Bazı Gernik Buğdayların iPBS Markörleri Kullanılarak Moleküler Karakterizasyonu

Year 2020, Issue: 20, 640 - 646, 31.12.2020

Fatih Demirel

https://doi.org/10.31590/ejosat.814537

Cited By: 2

Abstract

Toplam 21 buğday genotipi (emmer buğdayı olarak adlandırılan 16 Triticum dicoccum ve durum buğdayı olarak adlandırılan 5 Triticum durum) arasındaki genetik çeşitlilik 7 iPBS primeri kullanılarak araştırılmıştır. Mevcut çalışmada kullanılan iPBS'ler, buğday genotipleri için 136 banttan 134’ünü polimorfik olarak üretmiştir. Bu çalışmanın sonucunda genetik çeşitlilik parametrelerinin ortalaması; polimorfizm bilgi içeriği (PIC = 0.19), heterozigotluk (H = 0.23), polimorfizm oranı (P% = 97.92) ve polimorfizm (19.14) belirlenmiştir. Jaccard'ın çeşitlilik değeri, buğday genotipleri için ortalama 0.4677 olarak hesaplanmış ve 0.0222 ile 0.7843 arasında değiştiği saptanmıştır. AMOVA sonucuna göre gernik ve makarnalık buğdaylarındaki genetik çeşitlilik, popülasyon içinde %77 varyasyona sahip olduğu tespit edilmiştir. Öte yandan, popülasyonlar arasındaki genetik varyasyon %23 değeriyle orta düzeydeyde olduğu bulunmuştur. Popülasyonların genetik çeşitliliğini belirlemek için lokus başına ortalama alel sayısı (Na = 1.269), etkili alel sayısı (Ne = 1.31), Shannon bilgi indeksi (I = 0.29), Nei'nin genetik çeşitlilik seviyesi (h = 0.19) gibi parametrelerle hesaplanmıştır. Ayrıca, Nei'nin tarafsız genetik çeşitlilik seviyesi (uh) 0.218 olarak saptanmıştır. Bu çalışmadan elde edilen sonuçlara göre iPBS moleküler markörlerinin buğday genotipleri arasındaki genetik ilişkilerin belirlenmesinde faydalı olabileceğini göstermiştir.

Keywords

Gernik Buğday, Ekmeklik Buğday, Triticum dicoccum, Triticum durum, Genetik İlişki, iPBS

Genetic Diversity of Emmer Wheats Using iPBS Markers

Abstract

The genetic diversity among totally 21 wheat genotypes (16 Triticum dicoccum called emmer wheat and 5 Triticum durum called durum wheat) were investigated using 7 iPBS primers. iPBSs used in the current study generated 134 polymorphic from 136 bands for wheat genotypes. The mean of genetic diversity parameters were calculated such as; polymorphism information content (PIC= 0.19), heterozygosity (H= 0.23), polymorphism ratio (P%= 97.92) and average polymorphism (19.14). Jaccard's diversity index varied between 0.0222 and 0.7843 with a mean 0.4677 for wheat genotypes. According to the sum of AMOVA, genetic diversity in emmer and durum wheats was significantly high with 77% variation within the population. On the other hand, genetic variation among populations was moderate with 23% value. Genetic diversity of populations were calculated by parameters such as the mean number of alleles per locus (Na=1.269), effective allele number (Ne=1.31), Shannon information index (I=0.29), Nei’s genetic diversity level (h=0.19), and Nei’s unbiased genetic diversity level (uh=0.218). Results obtained from this study showed that iPBS molecular markers could be useful in determination of genetic relationships among wheat genotypes.

Keywords

Emmer Wheat, Durum Wheat, Triticum dicoccum, Triticum durum, Genetic Diversity, iPBS

