Research Article
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Determining the genetic diversity of some black cumin genotypes collected in different regions of Türkiye using RAPD markers

Year 2024, Volume: 8 Issue: 2, 294 - 300, 27.06.2024
https://doi.org/10.31015/jaefs.2024.2.6

Abstract

Black cumin is one of the important medicinal aromatic plants belonging to the Ranunculaceae family. It is mostly used in the Middle East and for some diseases, especially in the Iranian region. It is important to know the genetic resources of such important medicinal and aromatic plants. Characterization of genetic resources sheds light on both the conservation of genetic resources and the future breeding studies. In this study, a total of 8 black cumin plants were characterized with 17 RAPD primers. Presence (1) and absence (0) scoring of gel images was performed using the Agarose Gel Electrophoresis (AGE) method. In genetic characterization, phylogenetic dendrogram with Bayesian statistics and Principal Coordinate Analysis (PCoA) with Jaccard similarity index were performed. As a result of the findings, the Nigella damascena, one of the black cumin plant species, was 100% separated from the Nigella sativa species. Additionally, Nigella sativa species differed among Konya, Eskişehir and Çameli genotypes. It gave similar results to Bayesian statistics in PCoA. The analysis indicated that Konya, Eskişehir and Çameli genotypes of Nigella sativa species have a higher potential to be used in breeding studies compared to other genotypes.

Supporting Institution

The financial support of this study was supported by Iğdır University BAP coordination with the project number ZİF1223A09.

Project Number

ZİF1223A09

Thanks

I would like to thank Iğdır University for their financial support of this study.

