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:: Volume 9, Issue 1 (2022) ::
pgr 2022, 9(1): 117-134 Back to browse issues page
Investigating Genetic Diversity and Relationships in some Henbane (Hyoscyamus spp.) Populations Based on Polymorphisms Resulting from Retrotransposon Insertion
Alireza Asghari Mirak * , Seyed Siamak Alaviakia , Seyed Abolghasem Mohammadi
Department of Agriculture, Payame Noor University, Meshginshahr, Meshginshahr, Iran , alirezapnugen@pnu.ac.ir
Abstract:   (3267 Views)
Henbane has a high medicinal value due to the presence of hyoscyamine and scopolamine alkaloids. Improving the quality and quantity of henbane alkaloids using modern breeding methods requires evaluating the genetic diversity. The genetic diversity of henbane has been investigated using morphological, biochemical and molecular markers in several studies and the superiority of molecular markers over other markers has been proven. To this end, in 2018, the genetic diversity of 96 henbane genotypes collected from the habitats of northwest Iran was investigated using IRAP and REMAP molecular markers. For IRAP markers, out of 36 possible combinations obtained from eight LTR primers, seven combinations had a fine and scalable amplification. In the REMAP technique, the combination of 11 ISSR primers with eight LTR primers was used, and 12 combinations could be scored out of 88 possible combinations. The average amount of polymorphic information for IRAP and REMAP markers was 0.30 and 0.32, respectively, and the average marker index for these two markers was estimated as 2.59 and 2.47. Based on these criteria, REMAP marker was more efficient than IRAP in estimating the genetic diversity of henbane. In the analysis of molecular variance using IRAP and REMAP markers, intra-population variability was estimated to be higher than inter-population, which indicates the high diversity of these populations in northwestern Iran. Cluster analysis based on IRAP marker failed to separate species and populations, but REMAP marker was able to separate H. pusillus and H. reticulatus species to a high degree. A high shannon index in this research suggests that IRAP and REMAP retrotransposon markers resulted in a high genetic diversity within henbane populations with a high insertion in the genome of henbane populations.
Keywords: Henbane, Genetic diversity, IRAP and REMAP markers
Full-Text [PDF 972 kb]   (1004 Downloads)    
Type of Study: Research | Subject: Plant genetics
References
1. Afanasenko, O., Rozanova, I., Gofman, A., Lashina, N., Novakazi, F., Mironenko, N. and Zubkovich, A. (2022). Validation of molecular markers of barley net blotch resistance loci on chromosome 3h for marker-assisted selection. Agriculture, 12(4): 439.‌ [DOI:10.3390/agriculture12040439]
2. Alavikia, S., Mohammadi, S.A., Aharizad, S. and Moghaddam, M. (2008) Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using inter-retrotransposon amplified polymorphic. Biotecnology and Biotecnology Equipment, 22: 795-800. [DOI:10.1080/13102818.2008.10817555]
3. Baloch, F.S., Guizado, S.J.V., Altaf, M.T., Yuce, I., Çilesiz, Y., Bedir, M. and Gomez, J.C.C. (2022). Applicability of inter-primer binding site iPBS-retrotransposon marker system for the assessment of genetic diversity and population structure of Peruvian rosewood (Aniba rosaeodora Ducke) germplasm. Molecular Biology Reports, 49(4): 2553-2564.‌ [DOI:10.1007/s11033-021-07056-8]
4. Carracedo, M.G., Alonso, S.B., Cabrera, R.S.B., Jiménez-Arias, D. and Perez, J.A. (2022). Development of retrotransposon-based molecular markers for characterization of Persea americana (Avocado) cultivars and horticultural races. Agronomy, 12(7): 1510.‌ [DOI:10.3390/agronomy12071510]
5. Cayır, M.E. and Sevindik, E. (2022). Determining the genetic difference of some world cotton genotypes using iPbs (Inter-Primer Binding Sequences) retrotransposon markers. Journal of Natural Fibers, 19(17): 15213-15224.‌ [DOI:10.1080/15440478.2022.2120148]
6. Chadha, S. and Gopalakaishna, T. (2007). Comparative assessment of REMP and ISSR marker assays for genetic polymorphism studies in Magnaporthe grisea. Current Science, 93: 688-692.
