Genetic diversity and population structure of Fusarium oxysporum f. sp. cepae, the causal agent of Fusarium basal plate rot on onion, using RAPD markers

Fusarium oxysporum f. sp. cepae’ nın sebep olduğu Fusarium dip çürüklüğü, dünyanın birçok ülkesinde soğanbitkisinin önemli bir hastalığıdır. Türkiye’den yedi ve Colorado, ABD’den bir popülasyonu temsil eden toplam 116Fusarium oxysporum f. sp. cepae izolatı Random Amplified Polymorphic DNA (RAPD) tekniği kullanılarakmoleküler markör analizi ile incelenmiştir. Kullanılan 11 polimorfik primer ile 110 RAPD fragmenti elde edilmiştir(10 polimorfik bant/primer). Elde edilen verilerin UPGMA ile cluster analizi % 5 benzerlik seviyesinde 5 farklı soyortaya çıkarmıştır. Türkiye’den elde edilen Fusarium oxysporum f. sp. cepae izolatlarının büyük çoğunluğununmuhtemelen aynı klonal soydan türediği gözlemlenmiştir. Genetik değerlendirmeler ve popülasyon farklılıkları daTürkiye’ den elde edilen izolatların Colorado izolatlarından büyük ölçüde farklı olduğunu ve Bursa popülasyonununTürkiye popülasyonları arasında en farklı popülasyon olduğunu göstermitir. Nei’ nin genetik uzaklığına dayanancluster analizi ise coğrafik bölgelere göre popülasyon gruplanmasını desteklemiştir. Genetik farklılık değerlerinin (HT:0.140, HS: 0.124) karşılaştırılması ise Türkiye popülasyonları arasında düük seviyelerde genetik farklılıklar ortayaçıkarmıştır. Toplam genetik farklılığın sadece % 11.4’lük kısmının coğrafik popülasyonlar arasındaki farklılıklardankaynaklandığı gözlemlenmiştir. Moleküler varyans analizi de (AMOVA) popülasyonlar arasındaki düşük genetikfarklılıkları doğrulamıştır. Bu sonuçlar RAPD-PCR tekniğinin Fusarium oxysporum f. sp. cepae popülasyonlarıarasındaki ve içerisindeki genetik varyasyonun değerlendirilmesinde oldukça faydalı olduğunu göstermiştir.

Soğanda dip çürüklüğü etmeni Fusarium oxysporum f. sp. cepae’ daki genetik farklılığının ve popülasyon yapısının RAPD markörleri kullanılarak incelenmesi

Fusarium basal plate rot caused by Fusarium oxysporum f. sp. cepae is an important disease of onion in manycountries of the world. A total of 116 single spore isolates of Fusarium oxysporum f. sp. cepae representing sevenpopulations from Turkey and one population from Colorado, USA were subjected to molecular marker analysis usingRandom Amplified Polymorphic DNA (RAPD) technique. Using eleven polymorphic primers, 110 RAPD fragmentswere obtained with an average of 10 polymorphic bands per primer. Cluster analysis with UPGMA revealed fivedistinct lineages at arbitrary level of 65% similarity. The majority of F. oxysporum f. sp. cepae isolates from Turkeywere observed to derive probably from the same clonal lineage. Genetic estimates and population differencesdemonstrated that the isolates from Turkey were significantly distinct from Colorado isolates and that Bursapopulation was the most divergent among Turkish populations. Cluster analysis of Nei’s genetic distances supportedpopulations grouping according to the geographical regions. Comparison of genetic differentiation estimates (HT:0.140, HS: 0.124) revealed low levels of genetic differentiation among Turkish populations. Only, 11.4% of totalgenetic diversity (GST) attributed to differentiation among the geographical populations. Analysis of molecularvariance (AMOVA) confirmed that there was low genetic differentiation among populations. The results suggest thatRAPD-PCR is a useful method for analyzing genetic variation within and between populations of F. oxysporum f. sp.cepae.

