Investigation of molecular diversity of some coriander (Coriandrum sativum L.) populations using RAPD and SCoT markers

Document Type : Research Paper

Authors

1 Associate Professor, Department of Plant Production and Genetics, Faculty of Agriculture, University of Birjand, Birjand, Iran.

2 Former M.Sc. Student of Genetic and Plant Breeding, Department of Plant Production and Genetics, Faculty of Agriculture, University of Birjand, Birjand, Iran.

3 Department of Plant Production and Genetics, Faculty of Agriculture, University of Birjand, Birjand, Iran.

Abstract

Objective
Coriandrum sativum is a medicinal plant cultivated in various regions of Iran and worldwide for a long time. With a genomic formula of 2n=2x=22, coriander is a diploid plant, and Iran is the fourth largest producer of this crop in the world. This study aimed to investigate genetic diversity, assess similarities and differences of different coriander populations using RAPD and SCoT markers.
Materials and methods
Sixteen coriander populations were collected from various counties in three provinces: South Khorasan, Yazd, and Kerman. Twelve RAPD primers and 20 SCoT primers were used for molecular diversity analysis. Data analysis was performed using the software packages NTSYSpc2.2, SPSS v26, and Excel 2020.
Results
Of the 12 RAPD primers, 10 showed polymorphism, while 15 of the 20 SCoT primers displayed polymorphisms. In total, RAPD and SCoT primers produced 40 and 86 high-resolution bands, respectively. The polymorphism percentage was 100% for the RAPD and 97.67% for the SCoT markers. The RD6, RD8 (RAPD) and SC11, SC13 (SCoT) primers produced the highest number of bands (5 and 9 bands). The average values for the PIC, MI, EMR, and RP indices were 0.43, 1.69, 4, and 2.81, and 0.38, 2.09, 5.49, and 3.38 for RAPD and SCoT markers, respectively. The highest genetic similarity was found between Kerman-Zarand, Yazd-Bahabad, Sirjan-Baft, Kerman-Baft, and Birjand-Khusf populations. The lowest genetic similarity was observed between Sarbishe-Bahabad, Bahabad-Bam, Birjand-Bahabad, Birjand-Yazd, and Bahabad-Zarand populations. Cluster analysis on RAPD and SCOT data grouped the populations into three clusters.  Principal Coordinate Analysis (PCoA) according to RAPD and SCoT data explained 50.82% and 52.97% of the total variance, respectively.
Conclusions
The markers used in this study effectively distinguished the coriander populations from each other. The high polymorphism rate of the RAPD and SCoT markers demonstrated their efficiency for genetic diversity analysis in coriander populations. Both markers showed similar efficiency, but the SCoT marker slightly outperformed RAPD in distinguishing populations. The low percentage of variation explained by the components indicated that the primers had appropriate distribution across the genome and therefore were well chosen. The results revealed that genetic similarity was relatively high within populations of each province, while lower similarity was observed between populations from different provinces. To maximize diversity and heterosis, crossing populations such as Sarbishe × Bahabad, Bahabad × Bam, Birjand × Bahabad, Birjand × Yazd, and Bahabad × Zarand are recommended.

