Evaluation of molecular diversity and population structure analysis in some local black caraway (Nigella sativa L.) ecotypes using ISSR marker

Document Type : Research Paper

Authors

1 Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran

2 Assistant professor, Horticulture Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

3 Associate professor, Horticulture Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.

4 Researcher, Department of Genetics and National Plant Gene Bank of Iran, SPII., AREEO, Karaj, Iran

5 Graduated of M.Sc., Horticulture Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.

6 Seed and plant improvement institute, Agricultural research, education and extension (AREEO), Karaj, Iran

Abstract

Objective
Black cumin (Nigella sativa L.), a plant belonging to the Ranunculaceae family with a 3000-year history, has wide applications in the pharmaceutical industry. Despite the increasing global trend in the use of medicinal and aromatic plants in various pharmaceutical, health, and therapeutic industries, and despite numerous studies on the agronomy of medicinal plants, a significant gap is felt in breeding evaluations aimed at achieving high-yielding cultivars suitable for cultivation under different conditions in the country.
Materials and methods
In this study, the genetic diversity of 20 black cumin ecotypes collected from different regions of Iran was investigated using the ISSR molecular marker. Genomic DNA was extracted from young, fresh leaves using the CTAB protocol based on the modified method of Lodhi et al. (1994). The obtained data were analyzed to calculate various indices such as Polymorphic Information Content (PIC), Resolving Power (Rp), and Marker Index (MI). Grouping was performed using cluster analysis (based on Jaccard's dissimilarity matrix and the Neighbor-joining method) and Principal Coordinate Analysis (PCoA) with the Darwin software. The population structure of the molecular data was also investigated using the STRUCTURE software.
Results
Out of the 10 primers used, nine produced scorable bands. The primers collectively amplified 77 bands, of which 55 were polymorphic. The average number of bands produced per primer was 6.56. Primer 3 had the highest PIC value (0.408), and primer 4 had the lowest (0.217). Based on the calculated values of PIC, MI, and Rp indices, the ISSR-1 primer was identified as the most suitable primer for assessing the genetic diversity of black cumin in this study. The observed genetic similarity based on these markers ranged from 0.123 to 0.485, indicating high genetic diversity among the studied ecotypes. Cluster analysis separated the studied ecotypes into three distinct groups; however, population structure analysis identified eight different population groups.
Conclusions
Overall, the results of this research indicate the existence of high and potential genetic diversity among the studied black cumin ecotypes. Given that native ecotypes are highly adapted to their environment, this collection can be introduced as a valuable genetic resource for future black cumin breeding programs.

Keywords

References

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Agricultural Biotechnology Journal
Volume 18, Issue 4
August 2026
Pages 1-22

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