References

  • Abdulhamed, Z. A., Abas, S. A., & Kosaj, K. I. (2022). Genetic and Molecular Variations Using the Molecular Marker Rapd in Barley Yield. International Journal of Agricultural & Statistical Sciences, 18.
  • Al-Hadeithi, Z. S., & Jasim, S. A. (2021). Study of plant genetic variation through molecular markers: An overview. J. Pharm. Res. Int, 33(45B), 464-473.
  • Al-Khayri, J. M., Mahdy, E. M., Taha, H. S., Eldomiaty, A. S., Abd-Elfattah, M. A., Abdel Latef, A. A. H., ... & Hassanin, A. A. (2022). Genetic and morphological diversity assessment of five kalanchoe genotypes by SCoT, ISSR and RAPD-PCR markers. Plants, 11(13), 1722.
  • Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon, 7(10).
  • Aydin, A. (2023). Determination of Genetic Diversity of Some Upland and Sea Island Cotton Genotypes Using High-Resolution Capillary Electrophoresis Gel. Agronomy, 13(9), 2407.
  • Bi, D., Chen, D., Khayatnezhad, M., Hashjin, Z. S., Li, Z., & Ma, Y. (2021). Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers. Genetika, 53(1), 393-405.
  • Bourgou, S., Pichette, A., Marzouk, B., & Legault, J. (2010). Bioactivities of black cumin essential oil and its main terpenes from Tunisia. South African Journal of Botany, 76(2), 210-216.
  • El-Haggar, M. A., Mahgoub, Y. A., Aly, H. M., Ghazy, N. M., El-Fiky, F. K., & El-Hawiet, A. M. (2023). DNA barcodes, ISSR, RAPD and SCAR markers as potential quality control tools for molecular authentication of black and white mulberry. Food Control, 152, 109821.
  • Grover, A., & Sharma, P. C. (2016). Development and use of molecular markers: past and present. Critical reviews in biotechnology, 36(2), 290-302.
  • Gower, J. C. (2014). Principal coordinates analysis. Wiley StatsRef: statistics reference online, 1-7.
  • Han, C., Zhu, Q., Lu, H., Wang, C., Zhou, X., Peng, C., ... & Zhang, Y. (2020). Screening and characterization of sex-specific markers developed by a simple NGS method in mandarin fish (Siniperca chuatsi). Aquaculture, 527, 735495.
  • Hasan, N., Choudhary, S., Naaz, N., Sharma, N., & Laskar, R. A. (2021). Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. Journal of Genetic Engineering and Biotechnology, 19(1), 1-26.
  • Havlik, J., Kokoska, L., Vasickova, S., & Valterova, I. (2006). Chemical composition of essential oil from the seeds of Nigella arvensis L. and assessment of its actimicrobial activity. Flavour and fragrance journal, 21(4), 713-717.
  • Karaca, M., İnce, A. G., Elmasulu, S. Y., Onus, A. N., & Turgut, K. (2005). Coisolation of genomic and organelle DNAs from 15 genera and 31 species of plants. Analytical biochemistry, 343(2), 353-355.
  • Karaca, M., Ince, A. G., Aydin, A., & Ay, S. T. (2013). Cross‐genera transferable e‐microsatellite markers for 12 genera of the Lamiaceae family. Journal of the Science of Food and Agriculture, 93(8), 1869-1879.
  • Karaca, M., Ince, A. G., Aydin, A., Elmasulu, S. Y., & Turgut, K. (2015). Microsatellites for genetic and taxonomic research on thyme (Thymus L.). Turkish Journal of Biology, 39(1), 147-159.
  • Karaca, M., Aydin, A., & Ince, A. G. (2019). Cytosine methylation polymorphisms in cotton using TD-MS-RAPD-PCR. Modern Phytomorphology, 13, 13-19.
  • Luan Nguyen, T., Anam, A., Hofdey Megbes, F., Mourad Mohammed, I., Abed, A. S., Imran Mallhi, A., ... & Ha Pham Thi, H. (2023). Structural Diversity, Spectral Data, and Pharmacological Effects of Genus Nigella. Chemistry & Biodiversity, 20(7), e202300037.
  • Manjunathagowda, D. C. (2021). Perspective and application of molecular markers linked to the cytoplasm types and male‐fertility restorer locus in onion (Allium cepa). Plant Breeding, 140(5), 732-744.
  • Mei-Chao, D., Fan, Y. A. N. G., Xiao-meng, F. U., Jun-yan, G. A. O., Dong-guo, Z. H. O. U., Shao-hua, W. A. N. G., ... & Jian-qiang, Y. U. E. (2020). AFLP Molecular Markers-based Genetic Diversity Analysis on 90 Avocado Germplasms. 福建农业学报, 35(1), 13-19.
  • Meng, Y., Yang, C. B., Jiang, S. C., Huang, L. L., Kang, Z. S., & Zhan, G. M. (2022). Development and evaluation of SNP molecular markers of wheat strip rust based on KASP technology. Journal of plant protection, 47(1), 65-73
  • Ronquist, F. and Huelsenbeck, J.P. 2003. Mrbayes 3: Bayesian Phylogenetic Inference Under Mixed Models. Bioinformatics, 19, 1572-1574.
  • Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B., dos Santos Rabaiolli, S. M., & Stefanel, C. M. (2020). Determining the Polymorphism Information Content of a molecular marker. Gene, 726, 144175.
  • Soller, M. (2020). Mapping quantitative trait loci affecting traits of economic importance in animal populations using molecular markers. In Gene-mapping techniques and applications (pp. 21-49). CRC Press.
  • Song, L., Wang, R., Yang, X., Zhang, A., & Liu, D. (2023). Molecular Markers and Their Applications in Marker-Assisted Selection (MAS) in Bread Wheat (Triticum aestivum L.). Agriculture, 13(3), 642.
  • Srinivasan K (2018) Cumin (Cuminum cyminum) and black cumin (Nigella sativa) seeds: traditional uses, chemical constituents, and nutraceutical effects. Food Qual Saf 2(1):1–16
  • Türkoğlu, A., Haliloğlu, K., Demirel, F., Aydin, M., Çiçek, S., Yiğider, E., ... & Niedbała, G. (2023). Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat (Triticum aestivum L.): Callus Induction, Plant Regeneration, and DNA Methylation. Plants, 12(24), 4151.
  • Venkatesan, J., Ramu, V., Sethuraman, T., Sivagnanam, C., & Doss, G. (2021). Molecular marker for characterization of traditional and hybrid derivatives of Eleusine coracana (L.) using ISSR marker. Journal of Genetic Engineering and Biotechnology, 19, 1-12.
  • Yanez, J. M., Barria, A., Lopez, M. E., Moen, T., Garcia, B. F., Yoshida, G. M., & Xu, P. (2023). Genome‐wide association and genomic selection in aquaculture. Reviews in Aquaculture, 15(2), 645-675.
  • Xu, T., Yao, Z., Liu, J., Zhang, H., Din, G. M. U., Zhao, S., ... & Gao, L. (2020). Development of droplet digital PCR for the detection of Tilletia laevis, which causes common bunt of wheat, based on the SCAR marker derived from ISSR and real-time PCR. Scientific Reports, 10(1), 16106.
Year 2024, Volume: 8 Issue: 2, 294 - 300, 27.06.2024
https://doi.org/10.31015/jaefs.2024.2.6

Abstract

Ethical Statement

Etik beyanı gerektirecek bir çalışma değildir.

