Study on DNA polymorphism in populations of Rhizoctonia solani anastomosis group 4 using rDNA RFLP
Subject Areas : دو فصلنامه تحقیقات بیماریهای گیاهیF. Badpa 1 , G.R. Balali 2 , B. Sharifnabi 3
1 - دانش آموخته کارشناسی ارشد، گروه زیست شناسی، دانشگاه اصفهان، اصفهان، ایران.
2 - دانشیار، گروه زیست شناسی، دانشکده علوم، دانشگاه اصفهان، اصفهان، ایران.
3 - استاد، گروه گیاهپزشکی، دانشکده کشاورزی، دانشگاه صنعتی اصفهان، اصفهان، ایران
Keywords: genetic diversity, PCR, ITS-rDNA, Rhizoctonia solani AG4,
Abstract :
Ribosomal DNA (rDNA) sequences have been widely used to study the phylogenetic relationships in different fungi. Fungal nuclear rRNA genes are arranged as tandem repeats with several hundred copies per genome. These spacer regions are considerably more variable than the subunit sequences and have been widely used in studies on the relationships among species within a single genus or among intraspecific populations. To evaluate the polymorphism between 18S and 28S genes, 28 isolates of Rhizoctonia solani anastomosis group 4 were examined. Genomic DNA was extracted from the isolates and prepared for PCR reaction. The amplification was performed using internal transcribed spacer (ITS) ITS1 and ITS4 primers. A DNA fragment of 700 bp in size was detected in PCR products of all tested isolates. To assess existence of any further polymorphism in the ITS region, the PCR products were digested with restriction endonucleases. Although there were restriction sites for XbaI, HaeIII, BamHI, HindIII, SacI, PstI, and TaqI endonucleases, there were no restriction sites for NdeI, XhoI, HincII, HinfI, EcoRI and XhoI endonucleases. The endonuclease HincII recognized a restriction site on PCR products that discriminated the isolates belonging to AG4-HGII form isolates of AG4-HGI. Based on the results, it has been concluded that AG-4 isolates of Rhizoctonia solani wereheterogenic.
References
ahan, Iran. Mycopathologia 158: 377–384.
Boysen M, Borja M, Del Moral C, Salazar O and Rubio V. 1996. Identification at strain level of Rhizoctonia solani AG4 isolates by direct sequence of asymmetric PCR products of the ITS regions. Current Genetics 29: 174–181.
Bruns TD, White TJ and Taylor JW. 1991. Fungal molecular systematics. Annual Review of Ecology, Evolution and Systematics 22: 525–564.
Cubeta MA, Vilgalys R and González D. 1996. Molecular analysis of ribosomal RNA genes in Rhizoctonia fungi. pp. 81–86, In B Sneh, S Jabaji-Hare, S Neate and G Dijst (eds). Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control. Dordrecht: Kluwer Academic Publishers.
González D, Carling DE, Kuninaga S, Vilgalys R and Cubeta MA. 2001. Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs. Mycologia 93: 1138–1150.
González D, Cubeta MA and Vilgalys R. 2006. Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex. Molecular Phylogenetics and Evolution 40: 459–470.
González V, Salazar O, Julián MC, Acero J, Portal MA, Muñoz R, López-Córcoles H, Gómez-Acebo E, López-Fuster P and Rubio V. 2002. Ceratobasidium albasitensis, a new Rhizoctonia-like fungus isolated in Spain. Persoonia 17: 601–614.
Guillemaut C, Edel-Herman V, Comporota P, Alabouvette C, Richard-Molard M and Steinberg C. 2003. Typing of anastomosis groups of Rhizoctonia solani by restriction analysis of ribosomal DNA. Canadian Journal of Microbiology 49: 556–568.
Haratian M. 2012. Evaluation genetic structure populations Rhizoctonia solani AG4 in Iran [PhD]. [Tehran]: Tarbiat Modares University.
Jabaji-Hare S. 1996. Biochemical methods. pp. 65–71, In B Sneh, S Jabaji-Hare, S Neate and G Dijst (eds). Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control. Dordrecht: Kluwer Academic Publishers.
Kiliçoğlu Mc and Özkoç I. 2010. Molecular characterization of Rhizoctonia solani AG4 using PCR-RFLP of the rDNA-ITS region. Turkish. Journal of Biology 34: 261–269.
Kuninaga S 1996. DNA base sequence relatedness. pp. 74–78, In Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control. (B Sneh, S Jabaji-Hare, S Neate and G Dijst (eds). Dordrecht: Kluwer Academic Publishers.
