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Identification of Genetic Variations on Fritillaria imperialis L. Genotypes Collected from Van Lake Basin by iPBS-Retrotranspozon Markers

Yıl 2020, Cilt: 30 Sayı: 2, 398 - 406, 30.06.2020
https://doi.org/10.29133/yyutbd.705721

Öz

Fritillaria imperialis L. naturally grows in Turkey and it is used as an ornamental plant. This species harbored plentiful genetic variation for various morphological traits in its natural habitat. In this study, 19 different iPBS-Retrotransposon primers were used to identify genetic variation among 74 F. imperialis genotypes collected around Van lake basin. 19 primers amplified 94 bands, 100% polymorphism. The average number of bands per primer was 4.94 and the average polymorphism information content (PIC) was 0.58. Maximum number of polymorphic bands were 10 while the minimum number of polymorphic bands were 2. The mean effective number of alleles, Shannon information index and the gene diversity were 1.50, 0.47, and 0.30 respectively. The results reflected that genetic variations of F. imperialis genotypes collected from Van lake basin were significant. This is the first report identifying the genetic variations of F. imperialis genotypes by iPBS-Retrotransposon primers, and it proved that iPBS-Retrotransposon marker system could be applied successfully in F. imperialis for genetics and genomic studies. The data obtained from this study will provide preliminary information for future F. imperialis breeding activities. 

