Czech J. Genet. Plant Breed., 2023, 59(3):148-159 | DOI: 10.17221/112/2022-CJGPB

Assessment of genetic variation and population structure in Iraqi barley accessions using ISSR, CDDP, and SCoT markersOriginal Paper

Nawroz Tahir1, Djshwar Lateef2*, Kamaran Rasul1, Didar Rahim2, Kamil Mustafa2, Shokhan Sleman2, Avin Mirza3, Rebwar Aziz1
1 Horticulture Department, College of Agricultural Engineering Sciences, University of Sulaimani, Sulaimani, Iraq
2 Biotechnology and Crop Sciences Department, College of Agricultural Engineering Sciences, University of Sulaimani, Sulaimani, Iraq
3 General Directorate of Agriculture in Sulaimani, Ministry of Agricultural and Water Resources, Sulaimani, Iraq

The objective of this study was to investigate the diversity of 59 accessions of barley using inter simple sequence repeat (ISSR), conserved DNA-derived polymorphism (CDDP), and start codon targeted (SCoT) markers. A total of 391 amplified polymorphic bands were generated using 44 ISSR, 9 CDDP, and 12 SCoT primers that produced 255, 35, and 101 polymorphic bands, respectively. The average values of gene diversity were 0.77, 0.67, and 0.81 for ISSR, CDDP, and SCoT markers, respectively. The mean values of polymorphism information content for ISSR, CDDP and SCoT markers were 0.74, 0.63, and 0.80 respectively. The discrimination power of the three approaches for assessing allelic diversity in barley accessions ranked as follows: SCoT > ISSR > CDDP. The barley accessions were classified and clustered into two main groups. Molecular variance analysis revealed 15, 9, and 14% variability among populations with ISSR, CDDP, and SCoT markers, respectively. The Mantel test results revealed that the three molecular marker matrices had significant positive relationships. The SCoT markers might be useful tools for selecting appropriate parents for a breeding program.

Keywords: clustering; diversity; genetic differentiation; Hordeum vulgare; molecular markers

Received: December 15, 2022; Accepted: January 25, 2023; Prepublished online: April 14, 2023; Published: June 12, 2023  Show citation

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Tahir N, Lateef D, Rasul K, Rahim D, Mustafa K, Sleman S, et al.. Assessment of genetic variation and population structure in Iraqi barley accessions using ISSR, CDDP, and SCoT markers. Czech J. Genet. Plant Breed. 2023;59(3):148-159. doi: 10.17221/112/2022-CJGPB.
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    References

