Genetic Variation of Fusarium spp. Isolates Associated with Root and Crown Rot of Winter Wheat Using Retrotransposon-Based iPBS Assays

Abstract

Genetic variation among the isolates of Fusarium spp., causal agent of root and crown rot of winter wheat, was evaluated using retrotransposons-based inter-primer binding site (iPBS) markers in this study. Thirty-two isolates were isolated from diseased wheat plants obtained wheat growing areas in Turkey and Azerbaijan in 2017 and 2018, for this purpose. Among the isolates, F. culmorum was the most commonly found with 23 isolates, followed by F. pseudograminearum with five isolates, and F. graminearum with four isolates. The seven iPBS retrotransposon markers produced 114 bands, of which 99 were polymorphic (86.8%) with an average of 14.14 polymorphic bands per primer for the isolates. The polymorphism information contents (PIC) per markers ranged from 0.10 to 0.29 with the average being 0.17. The dendrogram derived from unweighted pair group method with arithmetic mean (UPGMA) cluster analyses based on the data of iPBS markers divided the isolates into three clusters in according to their taxonomic grouping at species level and their origin country in the groups. Population structure was estimated based on Bayesian modeling and the results showed three populations (K = 3) supporting the clustering of isolates in the dendrogram with the highest mean value of Ln likelihood of data (-476.0). Utilization of the iPBS markers produced high level of polymorphism at the interspecies level, which allows for the separation of species. This is the first study on genetic diversity and population structure of Fusarium spp. isolates on wheat using iPBS markers.

Keywords

• Wheat,Fusarium spp.,iPBS markers,retrotransposons

Kışlık Buğdaylarda Kök ve Kökboğazı Çürüklüğüne Sebep Olan Fusarium spp. İzolatları Arasındaki Genetik Varyasyonun Retrotranzpozon Temelli iPBS Markörleri ile İncelenmesi

Öz

Bu çalışmada, kışlık buğdaylarda kök ve kökboğazı çürüklüğüne sebep olan farklı Fusarium türlerine ait izolatlar arasındaki genetik çeşitlik, retrotranspozon temelli olan primerler arası bağlanma bölgesi (iPBS) markörleri kullanılarak incelenmiştir. Bu amaçla, 2017 ve 2018 yıllarında Türkiye ve Azerbaycan buğday yetiştirme alanlarından 32 Fusarium türü izolat elde edilmiştir.  İzolatlar arasında en yaygın bulunan tür 23 izolat ile F. culmorum olarak belirlenmiş, bunu beş izolat ile F. pseudograminearum ve dört izolat ile F. graminearum takip etmiştir. Yedi iPBS retrotranspozon markörü izolatlar için 99 adeti polimorfik (%86.8) olmak üzere 114 bant üretmiş, primer başına ortalama 14.14 polimorfik bant elde edilmiştir. Markörlerin polimorfik bilgi içeriği (PIC) ortalama 0.17 olup, bu değer 0.10 ile 0.29 arasında değişmiştir. iPBS markörleri ile elde edilen verilere dayalı ağırlıklı olmayan aritmetik ortalama eş grup metodu (UPGMA) küme analizlerinin sonrasında elde edilen dendrogramda, izolatlar tür seviyesinde ile üç gruba ayrılmıştır. Ayrıca grup içerisinde yer alan izolatlar ise orijini olan ülkeye göre dağılım sergilemiştir. Popülasyon yapısı, Bayesian modellemesine dayanılarak hesaplanmış ve sonuçlar dendrogramdaki izolatların kümelenmesini destekleyecek şekilde üç popülasyona ayrılmış (K = 3) ve Ln olasılığının en yüksek ortalama değeri (-476.0) eşlik etmiştir. iPBS markörlerinin kullanılması, türler arası seviyede oldukça yüksek düzeyde polimorfizm üretmiş olup türlerin birbirinden ayrılmasını sağlamıştır. Çalışma, buğdaydan elde edilmiş Fusarium spp. izolatlarının genetik çeşitliliğini ve popülasyon yapısını iPBS markörleri analizi ile ortaya koyan ilk çalışma olma özelliği taşımaktadır. 