Supporting Institution

Iğdır Üniversitesi

Project Number

ZİF1223A09

Thanks

Iğdır Üniversitesi BAP koordinasyon birimine mali desteklerinden dolayı teşekkür ederim.

References

  • Abdulhamed, Z. A., Abas, S. A., & Kosaj, K. I. (2022). Genetic and Molecular Variations Using the Molecular Marker Rapd in Barley Yield. International Journal of Agricultural & Statistical Sciences, 18.
  • Al-Hadeithi, Z. S., & Jasim, S. A. (2021). Study of plant genetic variation through molecular markers: An overview. J. Pharm. Res. Int, 33(45B), 464-473.
  • Al-Khayri, J. M., Mahdy, E. M., Taha, H. S., Eldomiaty, A. S., Abd-Elfattah, M. A., Abdel Latef, A. A. H., ... & Hassanin, A. A. (2022). Genetic and morphological diversity assessment of five kalanchoe genotypes by SCoT, ISSR and RAPD-PCR markers. Plants, 11(13), 1722.
  • Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon, 7(10).
  • Aydin, A. (2023). Determination of Genetic Diversity of Some Upland and Sea Island Cotton Genotypes Using High-Resolution Capillary Electrophoresis Gel. Agronomy, 13(9), 2407.
  • Bi, D., Chen, D., Khayatnezhad, M., Hashjin, Z. S., Li, Z., & Ma, Y. (2021). Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers. Genetika, 53(1), 393-405.
  • Bourgou, S., Pichette, A., Marzouk, B., & Legault, J. (2010). Bioactivities of black cumin essential oil and its main terpenes from Tunisia. South African Journal of Botany, 76(2), 210-216.
  • El-Haggar, M. A., Mahgoub, Y. A., Aly, H. M., Ghazy, N. M., El-Fiky, F. K., & El-Hawiet, A. M. (2023). DNA barcodes, ISSR, RAPD and SCAR markers as potential quality control tools for molecular authentication of black and white mulberry. Food Control, 152, 109821.
  • Grover, A., & Sharma, P. C. (2016). Development and use of molecular markers: past and present. Critical reviews in biotechnology, 36(2), 290-302.
  • Gower, J. C. (2014). Principal coordinates analysis. Wiley StatsRef: statistics reference online, 1-7.
  • Han, C., Zhu, Q., Lu, H., Wang, C., Zhou, X., Peng, C., ... & Zhang, Y. (2020). Screening and characterization of sex-specific markers developed by a simple NGS method in mandarin fish (Siniperca chuatsi). Aquaculture, 527, 735495.
  • Hasan, N., Choudhary, S., Naaz, N., Sharma, N., & Laskar, R. A. (2021). Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. Journal of Genetic Engineering and Biotechnology, 19(1), 1-26.
  • Havlik, J., Kokoska, L., Vasickova, S., & Valterova, I. (2006). Chemical composition of essential oil from the seeds of Nigella arvensis L. and assessment of its actimicrobial activity. Flavour and fragrance journal, 21(4), 713-717.
  • Karaca, M., İnce, A. G., Elmasulu, S. Y., Onus, A. N., & Turgut, K. (2005). Coisolation of genomic and organelle DNAs from 15 genera and 31 species of plants. Analytical biochemistry, 343(2), 353-355.
  • Karaca, M., Ince, A. G., Aydin, A., & Ay, S. T. (2013). Cross‐genera transferable e‐microsatellite markers for 12 genera of the Lamiaceae family. Journal of the Science of Food and Agriculture, 93(8), 1869-1879.
  • Karaca, M., Ince, A. G., Aydin, A., Elmasulu, S. Y., & Turgut, K. (2015). Microsatellites for genetic and taxonomic research on thyme (Thymus L.). Turkish Journal of Biology, 39(1), 147-159.
  • Karaca, M., Aydin, A., & Ince, A. G. (2019). Cytosine methylation polymorphisms in cotton using TD-MS-RAPD-PCR. Modern Phytomorphology, 13, 13-19.