References

• Ali, F., Yılmaz, A., Nadeem, M. A., Habyarimana, E., Subaşı, I., Nawaz, M. A., ... & Chung, G. (2019). Mobile genomic element diversity in world collection of safflower (Carthamus tinctorius L.) panel using iPBS-retrotransposon markers. PloS one, 14(2), e0211985.
• Andeden, E. E., Baloch, F. S., Derya, M., Kilian, B., & Özkan, H. (2013). iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. Journal of Plant Biochemistry and Biotechnology, 22(4), 453-466.
• Arystanbekkyzy, M., Nadeem, M. A., Aktas, H., Yeken, M. Z., Zencirci, N., Nawaz, M. A., ... & Baloch, F. S. (2019). Phylogenetic and taxonomic relationship of turkish wild and cultivated emmer (Triticum turgidum ssp. dicoccoides) revealed by iPBSretrotransposons markers. International Journal of Agriculture and Biology, 21(1), 155-63.
• Baloch, F. S., Alsaleh, A., de Miera, L. E. S., Hatipoğlu, R., Çiftçi, V., Karaköy, T., ... & Özkan, H. (2015). DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochemical Systematics and Ecology, 61, 244-252.
• Boczkowska, M., Nowosielski, J., Nowosielska, D., & Podyma, W. (2014). Assessing genetic diversity in 23 early Polish oat cultivars based on molecular and morphological studies. Genetic Resources and Crop Evolution, 61(5), 927-941.
• Borna, F., Luo, S., Ahmad, N. M., Nazeri, V., Shokrpour, M., & Trethowan, R. (2017). Genetic diversity in populations of the medicinal plant Leonurus cardiaca L. revealed by inter-primer binding site (iPBS) markers. Genetic Resources and Crop Evolution, 64(3), 479-492.
• Burkhamer, R. L., Lanning, S. P., Martens, R. J., Martin, J. M., & Talbert, L. E. (1998). Predicting progeny variance from parental divergence in hard red spring wheat. Crop Science, 38(1), 243-248.
• Carvalho, A., Lima-Brito, J., Maçãs, B., & Guedes-Pinto, H. (2009). Genetic diversity and variation among botanical varieties of old Portuguese wheat cultivars revealed by ISSR assays. Biochemical Genetics, 47(3-4), 276-294.
• Dashchi, S., Abdollahi Mandoulakanı, B., Darvishzadeh, R., & Bernousi, I. (2012). Molecular similarity relationships among Iranian bread wheat cultivars and breeding lines using ISSR markers. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 40(2), 254-260.
• Demirel, U., Tindas, I., Yavuz, C., Baloch, F. S., & Çaliskan, M. E. (2018). Assessing genetic diversity of potato genotypes using inter-PBS retrotransposon marker system. Plant Genetic Resources, 16(2), 137.
• 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 & Biotechnological Equipment, 30(6), 1075-1081.
• Fahima, T., Röder, M. S., Grama, A., & Nevo, E. (1998). Microsatellite DNA polymorphism divergence in Triticum dicoccoides accessions highly resistant to yellow rust. Theoretical and Applied Genetics, 96(2), 187-195.
• Frankel, O. H., & Bennett, E. (1970). Genetic resources in plants-their exploration and conservation. Genetic resources in plants-their exploration and conservation. Oxford. 1970;469-489.
• Ghonaim, M. M., Mohamed, H. I., & Omran, A. A. (2020). Evaluation of wheat (Triticum aestivum L.) salt stress tolerance using physiological parameters and retrotransposon-based markers. Genetic Resources and Crop Evolution, 1-16.
• Gurcan, K., Demirel, F., Tekin, M., Demirel, S., & Akar, T. (2017). Molecular and agro-morphological characterization of ancient wheat landraces of turkey. BMC plant biology, 17(1), 171.
• Hazen, S. P., Leroy, P., & Ward, R. W. (2002). AFLP in Triticum aestivum L.: patterns of genetic diversity and genome distribution. Euphytica, 125(1), 89-102.
• Hossein-Pour, A., Haliloglu, K., Ozkan, G., & Tan, M. (2019). Genetıc dıversıty and populatıon structure of quınoa (Chenopodıum quınoa wılld.) using iPBS-retrotransposons markers. Applıed Ecology And Envıronmental Research, 17(2), 1899-1911.
• Hou, Y. C., Yan, Z. H., Wei, Y. M., & Zheng, Y. L. (2005). Genetic diversity in barley from west China based on RAPD and ISSR analysis. Barley Genetics Newsletter, 35(1), 9-22.
• Jaccard, P. (1912). The distribution of the flora in the alpine zone. New Phytol. 11(2):37–50.
• Kalendar, R., Antonius, K., Smýkal, P., & Schulman, A. H. (2010): iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics, 121(8), 1419-1430.
• Karık, Ü., Nadeem, M. A., Habyarimana, E., Ercişli, S., Yildiz, M., Yılmaz, A., ... & Baloch, F. S. (2019). Exploring the genetic diversity and population structure of turkish laurel germplasm by the iPBS-Retrotransposon marker system. Agronomy, 9(10), 647.
• Khaled, A. G. A., Motawea, M. H., & Said, A. A. (2015). Identification of ISSR and RAPD markers linked to yield traits in bread wheat under normal and drought conditions. Journal of Genetic Engineering and Biotechnology, 13(2), 243-252.