Keywords

References

Aghaei, M., Darvishzadeh, R., & Hassani, A. (2012). Molecular characterization and similarity relationships among Iranian basil accessions using inter simple sequence repeat markers. Revista Ciência Agronômica, 43(2), 312-320. https://doi.org/10.1590/S1806-66902012000200014.
Agrama, H., & Tuinstra, M. (2003). Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs. African Journal of Biotechnology, 2, 334-340. https://doi.org/10.5897/AJB2003.000-1069.  
Akhtar, W., Qayyum, S., Ashraf, N., Qammar, K., Kiyani, W. K., Nazish, N., Kamal, A., Albasher, G., & Zaman, W. (2025). Molecular characterization of coriander (Coriandrum sativum L.) genotypes using inter simple sequence repeat (ISSR) and sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) markers. Genetic Resources and Crop Evolution, 72 (6): 7563-7576. https://doi.org/10.1007/s10722-025-02379-y.
Baruah, J., Gogoi, B., Das, K., Ahmed, N., Sarmah, D., Lal, M., & Bhau, B. (2017). Genetic diversity study amongst Cymbopogon species from NE-India using RAPD and ISSR markers. Industrial Crops and Products, 95, 235-243. https://doi.org/10.1016/j.indcrop.2016.10.022.
Basol, A., Yaldiz, G., & Camlica, M. (2024). Genetic diversity, analysis of some agro-morphological and quality traits, and utilization of plant resources of coriander (Coriandrum sativum L.) supported with cluster and multivariate analyses. Biology, 13, 866. https://doi.org/10.3390/biology13110866.
Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32, 314-322. PMCID: PMC1686077. PMID: 6247908.
Choudhary, S., Naika, M. B. N., & Meena., R. D. (2021). Development and characterization of genic SSR-FDM for stem gall disease resistance in coriander and its cross species transferability. Molecular Biology Reports, 48 (11):1-8. https://doi.org/10.1007/s11033-021-06396-9.
Choudhary, S., Sharma, R., Jethra, G., Vishal, M. K., & Tripathi, A. (2019). Molecular diversity in coriander (Coriandrum sativum) using RAPD and ISSR markers. Indian Journal of Agricultural Sciences, 89 (2), 193-198. https://doi.org/10.56093/ijas.v89i2.86983.
Choudhary, V., Verma, P., Sharma, S. C., Yadav, D L., & Narolia, R. S. (2022). Genetic divergence studies in coriander (Coriandrum sativum L.) genotypes. Journal of Pharmaceutical Innovation, 11 (12), 141-143.  https://HTTPS://DOI.org/10.55730/1300-011X.3227
Collard, B. C., & Mackill, D. J. (2009). Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter, 27 (1), 86-93. https://doi.org/10.1007/s11105-008-0060-5.
Coşkuner, Y., & Karababa, E. (2007). Physical properties of coriander seeds (Coriandrum sativum L.). Journal of Food Engineering, 80 (2), 408-416.  https://doi.org/10.1016/j.jfoodeng.2006.02.042.
Diederichsen, A., Heller, J., & Engels, J. (1996). Coriander. Coriandrum sativum L. Promoting the conservation and use of underutilized and neglected crops. 3. IPGRI Publication. 83 p.
Etesami, M, J., Naji, A, M., & Rezazadeh, A, R. (2020). Study of genetic diversity of coriander indigenous populations using SCoT molecular marker. The 7th National Congress of Biology and Natural Sciences of Iran, Tehran. (In Persian).
Ghasemi, M., Baghizadeh, A., & Mohammadabadi, M. R. (2010). Determination of genetic polymorphism in Kerman Holstein and Jersey Cattle population using ISSR markers. Australian Journal of Basic and Applied Sciences, 4 (12), 5758–5760. https://www.ajbasweb.com/old/ajbas/2010/5758-5760.pdf.
Hua, H. Q., Zhao, Z. Y., Zhang, Y., Hu, J., Zhangfan, Z. Z., & Xili, Y. (2018). Inter- and intra-specific differentiation of Trichogramma (Hymenoptera: Trichogrammatidae) species using PCR-RFLP targeting COI. Journal of Economic Entomology, 111(1). https://doi.org/10.1093/jee/toy119.
Jesus, O., Ferreira, C., Silva, S., Camara, T., Soares, T., & Pestana, K. (2009). Characterization of recommended banana cultivars using morphological and molecular descriptors. Crop Breeding and Applied Biotechnology, 9, 164-173. https://doi.org/10.1590/S1984-70332009000200003.
Jiang, G. L. (2013). Molecular markers and marker-assisted breeding in plants. In: Sven B. Andersen (ed.), Plant Breeding from Laboratories to Fields, In Tech, Croatia. 45-83.
Kalendar, R., Tselykh, T. V., Khassenov, B., & Ramanculov, E. M. (2017). Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis. Methods in Molecular Biology, 1620: 33-64. https://doi.org/10.1007/978-1-4939-7060-5_2.   
Kayis, S. A., Hakki, E. E., & Pinarkara, E.  (2010). Comparison of effectiveness of ISSR and RAPDmarkers in genetic characterization of seized marijuana in Turkey. African Journal of Agricultural Research, 5(21): 2925-2933. https://aperta.ulakbim.gov.tr/record/28211 adresinden erişildi.
Kebriyaee, D., Kordrostami, M., Rezadoost, M H., & Lahiji, H. S. (2012). QTL analysis of agronomic traits in rice using SSR and AFLP markers. Notulae Scientia Biologicae, 4 (2), 116-123. https://doi.org/10.15835/nsb427501.
Khosravi, H., Yaghoubi, F., & Mehrabi, M. (2021). Coriander, golden seed of Nahavand. The First National Conference on the Applications of Advanced Chemical and Agricultural Research for Development of Medicinal Plants (Focusing on the Coriandrum Sativum L.), Nahavand, Hamadan. Iran. https://civilica.com/doc/1377924. (In Persian).