Proje Numarası

2015-HIZ-ZF328

Kaynakça

  • Alp, Ş. (2006). “Doğal Çiçek Soğanları, Terslale Koruma Önlemleri ve Yetiştiriciliği”, Doğal Çiçek Soğancıları Derneği, Yayın No: 2, S. 44.
  • Andeden, E.E., Baloch, F.S., Derya, M., Kilian, M., Özkan, H. (2012). iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. J. Plant Biochem. Biotechnol., DOI 10.1007/s13562-012-0175-5.
  • Arslan, N., Sarıhan, E.O. (2002, Ekim). “Türkiye’nin Fritillaria türleri ve bunların tarımı konusunda yapılan çalısmalar”, II. Ulusal Süs Bitkileri Kongresi: 303-309. 22-24, Antalya.
  • Baloch, F.S.; Alsaleh, A.; de Miera, L.E.S.; Hatipoğlu, R.; Çiftçi, V.; Karaköy, T.; Yıldız, M.; Özkan, H. (2015). DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochem. Syst. Ecol., 61, 244–252.
  • Bingöl, F., Şener, B., Koyuncu, M., Faizi, S., Gilani, A. (1996).“Biological activities of some Frittilaria L. species growing in Turkey ’, GUEDE-J Journal of Faculty of Pharmacy of Gazı University, 13:45.
  • Boiteux, L.S., Fonseca, M.E.M., Simon, P.W. (1999). Effects of Plant Tissue and Purification Method on Randomly Amplified Polymorphic DNA-based Genetic Fingerprinting Analysis in Carrot. Journal of the American Society for Horticultural Science 124(1):32-38.
  • Chaleshtori, B.S., Shiran, B., Kohgard, M., Mommeni, H., Hafizi, A., Khodombashi, M., Mirakhorli, N., Sorkheh, N. (2012) Assessment of genetic diversity and structure of Imperial Crown (Fritillaria imperialis L.) populations in the Zagros region of Iran using AFLP, ISSR and RAPD markers and implications for its conservation. Biochem. Syst. Ecol., 42: 35–48.
  • Clark, T., Grey-Wilson, C. (2003). Crown imperials. The Plantsman, 2, Part 1:33-47.
  • Cömertpay, G., Baloch, F.S., Derya, M., Andeden, E.E., Alsaleh, A., Sürek, H., Özkan, H. (2016). Population structure of rice varieties used in Turkish rice breeding programs determined using simple sequence repeat and inter-primer binding site- retrotransposon data. Genet. Mol. Res., 15:1-4.
  • Davis, P.H. (1984). Flora of Turkey and East Aegean Islands. VIII Volume, Edinburgh Un. Press, s. 632.
  • De Riek, J., Calsyn, E., Everaert, I., Van Bocksteal, E., De Loose, M. (2001). AFLP based alternative for the assessment of the distinctness, uniformity and stability of sugar beat varieties. Theor. Appl. Genet. 103:1254-1256.
  • Doyle, J.J., Doyle, J.L. (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
  • Finnegan, D.J. (1989). Eukaryotic transposable elements and genome evolution. Trends Genet., 5, 103–107.
  • Guo, D.L.; Guo, M.X.; Hou, X.G.; Zhang, G.H. (2014). Molecular diversity analysis of grape varieties based on iPBS markers. Biochem. Syst. Ecol., 52, 27–32.
  • Gürlek, D. (2011). “Fritillaria imperialis L. ve Fritillaria persica L. türlerinde in vitro soğancık üretimi üzerine araştırmalar.” Doktora Tezi. Ankara Üniversitesi, Fen Bilimleri Enstitüsü, Ankara.
  • Huson, D.H., Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23: 254-267.
  • Kalendar, R., Antonius, K., Smykal, P., Schulman, A.H. (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet. 121:1419–1430.
  • Karık, Ü., Nadeem, M.A., Habyarimana, E., Ercişli, S., Yıldız, M., Yılmaz, A., Yang, S.H., Chung, G., Baloch, F.S. (2019). Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System. Agronomy-Basel, 9: 1-14.
  • Nei, M. (1987). Molecular evolutionary genetics. Columbia Univerisity Press, New York.
  • Rahimi, M., Daneshvar M.H., Heidari, M., Yari, F. (2013). “In vitro micropropagation of Fritillaria imperialis L. through induction of indirect organogenesis”, International Journal of Agronomy and Plant Production, 4(3): 418-424.
  • San Miguel, P., Tikhonov, A., Jin, Y.K., Motchoulskaia, N., Zakharov, D., Berhan-Melake, A., Springer, P.S., Lee, M., Avramova, Z., Bennetzen, JL. (1996). Nested retrotransposons in the intergenic regions of the maize genome. Science, 274, 765–768.
  • Tekşen, M., Aytaç, Z. (2011). “The revision of the genus Fritillaria L. (Liliaceae) in the Mediterranean region (Turkey)”, Turk. J. Bot., 35: 447-478.
  • Xu, J.Y., Yan, Z., Yı, Z., Wu, G., Xie, G.Y., Qin, M.J. (2018). Molecular diversity analysis of Tetradium ruticarpum (WuZhuYu) in China based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Chinese Journal of Natural Medicines, 16(1):1-9.
  • Yeh, F.C., Yang, R., Boyle, T.J., Ye, Z., Xiyan, J.M. PopGene32, Microsoft Windows-Based Freeware for Population Genetic Analysis, Version 1.32. Mol. Biology and Biotechnology Centre, University of Alberta: Edmonton, AB, Canada, 2000.
  • Yaldız, G.; Camlıca, M.; Nadeem, M.A.; Nawaz, M.A.; Baloch, F.S. (2018). Genetic diversity assessment in Nicotiana tabacum L. with iPBS-retrotransposons. Turk. J. Agric. For., 42, 154–164.
  • Yıldız, M.; Koçak, M.; Baloch, F.S. (2015). Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment. Genet. Mol. Res., 14, 10588–10602.
  • Yıldız, M., Koçak, M., Nadeem, M.A., Cavagnaro, P., Barboza, K., Baloch, F.S., Argün, D., Keleş, D. (2019). Genetic diversity analysis in the Turkish pepper germplasm using iPBS (inter-primer binding site) retrotransposon-based markers. Turkish Journal of Agriculture and Forestry, 43: 1-14.
  • Zampicinini, G., Blinov, A., Cervella, P., Guryev, V., Sella, G. (2004). Insertional polymorphism of a non-LTR mobile element (NLRCth1) in European populations of Chironomus riparius (Diptera, Chironomidae) as detected by transposon insertion display. Genome, 47, 1154–1163.

Van Gölü Havzasından Toplanan Terslale (Fritillaria imperialis L.) Genotiplerinde Genetik Farklılığın iPBS Retrotranspozon Markırları ile Belirlenmesi

Yıl 2020, Cilt: 30 Sayı: 2, 398 - 406, 30.06.2020
https://doi.org/10.29133/yyutbd.705721