Anahtar Kelimeler

• Buğday,Fusarium spp.,iPBS markörleri,Retrotranspozon

References

1. Agustí-Brisach, C., Raya-Ortega, M. C., Trapero, C., Roca, L. F., Luque, F., López-Moral, A., & Trapero A. (2018). First report of Fusarium pseudograminearum causing crown rot of wheat in Europe. Plant Disease, 102(8), 1670-1670.
2. Albayrak, G., Yörük, E., Gazdağli, A., & Sharifnabi, B. (2016). Genetic diversity among Fusarium graminearum and F. culmorum isolates based on ISSR markers. Archives of Biological Sciences, 68(2), 333-343.
3. Aoki, T., & O'Donnell, K. (1999). Morphological and molecular characterization of Fusarium pseudograminearum sp. nov., formerly recognized as the Group 1 population of F. graminearum. Mycologia, 91(4), 597-609.
4. Bayraktar, H., & Dolar, F. S. (2009). Genetic diversity of wilt and root rot pathogens of chickpea, as assessed by RAPD and ISSR. Turkish Journal of Agriculture and Forestry, 33(1), 1-10.
5. Chakraborty, S., Liu, C. J., Mitter, V., Scott, J. B., Akinsanmi, O. A., Ali, S., & Simpfendorfer, S. (2006). Pathogen population structure and epidemiology are keys to wheat crown rot and Fusarium head blight management. Australasian Plant Pathology, 35(6), 643-655.
6. Earl, D. A. (2012). Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359-361.
7. Finnegan, D. J. (1989). Eukaryotic transposable elements and genome evolution. Trends in Genetics, 5, 103-107.
8. Ji, L. J., Kong, L. X., Li, Q. S., Wang, L. S., Chen, D., & Ma, P. (2016). First report of Fusarium pseudograminearum causing Fusarium head blight of wheat in Hebei Province, China. Plant Disease, 100(1), 220-220.

