olup insan katılımcılar, deney hayvanları veya kişisel veri kullanımını içermediğinden etik kurul onayı gerektirmemektedir.

Thanks

Yazarlar, bu çalışmanın gerçekleştirilmesinde laboratuvar altyapısı ve teknik olanakları sağlayan Üsküdar Üniversitesi Bağımlılık ve Adli Bilimler Enstitüsü'ne teşekkür eder.

Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications

Abstract

Obtaining sufficient DNA from plant tissues is essential for molecular taxonomy, population genetics, conservation biology, and forensic botany. However, DNA extraction from conifer species remains challenging because their tissues contain high concentrations of polysaccharides, polyphenols, terpenoids, and resin compounds that may interfere with DNA isolation and downstream molecular analyses. This study aimed to evaluate the effects of sample condition and homogenization method on DNA concentration obtained from fresh and dried needles of Pinus brutia, one of the most widespread conifer species in Türkiye. Needle samples were collected from 24 individual trees in Çanakkale, Türkiye. Samples from 12 trees were processed fresh, whereas samples from the remaining 12 trees were air-dried for 20 days. Within each sample condition, samples were processed using two homogenization methods: mortar grinding followed by TissueLyser homogenization and blender homogenization. Genomic DNA was extracted using the i-genomic Plant DNA Extraction Mini Kit and quantified using a Qubit™ 4 Fluorometer with the dsDNA High Sensitivity Assay. Data were analyzed using two-way analysis of variance (ANOVA). Fresh samples showed higher DNA concentrations than dried samples, and mortar grinding followed by TissueLyser homogenization resulted in higher DNA concentrations than blender homogenization. Two-way ANOVA demonstrated significant main effects of sample condition and homogenization method on DNA concentration, as well as a significant interaction between the two factors. These findings indicate that both sample condition and homogenization method influence DNA concentration obtained from P. brutia needles and highlight the importance of sample-specific optimization of DNA extraction procedures for molecular plant research and forensic botanical applications.

Keywords

Supporting Institution

Üsküdar University Institute of Addiction and Forensic Sciences

Ethical Statement

Ethical approval was not required for this study because no human participants, animals, or personal data were involved.

Thanks

The authors would like to thank the Institute of Addiction and Forensic Sciences, Üsküdar University, for providing the laboratory facilities and technical infrastructure that supported this study.

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Details

Primary Language

English

Subjects

Plant Biotechnology, Plant Cell and Molecular Biology

Journal Section

Research Article

Authors

Tuğba Ünsal Sapan ^*
0000-0003-4744-2298
Türkiye

Nur Gizem Tanrıverdi
0009-0003-9690-0336
Türkiye

Publication Date

October 12, 2026

Submission Date

July 30, 2026

Acceptance Date

October 1, 2026

Published in Issue

Year 2026 Volume: 10 Number: 2

DOI

https://doi.org/10.30616/ajb.2006304

IZ

https://izlik.org/JA27RR25UU

Cite

RIS / Bibtex

APA

Ünsal Sapan, T., & Tanrıverdi, N. G. (2026). Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications. Anatolian Journal of Botany, 10(2), 237-242. https://doi.org/10.30616/ajb.2006304

AMA

1.Ünsal Sapan T, Tanrıverdi NG. Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications. Ant J Bot. 2026;10(2):237-242. doi:10.30616/ajb.2006304

Chicago

Ünsal Sapan, Tuğba, and Nur Gizem Tanrıverdi. 2026. “Optimization of DNA Extraction from Fresh and Dried Pinus Brutia Needles Using Different Homogenization Methods: An Approach for Forensic Botanical Applications”. Anatolian Journal of Botany 10 (2): 237-42. https://doi.org/10.30616/ajb.2006304.

EndNote

Ünsal Sapan T, Tanrıverdi NG (October 1, 2026) Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications. Anatolian Journal of Botany 10 2 237–242.