7. Chen, H., Guo, A., Wang, J., Gao, J., Zhang, S., Zheng, J. and Yi, K. (2020). Evaluation of genetic diversity within asparagus germplasm based on morphological traits and ISSR markers. Physiology and Molecular Biology of Plants, 26(2): 305-315.‌ [DOI:10.1007/s12298-019-00738-5]
8. Demirel, U., Tindas, I., Yavuz, C., Baloch, F.S. and Çaliskan, M.E. (2018). Assessing genetic diversity of potato genotypes using inter-PBS retrotransposon marker system. Plant Genetic Resources, 16(2): 137-145. [DOI:10.1017/S1479262117000041]
9. Excoffier, L., Smous, P.E. and Quattro, J.M. (1992). Analysis of molecular variance inferred from metric distance among DNA restriction data. Genetics, 131: 479-491. [DOI:10.1093/genetics/131.2.479]
10. Fazli, P. and HaghMyrza, K. (2011). Study of genetic diversity in native chickpea mass with markers ISSR. Modern Genetics, 6: 104-97.
11. Gorji, A.M., Poczai, P., Polgar, Z. and Taller, J. (2011). Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. American Journal of Potato Research, 88(3): 226-237.‌ [DOI:10.1007/s12230-011-9187-2]
12. Grandbastien, M.A., Spielmann, A. and Caboche, M. (1989). Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature, 337: 376-380. [DOI:10.1038/337376a0]
13. Hassani Tsieh, S.F., Samizadeh Lahiji, H., Shoaei Deilami, M. (2014). Investigation of genetic diversity between and within tobacco types using ISSR markers, New Genetics, 9(1): 1-12 (In Persian).
14. Hosseini, S., Rahgozar, M.R. and Badakhshan, H. (2021). Investigating the genetic diversity of Allium L. species based on ISSR markers in Kurdistan province. Plant Genetic Researches, 8(2): 57-68 (In Persian). [DOI:10.52547/pgr.8.2.5]
15. Huff, D.R., Peakal, R. and Smouse, P.E. (1993). RAPD variation within and among natural populations of outcrossing buffalograss Buchloe dactyloides Engelm. Theoretical and Applied Genetics, 86: 927-934. [DOI:10.1007/BF00211043]
16. Kalendar, R. and Schulman, A. (2006). IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 1: 2478-2484. [DOI:10.1038/nprot.2006.377]
17. Kharestani, H., Nejad Ghomi, N.A.A. and Mehrabi, A.A. (2013). Investigation of genetic diversity of incorn wheat using microsatellite markers, Electronic Journal of Crop Production, 2: 1-16 (In Persian).
18. Khosru Mehr, F., Jafari, A. and Hamdi, M. (2012). A comparative anatomy of the stems of two Henbane species in Khorasan Razavi, The First National Conference on Biological Sciences, Islamic Azad University, Falavarjan Branch, Falavarjan, Iran (In Persian).
19. Lightbourn, G.J., Jelesko, J.G. and Veilleux, R.E. (2007). Retrotransposon-based markers from potato monoploids used in somatic hybridization. Genome, 50: 492-501. [DOI:10.1139/G07-026]
20. Mahfouze, S.A. and Ottai, M. (2011). Assessment of genetic variability for some Hyoscymus species using biochemical and molecular markers. Journal of Applied Sciences Research, 7: 1752-1759.
21. Manetti, M.E., Rossi, M., Costa, A.P., Clausen, A.M. and Van Sluys, M.A. (2007). Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera. BMC Evolutionary Biology, 7: 34. [DOI:10.1186/1471-2148-7-34]
22. Mirzadeh Waqfi, S. (2013). Comparison of seed morphology of several species of Hyoscyamus. Journal of Plant Research (Iranian Biology), 26(4): 537-545 (In Persian).
23. Moghaddam, M., Ehdaie, B. and Waines, G. (2000). Genetic diversity in populations of wild diploid wheat (Triticum urartu Thum ex. Gandil.) revealed by Isozymes markers. Genetic Resources and Crop Evolution, 47: 323-332. [DOI:10.1023/A:1008782532505]
24. Mohsenzadeh Golfzaei, M., Samizadeh Lahiji, H., Alami, A., Shoaei Deilami, M. and Talesh Sasani, S. (2012). Investigation of genetic diversity of different greenhouse tobacco genotypes using ISSR and retrotransposon markers. Iranian Journal of Crop Science, 43(2): 371-380 (In Persian).