9. Leslie, J. F., & Summerell, B. A. (2006). The Fusarium laboratory manual. Blackwell Professional, Ames, 663 IA, USA; ISBN: 978-0-813-81919-8.
10. Mishra, P. K., Fox, R. T., & Culham, A. (2003). Inter‐simple sequence repeats and aggressiveness analyses revealed high genetic diversity, recombination and long‐range dispersal in Fusarium culmorum. Annals of Applied Biology, 143(3), 291-301.
11. Mishra, P. K., Tewari, J. P., Clear, R. M., & Turkington, T. K. (2006). Genetic diversity and recombination within populations of Fusarium pseudograminearum from western Canada. International Microbiology, 9(1), 65-68.
12. Monds, R. D., Cromey, M. G., Lauren, D. R., Di Menna, M., & Marshall, J. (2005). Fusarium graminearum, F. cortaderiae and F. pseudograminearum in New Zealand: molecular phylogenetic analysis, mycotoxin chemotypes and co-existence of species. Mycological Research, 109(4), 410-420.
13. Mueller, B. D., Groves, C. L., Holtz, D., Deutsch, A., & Smith, D. L. (2018). First report of Fusarium culmorum causing Fusarium head blight of wheat in Wisconsin. Plant Disease, 102(5), 1028-1028.
14. Muszewska, A., Hoffman-Sommer, M., & Grynberg, M. (2011). LTR retrotransposons in fungi. PLoS One, 6(12), e29425.
15. Nicholson, P., Simpson, D. R., Wilson, A. H., Chandler, E., & Thomsett, M. (2004). Detection and differentiation of trichothecene and enniatin-producing Fusarium species on small-grain cereals. In Molecular Diversity and PCR-detection of Toxigenic Fusarium Species and Ochratoxigenic Fungi, Springer, Dordrecht, pp. 503-514.
16. O'Donnell, K., Cigelnik, E., & Nirenberg, H. I. (1998). Molecular systematics and phylogeography of the Gibberella fujikuroi species complex. Mycologia, 90(3), 465-493. Özer, G., & Bayraktar, H. (2015). Intraspecific variation within Fusarium oxysporum f. sp. cumini from Cuminum cyminum in Turkey. International Journal of Agriculture and Biology, 17(2), 375-380.
17. Özer, G., Bayraktar, H., & Baloch, F. S. (2016). iPBS retrotransposons ‘A Universal Retrotransposons’ now in molecular phylogeny of fungal pathogens. Biochemical Systematics and Ecology, 68, 142-147.
18. Özer, G., Sameeullah, M., Bayraktar, H. & Göre, M. E. (2017). Genetic diversity among phytopathogenic Sclerotiniaceae, based on retrotransposon molecular markers. Phytopathologia Mediterranea, 56(2), 251-258.
19. Özer, G., & Bayraktar, H. (2018). Genetic diversity of Fusarium oxysporum f. sp. cumini isolates analyzed by vegetative compatibility, sequences analyses of the rDNA IGS region and iPBS retrotransposon markers. Journal of Plant Pathology, 2, 225-232.
20. Pourmahdi, A., & Taheri, P. (2015). Genetic Diversity of Thanatephorus cucumeris Infecting Tomato in Iran. Journal of Phytopathology, 163(1), 19-32.
21. Pritchard, J. K., Stephens, M., Rosenberg, N. A., & Donnelly, P. (2000). Association mapping in structured populations. The American Journal of Human Genetics, 67(1), 170-181.
22. Prevost, A., & Wilkinson, M. J. (1999). A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics, 98, 107–112.
23. Rohlf, F. J. (2000). NTSYS-pc, numerical taxonomy and multivariate analysis system, vol v. 2.1. Exceter Software, New York.
24. Roldan-Ruiz, I., Dendauw, J., Vanbockstaele, E., Depicker, A., & De Loose, M. (2000). AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Molecular Breeding, 6, 125–134.
25. Šķipars, V., Siaredzich, M., Belevich, V., Bruņeviča, N., Brūna, L., & Ruņģis, D.E. (2018). Genetic differentiation of Phoma sp. isolates using retrotransposon-based iPBS assays. Environmental and Experimental Biology 16(4), 307-314.
26. Pettitt, T., Xu, X., & Parry, D. (2003). Association of Fusarium species in the wheat stem rot complex. European journal of plant pathology, 109(7), 769-774.
27. Pettitt, T. R., Parry, D. W., & Polley, R. W. (1996). Effect of temperature on the incidence of nodal foot rot symptoms in winter wheat crops in England and Wales caused by Fusarium culmorum and Microdochium nivale. Agricultural and Forest Meteorology, 79(4), 233-242.
28. Rohweder, D., Valenta, H., Sondermann, S., Schollenberger, M., Drochner, W., Pahlow, G., & Dänicke, S. (2011). Effect of different storage conditions on the mycotoxin contamination of Fusarium culmorum-infected and non-infected wheat straw. Mycotoxin Research, 27(2), 145-153.
29. Schulman, A. H., Flavell, A. J., & Ellis, T. H. N. (2004). The application of LTR retrotransposons as molecular markers in plants. Methods in Molecular Biology, 260, 145-175.
30. Tunali, B., Nicol, J. M., Hodson, D., Uckun, Z., Büyük, O., Erdurmuş, D., & Bağci, S. A. (2008). Root and crown rot fungi associated with spring, facultative, and winter wheat in Turkey. Plant Disease, 92(9), 1299-1306.
31. Voigt, K., Schleier, S., & Brückner, B. (1995). Genetic variability in Gibberella fujikuroi and some related species of the genus Fusarium based on random amplification of polymorphic DNA (RAPD). Current genetics, 27(6), 528-535.
32. Waalwijk, C., de Koning, J. R., Baayen, R. P., & Gams, W. (1996). Discordant groupings of Fusarium spp. from sections Elegans, Liseola and Dlaminia based on ribosomal ITS1 and ITS2 sequences. Mycologia, 88(3), 361-368.
33. Wu, J., Xie, X., Shi, Y., Chai, A., Wang, Q., & Li, B. (2019). Analysis of pathogenic and genetic variability of Corynespora cassiicola based on iPBS retrotransposons. Canadian Journal of Plant Pathology, 41(1), 76-86.
34. Wulff, E. G., Sørensen, J. L., Lübeck, M., Nielsen, K. F., Thrane, U., & Torp, J. (2010). Fusarium spp. associated with rice Bakanae: ecology, genetic diversity, pathogenicity and toxigenicity. Environmental Microbiology, 12(3), 649-657.