Öz

Fritillaria imperialis L. (Terslale) Türkiye’de doğal olarak yetişen ve süs bitkisi olarak kullanılan bir türdür. Bu tür doğada morfolojik olarak yüksek bir genetik varyasyon göstermektedir. Van Gölü havzasından toplanan 74 F. imperialis genotipi arasındaki genetik çeşitliliği belirlemek amacıyla yürütülen bu çalışmada, 19 farklı iPBS-Retrotranspozon primeri kullanılmıştır. Kullanılan 19 primerin tamamı %100 oranında polimorfizm gösteren toplam 94 bant oluşturmuştur. Primer başına düşen ortalama bant sayısının 4.94, ortalama polimorfizm bilgi içeriğinin (PIC) ise 0.58 olduğu belirlenmiştir. En düşük bant veren primer 2 bant oluştururken, en yüksek bant veren primer 10 bant oluşturmuştur. Ortalama etkili allel sayısının 1.50, Shannon bilgi indeksinin 0.47, gen çeşitliliğinin ise 0.30 olduğu saptanmıştır. Elde edilen sonuçlar, Van Gölü havzasından toplanan ters lale genotiplerindeki genetik farklılığın önemli düzeyde olduğunu ortaya koymuştur. Terslale genotiplerinde ilk kez iPBS-Retrotranspozon markırları kullanılarak genetik çeşitliliğin belirlenmesine yönelik olarak yürütülen bu çalışma, iPBS-Retrotranspozon markır sisteminin bu türde başarılı bir şekilde uygulanabileceğini ortaya koymuştur. Elde edilen veriler, terslale üzerinde yürütülecek ıslah çalışmaları için ön bilgi oluşturacak niteliktedir.