Kuninaga S and Yokosawa R. 1984a. DNA base sequence homology in Rhizoctonia solani Ktihn. IV. Genetic relatedness within AG4. Annals of the Phytopathological society of Japan 50: 322–330.
Kuninaga S and Yokosawa R. 1984b. DNA base sequence homology in Rhizoctonia solani Ktihn. V. Genetic relatedness within AG6. Annals of the Phytopathological society of Japan 50: 346–352.
Lübeck M. 2004. Molecular characterization of Rhizoctonia solani. Applied Mycology and Biotechnology 4: 205–224.
McDonald HJ and Rovira AD. 1985. Development of inoculation technique for Rhizoctonia solani and its application to screening cereal cultivars for resistance. pp. 174–176, In CA Parker, AD Rovira, KJ Moore, PTW Wong and JF Kollmorgen (eds.). Ecology and Management of Soilborne Plant Pathogens. St. Paul (MN): American Phytopathological Society.
Meinhardt LW, Wulff NA, Bellato CM and Tsai SM. 2002. Genetic analyses of Rhizoctonia solani isolates from Phaseolus vulgaris grown in the Atlantic rainforest region of Sao Paulo, Brazil. Fitopatologia Brasileira 27: 259–267.
Menzies JD. 1970 Introduction: The first century of Rhizoctonia solani. pp. 3–5 In Parmeter JR (ed.). Rhizoctonia solani: Biology and Pathology. Berkeley (CA): University of California Press.
Moore RT. 1996. The dolipore/parenthesome septum in modern taxonomy. pp. 13–35, In B Sneh, S Jabaji-Hare, S Neate and G Dijst (eds). Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control. Dordrecht: Kluwer Academic Publishers.
Pannecoucque J, Van Beneden S and Hofte M. 2008. Characterization and pathogenicity of Rhizoctonia isolates associated with cauliflower in Belgium. Plant Pathology 57: 737–746.
Parmeter JR and Whitney HS. 1970. Taxonomy and nomenclature of the perfect state. pp. 7–19 In Parmeter JR (ed.). Rhizoctonia solani: Biology and Pathology. Berkeley (CA): University of California Press.
Parmeter JR, Sherwood, RT and Platt WD. 1969. Anastomosis grouping among isolates of Thanatephorus cucumeris. Phytopathology 59: 1270–1278.
Puhalla J and Carter W. 1976. The role of the H locus in heterokaryosis in Rhizoctonia solani [from soil of a cotton field, fungal diseases]. Phytopathology 66: 1348–1353.
Rahimian H. 1986. Rhizoctonia soil rot of tomato. Paper presented at: 8th Iranian Plant Protection Congress; 30 August-4 September; Isfahan, Iran.
Rosewich UL, Pettway RE, McDonald BA and Kistler HC. 1999. High levels of gene flow and heterozygote excess characterize Rhizoctonia solani AG 1-1A (Thanatephorus cucumeris)from Texas. Fungal Genetics Biology 28: 148–159.
Schneider J, Salazar O, Rubio V and Keijer J. 1997. Identification of Rhizoctonia solani associated with field-grown tulips using ITS rDNA polymorphism and pectic zymograms. European Journal of Plant Pathology 103: 607–622.
Sneh B, Burpee I and Ogoshi A (eds). 1991. Identification of Rhizoctonia species. St. Paul (Mn): American Phytopathology Society Press.
Taylor JW, Jacobsen DJ and Fisher MC. 1999. The evolution of asexual fungi: reproduction, speciation and classification. Annual Review Phytopathology 37: 197–246.
Vilgalys R and Cubeta M. 1994. Molecular systematics and population biology of Rhizoctonia. Annual Review of Phytopathology 32: 135–155.
Vilgalys R and Gonzalez D. 1990. Ribosomal DNA restriction fragment length polymorphisms in Rhizoctonia solani. Phytopathology 80: 151–158.
Vilgalys R. 1988. Genetic relatedness among anastomosis groups in Rhizoctonia as measured by DNA/DNA hybridization. Phytopathology 78: 698–702.
Visscher H, Sephton MA and Looy CV. 2011. Fungal virulence at the time of the end-Permian biosphere crisis? Geology 39: 883–886.
White TJ, Burns T, Lee S and Talor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. pp 315–322, In MA Innis (ed). PCR Protocols: A Guide to Methods and Applications. San Diego (CA): Academic Press.
_||_