IEEE

[1]T. Ünsal Sapan and N. G. Tanrıverdi, “Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications”, Ant J Bot, vol. 10, no. 2, pp. 237–242, Oct. 2026, doi: 10.30616/ajb.2006304.

ISNAD

Ünsal Sapan, Tuğba - Tanrıverdi, Nur Gizem. “Optimization of DNA Extraction from Fresh and Dried Pinus Brutia Needles Using Different Homogenization Methods: An Approach for Forensic Botanical Applications”. Anatolian Journal of Botany 10/2 (October 1, 2026): 237-242. https://doi.org/10.30616/ajb.2006304.

JAMA

1.Ünsal Sapan T, Tanrıverdi NG. Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications. Ant J Bot. 2026;10:237–242.

MLA

Ünsal Sapan, Tuğba, and Nur Gizem Tanrıverdi. “Optimization of DNA Extraction from Fresh and Dried Pinus Brutia Needles Using Different Homogenization Methods: An Approach for Forensic Botanical Applications”. Anatolian Journal of Botany, vol. 10, no. 2, Oct. 2026, pp. 237-42, doi:10.30616/ajb.2006304.

Vancouver

1.Tuğba Ünsal Sapan, Nur Gizem Tanrıverdi. Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications. Ant J Bot. 2026 Oct. 1;10(2):237-42. doi:10.30616/ajb.2006304

Anatolian Journal of Botany (Ant J Bot) is an open-access, peer-reviewed journal. It publishes original articles, reviews or short communications in all areas of plant biology (biotechnology, diversity, ecology, function, genetics, physiology, structure and systematics) including algae, fungi, lichens and mosses, and chemistry of all above organisms. The journal have been published biannually until the end of 2025. Starting from 2026 the journal publishes continiously.
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Kaya A (2015). Contributions to the macrofungal diversity of Atatürk Dam Lake basin. Turkish Journal of Botany 39(1): 162-172.

Uzun Y, Karacan İH, Yakar S, Kaya A (2017). Octospora Hedw., A new genus record for Turkish Pyronemataceae. Anatolian Journal of Botany 1(1): 18-20.

Uzun Y, Kaya A (2019). New additions to Turkish Pezizales from East Blacksea Region. Turkish Journal of Botany (DOI: 10.3906/bot-1802-34 / online)

Breitenbach J, Kränzlin F (1984). Fungi of Switzerland,Vol. 1. Lucerne: Verlag Mykologia.

Davis PH (1965). Flora of Turkey and the East Aegean Islands, Vol. 1. Edinburgh: Edinburgh University Press.

Kaya A (2011). Mantarlar. In: Özuslu E, Tel AZ (eds.). Gaziantep’in Biyolojik Çeşitliliği. Gaziantep: Doğa Koruma Derneği. pp. 29-60.

Kaya A (2009). Contributions to the macrofungi flora of Muş (Turkey) province. In: Ivanova D (ed.). Plant, fungal and habitat diversity investigation and conservation. Proceedings of IV Balkan Botanical Congress, Sofia 2006. Pp. 455–458.

Index Fungorum. http://www.indexfungorum.org/names/Names.asp / [accessed 10 December 2016].

Kuo M (2007). Key to major groups of mushrooms. MushroomExpert.Com Website: http://www.mushroomexpert.com/major_groups.html / [accessed 15 December 2016].

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Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications

Taze ve kurutulmuş Pinus brutia iğne yapraklarından DNA ekstraksiyonunun farklı homojenizasyon yöntemleriyle optimizasyonu: Adli botanik uygulamaları için bir yaklaşım

Abstract

Keywords

Supporting Institution

Ethical Statement

Thanks

Optimization of DNA extraction from fresh and dried Pinus brutia needles using different homogenization methods: An approach for forensic botanical applications

Abstract

Keywords

Supporting Institution

Ethical Statement

Thanks

References

Details

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Acceptance Date

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