  • Luan Nguyen, T., Anam, A., Hofdey Megbes, F., Mourad Mohammed, I., Abed, A. S., Imran Mallhi, A., ... & Ha Pham Thi, H. (2023). Structural Diversity, Spectral Data, and Pharmacological Effects of Genus Nigella. Chemistry & Biodiversity, 20(7), e202300037.
  • Manjunathagowda, D. C. (2021). Perspective and application of molecular markers linked to the cytoplasm types and male‐fertility restorer locus in onion (Allium cepa). Plant Breeding, 140(5), 732-744.
  • Mei-Chao, D., Fan, Y. A. N. G., Xiao-meng, F. U., Jun-yan, G. A. O., Dong-guo, Z. H. O. U., Shao-hua, W. A. N. G., ... & Jian-qiang, Y. U. E. (2020). AFLP Molecular Markers-based Genetic Diversity Analysis on 90 Avocado Germplasms. 福建农业学报, 35(1), 13-19.
  • Meng, Y., Yang, C. B., Jiang, S. C., Huang, L. L., Kang, Z. S., & Zhan, G. M. (2022). Development and evaluation of SNP molecular markers of wheat strip rust based on KASP technology. Journal of plant protection, 47(1), 65-73
  • Ronquist, F. and Huelsenbeck, J.P. 2003. Mrbayes 3: Bayesian Phylogenetic Inference Under Mixed Models. Bioinformatics, 19, 1572-1574.
  • Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B., dos Santos Rabaiolli, S. M., & Stefanel, C. M. (2020). Determining the Polymorphism Information Content of a molecular marker. Gene, 726, 144175.
  • Soller, M. (2020). Mapping quantitative trait loci affecting traits of economic importance in animal populations using molecular markers. In Gene-mapping techniques and applications (pp. 21-49). CRC Press.
  • Song, L., Wang, R., Yang, X., Zhang, A., & Liu, D. (2023). Molecular Markers and Their Applications in Marker-Assisted Selection (MAS) in Bread Wheat (Triticum aestivum L.). Agriculture, 13(3), 642.
  • Srinivasan K (2018) Cumin (Cuminum cyminum) and black cumin (Nigella sativa) seeds: traditional uses, chemical constituents, and nutraceutical effects. Food Qual Saf 2(1):1–16
  • Türkoğlu, A., Haliloğlu, K., Demirel, F., Aydin, M., Çiçek, S., Yiğider, E., ... & Niedbała, G. (2023). Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat (Triticum aestivum L.): Callus Induction, Plant Regeneration, and DNA Methylation. Plants, 12(24), 4151.
  • Venkatesan, J., Ramu, V., Sethuraman, T., Sivagnanam, C., & Doss, G. (2021). Molecular marker for characterization of traditional and hybrid derivatives of Eleusine coracana (L.) using ISSR marker. Journal of Genetic Engineering and Biotechnology, 19, 1-12.
  • Yanez, J. M., Barria, A., Lopez, M. E., Moen, T., Garcia, B. F., Yoshida, G. M., & Xu, P. (2023). Genome‐wide association and genomic selection in aquaculture. Reviews in Aquaculture, 15(2), 645-675.
  • Xu, T., Yao, Z., Liu, J., Zhang, H., Din, G. M. U., Zhao, S., ... & Gao, L. (2020). Development of droplet digital PCR for the detection of Tilletia laevis, which causes common bunt of wheat, based on the SCAR marker derived from ISSR and real-time PCR. Scientific Reports, 10(1), 16106.
There are 30 citations in total.

Details

Primary Language English
Subjects Plant Biotechnology
Journal Section Research Articles
Authors

Adnan Aydın 0000-0002-8284-3751

Project Number ZİF1223A09
Early Pub Date June 7, 2024
Publication Date June 27, 2024
Submission Date February 9, 2024
Acceptance Date May 4, 2024
Published in Issue Year 2024 Volume: 8 Issue: 2

Cite

APA Aydın, A. (2024). Determining the genetic diversity of some black cumin genotypes collected in different regions of Türkiye using RAPD markers. International Journal of Agriculture Environment and Food Sciences, 8(2), 294-300. https://doi.org/10.31015/jaefs.2024.2.6


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