    1. Adhikari S., Saha S., Biswas A., Rana T.S., Bandyopadhyay T.K., Ghosh P. (2017): Application of molecular markers in plant genome analysis: A review. Nucleus, 60: 283-297. Go to original source...
    2. Agarwal M., Shrivastava N., Padh H. (2008): Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27: 617-631. Go to original source... Go to PubMed...
    3. Ahmed D.A., Razzak Tahir N.A., Salih S.H., Talebi R. (2021): Genome diversity and population structure analysis of Iranian landrace and improved barley (Hordeum vulgare L.) genotypes using arbitrary functional gene-based molecular markers. Genetic Resources and Crop Evolution, 68: 1045-1060. Go to original source...
    4. Ahmed A.A., Qadir S.A., Tahir N.A.R. (2022): Genetic variation and structure analysis of Iraqi Valonia oak (Quercus aegilops L.) populations using conserved DNA-derived polymorphism and inter-simple sequence repeats markers. Plant Molecular Biology Reporter, 41: 1-14. Go to original source...
    5. Al-Hadeithi Z.S.M. (2015): Using ISSR markers to build a phylogenetic of barley genotypes. Iraqi Journal of Agricultural Sciences, 56: 1682-1688.
    6. Al-Hadeithi Z.S.M. (2016): Detection of genetic polymorphism in Iraqi barley using SSR-PCR analysis. Iraqi Journal of Agricultural Sciences, 57: 1158-1164.
    7. Amom T., Nongdam P. (2017): The use of molecular marker methods in plants: A review. Journal of Current Research and Review, 9: 1-7.
    8. Aziz R.R., Tahir N.A.R. (2022): Genetic diversity and structure analysis of melon (Cucumis melon L.) genotypes using URP, SRAP, and CDDP markers. Genetic Resources and Crop Evolution, 70: 799-813. Go to original source...
    9. Baum M., Grando S., Ceccarelli S., Backes G., Jahoor A. (2015): Localization of quantitative trait loci for dryland characters in barley by linkage mapping. Challenges and Strategies of Dryl and Agriculture, 32: 191-202. Go to original source...
    10. Brantestam A.K., Von Bothmer R., Dayteg C., Rashal I., Tuvesson S., Weibull J. (2007): Genetic diversity changes and relationships in spring barley (Hordeum vulgare L.) germplasm of Nordic and Baltic areas as shown by SSR markers. Genetic Resources and Crop Evolution, 54: 749-758. Go to original source...
    11. Cai K., Chen X., Han Z., Wu X., Zhang S., Li Q., Nazir M.M., Zhang G., Zeng F. (2020): Screening of worldwide barley collection for drought tolerance: The assessment of various physiological measures as the selection criteria. Frontiers in Plant Science, 11: 1159. Go to original source... Go to PubMed...
    12. Collard B.C.Y., Mackill D.J. (2009): Conserved DNA-derived polymorphism (CDDP): A simple and novel method for generating DNA markers in plants. Plant Molecular Biology Reports, 27: 558-562. Go to original source...
    13. Cullingham C.I., Miller J.M., Peery R.M., Dupuis J.R., Malenfant R.M., Gorrell J.C., Janes J.K. (2020): Confidently identifying the correct K value using the ΔK method: When does K = 2? Molecular Ecology, 29: 862-869. Go to original source... Go to PubMed...
    14. Etminan A., Pour-Aboughadareh A., Mohammadi R., Ahmadi-Rad A., Noori A., Mahdavian Z., Moradi Z. (2016): Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnology and Biotechnological. Equipment, 30: 1075-1081. Go to original source...
    15. Evanno G., Regnaut S., Goudet (2005): Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14: 2611-2620. Go to original source... Go to PubMed...
    16. Gholamian F., Etminan A., Changizi M., Khaghani S., Gomarian M. (2019): Assessment of genetic diversity in Triticum urartu Thumanjan ex Gandilyan accessions using start codon targeted polymorphism (SCoT) and CAAT-box derived polymorphism (CBDP) markers. Biotechnology & Biotechnological Equipment, 33: 1653-1662. Go to original source...
    17. Govindaraj M., Vetriventhan M., Srinivasan M. (2015): Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015: 431-487. Go to original source... Go to PubMed...
    18. Hagenblad J., Leino M.W., Afonso G.H. (2019): Morphological and genetic characterization of barley (Hordeum vulgare L.) landraces in the Canary Islands. Genetic Resources and Crop Evolution, 66: 465-480. Go to original source...
    19. Hernandez J., Meints B., Hayes P. (2020): Introgression breeding in barley: Perspectives and case studies. Frontiers in Plant Science, 11: 761. Go to original source... Go to PubMed...
    20. Igwe D.O., Ihearahu O.C., Osano A.A., Acquaah G., Ude G.N. (2021): Genetic diversity and population assessment of Musa L.(Musaceae) employing CDDP markers. Plant Molecular Biology Reporter, 39: 801-820. Go to original source...
    21. Khodaee L., Azizinezhad R., Etminan A.R., Khosroshahi M. (2021): Assessment of genetic diversity among Iranian Aegilops triuncialis accessions using ISSR, SCoT, and CBDP markers. Journal of Genetic Engineering and Biotechnology, 19: 1-9. Go to original source... Go to PubMed...
    22. Lateef D.D. (2015): DNA marker technologies in plants and applications for crop improvements. Journal of Biosciences and Medicines, 3: 7-18. Go to original source...