Lewontin, R. C. (1972). The Apportionment of Human Diversity. Evolutionary Biology, 6: 381–398. https://doi.org/10.1007/978-1-4684-9063-3_14.
López, P., Widrlechner, M., Simon, P., Rai, S., Bailey, T., & Gardner, C. (2009). Applying molecular markers in coriander populations with diverse geographical origins. Paper presented at the Proceedings of the XIII National Congress of Mexican Society of Horticultural Sciences, Torreon, Coahuila, Mexico.
Milbourne, D., Meyer, R., Bradshaw, J. E., Baird, E., Bonar, N., Provan, J., Powell, W., & Waugh, R. (1997). Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato. Journal of Plant Molecular Breeding, 3, 127–136. https://doi.org/10.1023/A:1009633005390.
Mohammadabadi, M. R (2016). Inter-simple sequence repeat loci associations with predicted breeding values of body weight in Kermani sheep. Genetics in the Third Millennium, 14(4), 4386–4393. https://doi.org/472-591-539-924.   
Mohammadabadi, M. R, Oleshko, V., Oleshko, O., Heiko, L., Starostenko, I., Kunovskii, J., Bazaeva, A., & Roudbari, Z. (2021). Using Inter Simple Sequence Repeat Multi-Loci Markers for Studying Genetic Diversity in Guppy Fish. Turkish Journal of Fisheries and Aquatic Sciences, 21, 603-613.  https://doi.org/10.4194/1303-2712-v21 12_03.  
Mohammadi, S. A. (2006). The analysis of molecular data from the point of view of studying genetic diversity. The 9th Iranian Congress of Crop Science and Plant Breeding, 96- 119 (In Persian).
Moradi Behjo, A., Amin Amlashi, H., & Khosravi, H. (2021). Investigating the situation of coriander production and trade in the world and Iran. The First National Conference on the Applications of Advanced Chemical and Agricultural Research for Development of Medicinal Plants (Focusing on the Coriandrum Sativum L.), Nahavand, Hamadan. (In Persian).
Nadi, S., Saba, J., Jafaraghae, M., & Andalibi, B. (2023). Investigating of genetic diversity of some coriander (Coriandrum sativum L.) landraces in Iran for phenological, morphological and agronomic traits. Journal of Crop Breeding, 15 (47): 103-112. https://doi.org/10.61186/jcb.15.47.103. (In Persian).
Narzary, D., Verma, S., Mahar, K. S., & Rana, T. S. (2015). A Rapid and Effective Method for Isolation of Genomic DNA from Small Amount of Silica-Dried Leaf Tissues. National Academy Science Letters, 38(5):441-444. https://doi.org/10.1007/s40009-015-0357-5.
Nezafat, S., Mohebodini, M., Azarmi, R., Ebadi Segherloo, A., & Fathi, R. (2023). Evaluation of genetic diversity of some native populations of Iranian coriander (Coriandrum sativum L.) based on morphological and physiological traits. Plant Products, 45 (4), 449-461. https://doi.org/10.22055/PPD.2023.37678.1984.
Omid Beigi, R. (2022). Production and processing of medicinal plants (Volume I). Beh-Nashr Publications, page 347. (In Persian).
Pullaiah. T., Bahadur, B., & Krishnamurthy, K. (2015). Plant biodiversity. In Plant Biology and Biotechnology: Volume I: Plant Diversity, Organization, Function and Improvement. Springer Publications, pp. 177-195. https://doi.org/10.1007/978-81-322-2286-6_6.
Sankhla, A. K., Malik. C., & Parashar, M. (2015). A review on start codon targeted (SCoT) marker. Plant Science Research, 31(2). https://doi.org/2022.17340.1316IJGPB10.30479.
Sharangi, A. B., Bal, S., Maji, A., Upadhyay, T. K., Binsuwaidan, R., Alshammari, N., Alabdallah, N. M., Kolapkar, A., & Saeed, M. (2024). Coriander (Coriandrum sativum L.) diversity analysis: insights from germplasm resources leading to crop improvement. Turkish Journal of Agriculture, 48 (6), 6. https://doi.org/10.55730/1300-011X.3227.
Sharma, A. (2020). Morphological, biochemical and molecular characterizations in Coriander (Coriandrum sativum L.) genotype. Thesis Submitted to the Maharana Pratap University of Agriculture and Technology, Udaipur in partial fulfillment of the requirements for the Degree of Doctorate of Philosophy in Agriculture (Molecular Biology and Biotechnology). P, 123.
Sowmya, M., Giridhar, K., Priya, B. T., Lakshmi, T. V. & Kalpana, M. (2025). Biochemical, histological and molecular investigations of coriander genotypes against Fusarium wilt. Plant Science Today, 11 (sp3). https://doi.org/10.14719/pst.4211.
Thimmappaiah, W., Santhosh, G., Shobha, D., & Melwyn, G. S. (2009). Assessment of genetic diversity in cashew germplasm using RAPD and ISSR markers. Scientia Horticulturae, 120 (3), 411-417. https://doi.org/10.1016/j.scienta.2008.11.022.
Wei, Y. M., Hou, Y. C., Yan, Z. H., Zhi-Qing Zhang, W. W., Liu, D. C., & Zheng, Y. L. (2005). Microsatellite DNA polymorphism divergence in Chinese wheat landraces highly resistant to Fusarium head blight. Journal of Applied Genetics, 46 (1), 3-9. PMID: 15741658
Wright, S. (1943). Isolation by distance. Genetics, 28 (2),114–138. https://doi.org/10.1093/genetics/28.2.114.
Zabet, M., Akbari, M., & Izanloo, A. (2025). Investigating the Efficiency of ISSR and ScoT Markers in Studying the Genetic Diversity of Some Coriander (Coriandrum sativum L.) Populations. Plant Genetic Researches, 11 (2): 83-98. https://doi.org/10.22034/PGR.11.2.6.
Agricultural Biotechnology Journal
Volume 17, Issue 4
November 2025
Pages 71-98

Files

Share

How to cite

Statistics