Proje Numarası

2015-HIZ-ZF328

Kaynakça

  • Alp, Ş. (2006). “Doğal Çiçek Soğanları, Terslale Koruma Önlemleri ve Yetiştiriciliği”, Doğal Çiçek Soğancıları Derneği, Yayın No: 2, S. 44.
  • Andeden, E.E., Baloch, F.S., Derya, M., Kilian, M., Özkan, H. (2012). iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. J. Plant Biochem. Biotechnol., DOI 10.1007/s13562-012-0175-5.
  • Arslan, N., Sarıhan, E.O. (2002, Ekim). “Türkiye’nin Fritillaria türleri ve bunların tarımı konusunda yapılan çalısmalar”, II. Ulusal Süs Bitkileri Kongresi: 303-309. 22-24, Antalya.
  • Baloch, F.S.; Alsaleh, A.; de Miera, L.E.S.; Hatipoğlu, R.; Çiftçi, V.; Karaköy, T.; Yıldız, M.; Özkan, H. (2015). DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochem. Syst. Ecol., 61, 244–252.
  • Bingöl, F., Şener, B., Koyuncu, M., Faizi, S., Gilani, A. (1996).“Biological activities of some Frittilaria L. species growing in Turkey ’, GUEDE-J Journal of Faculty of Pharmacy of Gazı University, 13:45.
  • Boiteux, L.S., Fonseca, M.E.M., Simon, P.W. (1999). Effects of Plant Tissue and Purification Method on Randomly Amplified Polymorphic DNA-based Genetic Fingerprinting Analysis in Carrot. Journal of the American Society for Horticultural Science 124(1):32-38.
  • Chaleshtori, B.S., Shiran, B., Kohgard, M., Mommeni, H., Hafizi, A., Khodombashi, M., Mirakhorli, N., Sorkheh, N. (2012) Assessment of genetic diversity and structure of Imperial Crown (Fritillaria imperialis L.) populations in the Zagros region of Iran using AFLP, ISSR and RAPD markers and implications for its conservation. Biochem. Syst. Ecol., 42: 35–48.
  • Clark, T., Grey-Wilson, C. (2003). Crown imperials. The Plantsman, 2, Part 1:33-47.
  • Cömertpay, G., Baloch, F.S., Derya, M., Andeden, E.E., Alsaleh, A., Sürek, H., Özkan, H. (2016). Population structure of rice varieties used in Turkish rice breeding programs determined using simple sequence repeat and inter-primer binding site- retrotransposon data. Genet. Mol. Res., 15:1-4.
  • Davis, P.H. (1984). Flora of Turkey and East Aegean Islands. VIII Volume, Edinburgh Un. Press, s. 632.
  • De Riek, J., Calsyn, E., Everaert, I., Van Bocksteal, E., De Loose, M. (2001). AFLP based alternative for the assessment of the distinctness, uniformity and stability of sugar beat varieties. Theor. Appl. Genet. 103:1254-1256.
  • Doyle, J.J., Doyle, J.L. (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
  • Finnegan, D.J. (1989). Eukaryotic transposable elements and genome evolution. Trends Genet., 5, 103–107.
  • Guo, D.L.; Guo, M.X.; Hou, X.G.; Zhang, G.H. (2014). Molecular diversity analysis of grape varieties based on iPBS markers. Biochem. Syst. Ecol., 52, 27–32.
  • Gürlek, D. (2011). “Fritillaria imperialis L. ve Fritillaria persica L. türlerinde in vitro soğancık üretimi üzerine araştırmalar.” Doktora Tezi. Ankara Üniversitesi, Fen Bilimleri Enstitüsü, Ankara.
  • Huson, D.H., Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23: 254-267.
  • Kalendar, R., Antonius, K., Smykal, P., Schulman, A.H. (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet. 121:1419–1430.
  • Karık, Ü., Nadeem, M.A., Habyarimana, E., Ercişli, S., Yıldız, M., Yılmaz, A., Yang, S.H., Chung, G., Baloch, F.S. (2019). Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System. Agronomy-Basel, 9: 1-14.
  • Nei, M. (1987). Molecular evolutionary genetics. Columbia Univerisity Press, New York.
  • Rahimi, M., Daneshvar M.H., Heidari, M., Yari, F. (2013). “In vitro micropropagation of Fritillaria imperialis L. through induction of indirect organogenesis”, International Journal of Agronomy and Plant Production, 4(3): 418-424.
  • San Miguel, P., Tikhonov, A., Jin, Y.K., Motchoulskaia, N., Zakharov, D., Berhan-Melake, A., Springer, P.S., Lee, M., Avramova, Z., Bennetzen, JL. (1996). Nested retrotransposons in the intergenic regions of the maize genome. Science, 274, 765–768.
  • Tekşen, M., Aytaç, Z. (2011). “The revision of the genus Fritillaria L. (Liliaceae) in the Mediterranean region (Turkey)”, Turk. J. Bot., 35: 447-478.
  • Xu, J.Y., Yan, Z., Yı, Z., Wu, G., Xie, G.Y., Qin, M.J. (2018). Molecular diversity analysis of Tetradium ruticarpum (WuZhuYu) in China based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Chinese Journal of Natural Medicines, 16(1):1-9.
  • Yeh, F.C., Yang, R., Boyle, T.J., Ye, Z., Xiyan, J.M. PopGene32, Microsoft Windows-Based Freeware for Population Genetic Analysis, Version 1.32. Mol. Biology and Biotechnology Centre, University of Alberta: Edmonton, AB, Canada, 2000.
  • Yaldız, G.; Camlıca, M.; Nadeem, M.A.; Nawaz, M.A.; Baloch, F.S. (2018). Genetic diversity assessment in Nicotiana tabacum L. with iPBS-retrotransposons. Turk. J. Agric. For., 42, 154–164.
  • Yıldız, M.; Koçak, M.; Baloch, F.S. (2015). Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment. Genet. Mol. Res., 14, 10588–10602.
  • Yıldız, M., Koçak, M., Nadeem, M.A., Cavagnaro, P., Barboza, K., Baloch, F.S., Argün, D., Keleş, D. (2019). Genetic diversity analysis in the Turkish pepper germplasm using iPBS (inter-primer binding site) retrotransposon-based markers. Turkish Journal of Agriculture and Forestry, 43: 1-14.
  • Zampicinini, G., Blinov, A., Cervella, P., Guryev, V., Sella, G. (2004). Insertional polymorphism of a non-LTR mobile element (NLRCth1) in European populations of Chironomus riparius (Diptera, Chironomidae) as detected by transposon insertion display. Genome, 47, 1154–1163.
Toplam 28 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Ziraat, Veterinerlik ve Gıda Bilimleri
Bölüm Makaleler
Yazarlar

Metin Koçak Bu kişi benim 0000-0002-8109-5245

Merve Karataş 0000-0002-1076-3648

Şevket Alp 0000-0002-9552-4848

Faheem Baloch 0000-0002-7470-0080

Mehtap Yıldız 0000-0001-6534-5286

Proje Numarası 2015-HIZ-ZF328
Yayımlanma Tarihi 30 Haziran 2020
Kabul Tarihi 29 Mayıs 2020
Yayımlandığı Sayı Yıl 2020 Cilt: 30 Sayı: 2

Kaynak Göster

APA Koçak, M., Karataş, M., Alp, Ş., Baloch, F., vd. (2020). Van Gölü Havzasından Toplanan Terslale (Fritillaria imperialis L.) Genotiplerinde Genetik Farklılığın iPBS Retrotranspozon Markırları ile Belirlenmesi. Yuzuncu Yıl University Journal of Agricultural Sciences, 30(2), 398-406. https://doi.org/10.29133/yyutbd.705721

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