• Khazaei, H., Caron, C. T., Fedoruk, M., Diapari, M., Vandenberg, A., Coyne, C. J., ... & Bett, K. E. (2016). Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world's agro-ecological zones. Frontiers in plant science, 7, 1093.
• Kumar, S., Tamura, K., & Nei, M. (1994). MEGA: molecular evolutionary genetics analysis software for microcomputers. Bioinformatics, 10(2), 189-191.
• Liu, K., & Muse, S. V. (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128-2129.
• Matsuoka, Y. (2011). Evaluation of polyploid Triticum wheats under cultivation: The role of domestication, natural hybridization and allopolyploid specification in their diversification. Plant and Cell Physiology, 52(5), 750-764.
• Mehmood, A., Luo, S., Ahmad, N. M., Dong, C., Mahmood, T., Sajjad, Y., ... & Sharp, P. (2016). Molecular variability and phylogenetic relationships of guava (Psidium guajava L.) cultivars using inter-primer binding site (iPBS) and microsatellite (SSR) markers. Genetic Resources and Crop Evolution, 63(8), 1345-1361.
• Mir, R. R., Kumar, J., Balyan, H. S., & Gupta, P. K. (2012). A study of genetic diversity among Indian bread wheat (Triticum aestivum L.) cultivars released during last 100 years. Genetic Resources and Crop Evolution, 59(5), 717-726.
• Moragues, M., Moralejo, M., Sorrells, M. E., & Royo, C. (2007). Dispersal of durum wheat [Triticum turgidum L. ssp. turgidum convar. durum (Desf.) MacKey] landraces across the Mediterranean basin assessed by AFLPs and microsatellites. Genetic Resources and Crop Evolution, 54(5), 1133-1144.
• Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Doğan, Y., Comertpay, G., Yıldız, M., ... & Özkan, H. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32(2), 261-285.
• Najaphy, A., Parchin, R. A., & Farshadfar, E. (2011). Evaluation of genetic diversity in wheat cultivars and breeding lines using inter simple sequence repeat markers. Biotechnology & Biotechnological Equipment, 25(4), 2634-2638.
• Nei, M. (1987). Molecular evalutionary genetics. Columbia University Press, New York. 512 p. Öztürk, H. İ., Dursun, A., Hosseınpour, A., & Haliloğlu, K. (2020). Genetic diversity of pinto and fresh bean (Phaseolus vulgaris L.) germplasm collected from Erzincan province of Turkey by inter-primer binding site (iPBS) retrotransposon markers. Turkish Journal of Agriculture and Forestry, 44(4), 417-427.
• Peakall, R. O. D., & Smouse, P. E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular ecology notes, 6(1), 288-295.
• Peng, J., Sun, D., & Nevo, E. (2011a). Wild emmer wheat,'Triticum dicoccoides', occupies a pivotal position in wheat domestication process. Australian Journal of Crop Science, 5(9), 1127.
• Peng, J. H., Sun, D., & Nevo, E. (2011b). Domestication, evaluation, genetics and genomics in wheat. Molcular Breeding, 28,281-301.
• Provan, J., Wolters, P., Caldwell, K. H., & Powell, W. (2004). High-resolution organellar genome analysis of Triticum and Aegilops sheds new light on cytoplasm evolution in wheat. Theoretical and applied genetics, 108(6), 1182-1190.
• Rohlf, J.F. (2000). NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System. Exeter Software, Setauket, New York.
• Salem, K. F. M., El-Zanaty, A. M., & Esmail, R. M. (2008). Assessing wheat (Triticum aestivum L.) genetic diversity using morphological characters and microsatellite markers. World Journal of Agricultural Sciences, 4(5), 538-544.
• Shirmohammadli, S., Sabouri, H., Ahangar, L., Ebadi, A. A., & Sajjadi, S. J. (2018). Genetic diversity and association analysis of rice genotypes for grain physical quality using iPBS, IRAP, and ISSR markers. Journal of Genetic Resources, 4(2), 122-129.
• Sipahi, H., & Yumurtacı, A. (2020) Retrotranspozon temelli moleküler belirteçler kullanılarak Türk arpa (Hordeum vulgare L.) çeşitlerinin genomik karakterizasyonu. Mediterranean Agricultural Sciences, 33(2), 275-283.
• Tanksley, S. D., & McCouch, S. R. (1997). Seed banks and molecular maps: unlocking genetic potential from the wild. science, 277(5329), 1063-1066.
• Tarang, A., Kordrostami, M., Kumleh, A. S., Chaleshtori, M. H., Saravani, A. F., Ghanbarzadeh, M., & Sattari, M. (2020). Study of genetic diversity in rice (Oryza sativa L.) cultivars of Central and Western Asia using microsatellite markers tightly linked to important quality and yield related traits. Genetic Resources and Crop Evolution, 67(6), 1537-1550.
• Uddin, M. S., & Boerner, A. (2008). Genetic diversity in hexaploid and tetraploid wheat genotypes using microsatellite markers. Plant Tissue Culture and Biotechnology, 18(1), 65-73.
• Yagdi, E. A. C. K. (2012). Study of genetic diversity in wheat (Triticum aestivum) varities using Random Amplified Polymorphic DNA (RAPD) analysis. Turkish Journal of Field Crops, 17(1), 91-95.
• Yıldız, M., Koçak, M., & Baloch, F. S. (2015). Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment. Genetics and Molecular Research, 14(3), 10588-10602.