25. Kaab Omeer, A., Pourmohammadi, P., Gilani, A., Alami, S.K., Farkhari, M. (2021). Investigation of genetic diversity and classification of aerobic and local rice cultivars of Khuzestan province. Plant Genetic Researches, 8(2): 103-116 (In Persian). [DOI:10.52547/pgr.8.2.8]
26. Kouhsari, S.M., Sharifi, G., Ebrahimzadeh, H. and Khatamsaz, M. (2006). Comparative study of six isoenzyme systems in some species of Hyoscyamus L., from Iran. Pakistan Journal of Botany, 38: 107-119.
27. Nejad Habib Vash, F., Rahman, F., Heidari, R. and Jamei, R. (2012). Investigation of genetic diversity of henbane genotypes using ISSR molecular markers. 12th Iranian Genetic Congress, Tehran, Iran (In Persian).
28. Niu, Y.X. and Zhao, F.K. (2010). Clustering Analysis and identification of genetic diversities in eggplant (Solanum melongena L.) varieties with REMAP. 4th International Conference on Bioinformatics and Biomedical Engineering, Bali, Indonesia. [DOI:10.1109/ICBBE.2010.5516571]
29. Peakall, R.O.D. and Smouse, P.E. (2006). GenAlex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6: 288-295. [DOI:10.1111/j.1471-8286.2005.01155.x]
30. Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S. and Rafalski, A. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding, 2: 225-238. [DOI:10.1007/BF00564200]
31. Prasad, P., Srivastava, A., Singh, V., Kushwaha, H. K., Kishor, R., Aftab, N. and Kumar, B. (2022). Genetic diversity analysis of Prishniparni, Uraria picta Desv: A Dashmoola ingredient, to realize high yielding accessions. The Nucleus, 65(3): 341-350.‌ [DOI:10.1007/s13237-022-00402-6]
32. Probeski, S., Grant Bialey, L. and Baun, B.R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter, 15: 8-15. [DOI:10.1007/BF02772108]
33. Rogers, S.A. and Pauls, K.P. (2000). Ty1-copia-like retrotransposons of tomato (Lycopersicon esculentum Mill.). Genome, 43: 887-894. [DOI:10.1139/g00-056]
34. Saghai-Maroof, M.A., Soliman, K., Jorgensen, R.A. and Allard, R.W. (1984). Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Procceeding of National Academy of Science, 81: 8014-8018. [DOI:10.1073/pnas.81.24.8014]
35. Shajdehahmadi, M. and Kharazi, M. (2015). The use of ISSR molecular markers in the study of genetic diversity of some tobacco genotypes, Plant Genetics Researches, 2(2): 33-46 (In Persian). [DOI:10.29252/pgr.2.2.33]
36. Sokhdari, A., Malekzadeh Shafaroodi, S., Asghari, A. and Kiani Freeze, M. (2013). Analysis of the relationship between some agronomic traits with ISSR markers in 20 potato genotypes. 8th National Conference on Biotechnology of the Islamic Republic of Iran and the 4th National Conference on Biosafety, University of Tehran, Tehran, Iran (In Persian).
37. Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version4.0. Molecular Biology and Evolution, 24: 1596-1599. [DOI:10.1093/molbev/msm092]
38. Yadav, R., Lal, R.K. and Gupta, M.M. (2018). Prediction of morpho-genetic variability at intra-specific level and elite line selection in black henbane (Hyoscyamus niger L.). Acta Scientific Agriculture, 2(9): 94-103.
39. Yousefi, M.J. (2009). Evaluation of genetic diversity of some Iranian black henbane accessions (Hyoscyamus niger) based on RAPD markers and seed proteins fingerprinting. M.Sc. Thesis, Tehran University, Tehran, Iran (In Persian).
40. Zanganeh, F. and Sheidai, M. (2022). Population genetic diversity and genetic affinity analyses of sweet orange cultivars (Citrus sinensis (L.) Osbeck) by using IRAP molecular markers. Genetic Resources and Crop Evolution, 69: 2437-2446. [DOI:10.1007/s10722-022-01382-x]
41. Zhu, J., Gale, M.D., Quarrie, S., Jackson, M.T. and Bryan, G.J. (1998). AFLP markers for the study of rice biodiversity. Theoretical and Applied Genetics, 96: 602-611. [DOI:10.1007/s001220050778]
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Asghari Mirak A, Alaviakia S S, Mohammadi S A. Investigating Genetic Diversity and Relationships in some Henbane (Hyoscyamus spp.) Populations Based on Polymorphisms Resulting from Retrotransposon Insertion. pgr 2022; 9 (1) :117-134
URL: http://pgr.lu.ac.ir/article-1-248-en.html


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