PDF

___

Abawi G S & Lorbeer J W (1971). Reaction of selected onion varieties to infection by Fusarium oxysporum f. sp. cepae. Plant Disease Reporter 55: 1000-1004
Assigbetse K B, Fernandez D, Dubois M P & Geiger J P (1994). Differentiation of Fusarium oxysporum f. sp. vasinfectum races on cotton by Random Amplified Polymorphic DNA (RAPD) analysis. Phytopathology 84: 622-626
Bayraktar H, Türkkan M & Dolar F S (2010). Characterization of Fusarium oxysporum f. sp. cepae from onion in Turkey based on vegetative compatibility and rDNA RFLP analysis. Journal of Phytopathology 158: 691-697
Bentley S, Pegg K G & Dale J L (1994). Optimization of RAPD-fingerprinting to analyze genetic variation within populations of Fusarium oxysporum f. sp. cubense. Journal of Phytopathology 142: 64-78
Cramer C S (2000). Breeding and genetics of Fusarium basal rot resistance in onion. Euphytica 115: 159-166
Cramer R A, Byrne P F, Brick M A, Panella L, Wickliffe E & Schwartz H F (2003). Characterization of Fusarium oxysporum isolates from common bean and sugar beet using pathogenicity assays and random- amplified polymorphic DNA markers. Journal of Phytopathology 151: 352–360
Dissanayake M L M, Kashima R, Tanaka S & Ito S I (2009). Pathogenic variation and molecular characterization of Fusarium species isolated from wilted Welsh onion in Japan. Journal of General Plant Pathology 75: 37-45
Excoffier L, Laval G & Schneider S (2005). Arlequin ver. 3.0: An Integrated Software Package for Population Genetics Data Analysis: University of Berne Switzerland
Faostat (2010). Statistical database. Available: http://faostat.fao.org
Freeman S & Maymon M (2000). Reliable detection of the fungal Fusarium oxysporum f. sp. albedinis, causal agent of bayoud disease of date palm, using molecular techniques. Phytoparasitica 28(4): 341- 348
Galván G A, Koning-Boucoiran C F S, Kopman W J M, Burger-Meijer K, González P H, Waalwijk C, Kik C & Scholten O E (2008). Genetic variation among Fusarium isolates from onion and resistance to Fusarium basal rot in related Allium species. European Journal of Plant Pathology 121: 499-512
Gargouri S, Bernier L, Hajlaoui M R & Marrakchi M (2003). Genetic variability and population structure of the wheat foot rot fungus, Fusarium culmorum, in Tunisia. European Journal of Plant Pathology 109: 807-815
Hernandez J F, Posada M A & Arbelaez G (1999). Identification of molecular markers of Fusarium oxysporum f. sp. dianthi by RAPD. Proceedings of the International Symposium on cut flowers in the Tropics, pp 123-131
Leslie J F & Summerell B A (2006). The Fusarium laboratory manual. Blackwell, Ames, pp 388.
Lewontin R C (1972). The apportionment of human diversity. Evolutionary Biology 6: 381-398
Migheli Q, Briatore E & Garibaldi A (1998). Use of random amplified polymorphic DNA (RAPD) to identify races 1, 2, 4 and 8 of Fusarium oxysporum f. sp. dianthi in Italy. European Journal of Plant Pathology 104: 49-57
Mishra P K, Fox R T V & Culham A (2003). Development of a PCR-based assay for rapid and reliable identification of pathogenic Fusaria. FEMS Microbiology Letters 218: 329-332
Nagarajan G, Kang S W, Nam M H, Song J Y, Yoo S J & Kim H G (2006). Characterization of Fusarium oxysporum f. sp. fragariae based on vegetative compatibility group, random amplified polymorphic DNA and pathogenicity. The Plant Pathology Journal 22(3): 222-229
Nei M (1972). Genetic distance between populations. American Naturalist 106: 283-292
Nei M (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences USA 70: 3321-3323
Nelson P E, Toussoun T A & Marasas W F O (1983). Fusarium Species. An illustrated manual for identification. Pennsylvania State University Press, pp 193
Özer N, Koycu D, Chilosi D & Magro P (2004). Resistance to Fusarium basal rot of onion in greenhouse and field and associated expression of antifungal compounds. Phytoparasitica 32: 388-394
Pekarek E, Jacobson K & Donovan A (2006). High levels of genetic variation exist in Aspergillus niger populations infecting welwitschia mirabilis hook. Journal of Heredity 97(3): 270-278
Reader U & Broda P (1985). Rapid preparation of DNA from filamentous fungi. Letters in Applied Microbiology 1: 17-20
Rohlf F I (1998). NTSYS-pc. Numerical taxonomy and multivariate analysis system, version 2.0. Applied Biostatistics, New York, USA
Sambrook J, Fritsch E F & Maniatis T (1989). Molecular cloning: A laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York, pp 1659
Sumner D R (1995). Fusarium basal plate rot, In: Schwartz H.F. and Mohan S.K. (eds.). Compendium of Onion and Garlic Diseases. St. Paul, MN, USA, APS press, pp 10-11
Swift C E, Wickliffe E R & Schwartz H F (2002). Vegetative compatibility groups of Fusarium oxysporum f. sp. cepae from onion in Colorado. Plant Disease 86: 606-610
Vakalounakis D J & Fragkiadakis G A (1999). Genetic diversity of Fusarium oxysporum isolates from cucumber: differentiation by pathogenicity, vegetative compatibility, and RAPD fingerprinting. Phytopathology 89: 161-168
Wang B, Brubaker C L, Tate W, Woods M J, Matheson B A & Burdon J J (2006). Genetic variation and population structure of Fusarium oxysporum f. sp. vasinfectum in Australia. Plant Pathology 55: 746- 755
Woo S L, Zoina A, Del Sorbo G, Lorito M, Nanni B, Scala F & Noviello C (1996). Characterization of Fusarium oxysporum f. sp. phaseoli by pathogenic races, VCGs, RFLPs, and RAPD. Phytopathology 86: 966-973
Yeh F C, Yang R C, Boyle T J, Ye Z H & Mao J X (1999). Popgene ver. 1.32, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Canada