    23. Liu H., Zang F., Wu Q., Ma Y., Zheng Y., Zang D. (2020): Genetic diversity and population structure of the endangered plant Salix taishanensis based on CDDP markers. Global Ecology and Conservation, 24: e01242. Go to original source...
    24. Mzid R., Chibani F., Ayed R.B., Hanana M., Breidi J., Kabalan R., El-Hajj S., Machlab H., Rebai A., Chalak L. (2016): Genetic diversity in barley landraces (Hordeum vulgare L. subsp. vulgare) originated from crescent fertile region as detected by seed storage proteins. Journal of Genetics, 95: 733-739. Go to original source... Go to PubMed...
    25. Naceur A.B., Chaabane R., El-Faleh M., Abdelly C., Ramla D., Nada A., Sakr M. (2012): Genetic diversity analysis of North Africa's barley using SSR markers. Journal of Genetic Engineering and Biotechnology, 10: 13-21. Go to original source...
    26. Nair S.K., Wang N., Turuspekov Y., Pourkheirandish M., Sinsuwongwat S., Chen G., Sameri M., Tagiri A., Honda I., Watanabe Y. (2010): Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proceedings of the National Academy Sciences, 107: 490-495. Go to original source... Go to PubMed...
    27. Pour-Aboughadareh A., Ahmadi J., Mehrabi A.A., Etminan A., Moghaddam M. (2018): Insight into the genetic variability analysis and relationships among some Aegilops and Triticum species, as genome progenitors of bread wheat, using SCoT markers. Plant Biosystems, 152: 694-703. Go to original source...
    28. Pritchard J.K., Stephens M., Donnelly P. (2000): Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. Go to original source... Go to PubMed...
    29. Rasul K.S., Grundler F.M., Abdul-Razzak Tahir N. (2022): Genetic diversity and population structure assessment of Iraqi tomato accessions using fruit characteristics and molecular markers. Horticulture Environment and Biotechnology, 63: 523-538. Go to original source...
    30. Saidi A., Jabalameli Z., Ghalamboran M. (2018): Evaluation of genetic diversity of carnation cultivars using CDDP and DAMD markers and morphological traits. Nucleus, 61: 129-135. Go to original source...
    31. Serrote C.M.L., Reiniger L.R.S., Silva K.B., Rabaiolli S.M.D.S., Stefanel C.M. (2020): Determining the polymorphism information content of a molecular marker. Gene, 726: 144175. Go to original source... Go to PubMed...
    32. Skroch P.W., Nienhuis J. (1995): Qualitative and quantitative characterization of RAPD variation among snap bean (Phaseolus vulgaris) genotypes. Theoretical and Applied Genetics, 91: 1078-1085. Go to original source... Go to PubMed...
    33. Tahir N.A.-R. (2014): Comparison of RAPD-PCR and SDS-page techniques to evaluate genetic variation among nine barley varieties (Hordeum spp). Malaysian Applied Biology, 43: 107-117.
    34. Tahir N.A.-R. (2015): Identification of genetic variation in some faba bean (Vicia faba L.) genotypes grown in Iraq estimated with RAPD and SDS-PAGE of seed proteins. Indian Journal of Biotechnology, 14: 351-356.
    35. Tahir N.A.-R., Omer D.A. (2017): Genetic variation in lentil genotypes by morpho-agronomic traits and RAPD-PCR. The Journal of Animal and Plant Sciences, 27: 468-480.
    36. Tahir N.A.-R., Ahmad N.S., Mustafa K.M., Kareem D.D.L. (2021): Diversity maintenance of some barley (Hordeum spp) genetic resources using SSR-based marker. The Journal of Animal and Plant Sciences, 31: 221-234. Go to original source...
    37. Talebi R., Nosrati S., Etminan A., Naji A.M. (2018): Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers. Biotechnology and Biotechnological Equipments, 32: 1183-1194. Go to original source...
    38. Tiwari G., Singh R., Singh N., Choudhury D.R., Paliwal R., Kumar A., Gupta V. (2016): Study of arbitrarily amplified (RAPD and ISSR) and gene targeted (SCoT and CBDP) markers for genetic diversity and population structure in Kalmegh [Andrographis paniculata (Burm. f.) Nees]. Industrial Crops Products, 86: 1-11. Go to original source...
    39. Vieira E.A., Carvalho F.I.F., Bertan I., Kopp M.M., Zimmer P.D., Benin G., Silva J.A.G., Hartwig I., Malone G., Oliveira A.C. (2007): Association between genetic distances in wheat (Triticum aestivum L.) as estimated by AFLP and morphological markers. Genetics and Molecular Biology, 30: 392-399. Go to original source...
    40. Vinceti B., Loo J., Gaisberger H., van Zonneveld M.J., Schueler S., Konrad H., Kadu C.A.C., Geburek T. (2013): Conservation priorities for Prunus africana defined with the aid of spatial analysis of genetic data and climatic variables. PLoS ONE, 8: 59987. Go to original source... Go to PubMed...
    41. Wang A., Yu Z., Ding Y. (2009): Genetic diversity analysis of wild close relatives of barley from Tibet and the Middle East by ISSR and SSR markers. Comptes Rendus Biologies, 332: 393-403. Go to original source... Go to PubMed...
    42. Xie Z., Zhang Z.L., Zou X., Huang J., Ruas P., Thompson D., Shen Q.J. (2005): Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiology, 137: 176-189. Go to original source... Go to PubMed...
    43. Yongcui H., Zehong Y., Xiujin L. (2005): Genetic diversity among barley germplasm with known origins based on the RAMP and ISSR markers. Scientia Agricultura Sinica, 38: 2555-2565.

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