Using ISSR and URP-PCR markers in detecting genetic diversity among Macrophomina phaseolina isolates of sesame in Iran

Volume 8, Issue 3
June 2019
Pages 293-309

Document Type : Original Research

Authors

1 Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

2 Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

Abstract
To assess the variability of Macrophomina phaseolina (Tassi) Goid, the causal agent of charcoal rot of Sesame, sixty isolates recovered from ten geographic regions, were analyzed using inter simple sequence repeat (ISSR) and universal rice primer (URP) markers. Isolates were grouped into eight clusters at 78% genetic similarity level. Our results showed that the five ISSR primers produced 105 bands of which 77.11% were polymorphic and eight URP-PCR primers generated 135 bands of which 66.84% were polymorphic. These methods showed a considerable genetic diversity among Iranian isolates, but no correlation was found between genetic diversity and geographical origins of the isolates. Analysis of molecular variance revealed that a large proportion of genetic variability resulted from the differences among isolates within regions. The findings of this study demonstrated that the low-genetic differentiation (GST) and high gene flow (Nm) among populations had a significant effect on the emergence and evolutionary development of M. phaseolina.


Keywords

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Aboshosha, S. S., Attaalla, S.I., El-Korany, A. E. and El-argawy, E. 2007. Characterization of Macrophomina phaseolina isolates affecting sunflower growth in El-Behera governorate. International Journal of Agriculture and Biology, 9: 807−815.
Aghakhani, M. and Dubey, S. C. 2009. Determination of genetic diversity among Indian isolates of Rhizoctonia bataticola causing dry root rot of chickpea. Antonie van Leeuwenhoek, 96: 607−619.
Almeida, M. R., Abdelnoor, R. V., Arias, C. A. A., Carvalho, V.P., Martin, S. R. R., Benato, L. C., Pinto, M. C. and Carvalho, C. G. P. 2003. Genotypic diversity among brazilian isolates of Macrophomina phaseolina revealed by RAPD. Fitopatologia Brasileira, 28: 279−285.
Almeida, M. R., Sosa-Gomez, D. R., Binneck, E., Marin, S. R. R., Zucchi, M.I., Abdelnoor, R. V. and Souto, E. R. 2008. Effect of crop rotation on specialization and genetic diversity of Macrophomina phaseolina. Tropical Plant Pathology, 33: 257−264.
Ahmad, I. and Burney, K. 1990. In: Ooi P, Lim G-S, Teng PS, editors. Macrophomina phaseolina infection and charcoal rot development in sunflower under field conditions. Proceedings of the Third International Conference Plant Protection in the Tropics; 1990 March 20–23; Malaysia. Kuala Lumpur: Genting Highlands.
Babu, B. K., Saxena, A. K., Srivastava, A. K. and Arora, D. K. 2007. Identification and detection of Macrophomina phaseolina by using species-specific oligonucleotide primers and probe. Mycologia, 99: 797−803.
Baird, R. E., Wadl, P. A., Allen, T., McNeill, D., Wang, X. W., Moulton, J. K., Rinehart, T. A., Abbas, H. K., Shier, T. and Trigiano, R. N. 2010. Variability of United States isolates of Macrophomina phaseolina based on simple sequence repeats and cross genus transferability to related genera within Botryosphaeriaceae. Mycopathologia, 170: 169−180.
Bornet, B. and Branchard, M. 2001. Nonanchored Inter Simple Sequence Repeat (ISSR) markers: reproducible and specific tools for genome fingerprinting. Plant Molecular Biology Reporter. 19: 209-215.
Broglie, K.E., Gaynor, J. J. and Broglie, R. M. 1986. Ethylene-regulated gene expression: molecular cloning of the genes encoding an endochitinase from Phaseolus vulgaris. Proceedings of the National Academy of Science of the United States of America. 1986 Sept 9; America. United States.
Carlile, M. J. 1986. Genetic Exchange and Gene Flow: Their Promotion and Prevention. In: Evolutionary Biological of the Fungi. Rayner ADM, Moore D, editors. Cambridge: Cambridge University Press; p. 203-214.
Chakravarthi, B. K. and Naravaneni, R. 2006. SSR Marker Based DNA Fingerprinting and Diversity Study in Rice (Oryza sativa. L.). African Journal of Biotechnology, 5: 684–688.
Dhingra, O.D. and Sinclair, J. B. 1978. Biology and Pathology of Macrophomina phaseolina. Vic¸osa (Brasil): Imprensa Universita´ ria, Universidade Federal de Vic¸osa.
Geo, P., Yao, Q., Ding, B., Zeng, H., Zhong, Y., Fu, C. and Jin, X. 2006. Genetic diversity of Sinojackia dolichocarpa (Styracaceae), a species endangered and endemic to China, detected by inter-simple sequence repeat (ISSR). Biochemical Systematics and Ecology, 34: 231-239.
Gordon, T. R. and Martyn. R. D. 1997. The evolutionary biology of Fusarium oxysporum. Annual Review of Phytopathology, 35:111-128.
Hamer, J. E., Farrall, L., Orbach, M. J., Valent, B. and Chumley, F. G. 1989. Host species-specific conservation of a family of repeated DNA sequences in the genome of a fungal plant pathogen. Proc Natl Acad Sci USA. 86: 9981–9985.
Hlinkova, E. and Sykora, M. 1996. Changes in extracellular protein patterns induced by powdery mildew (Erysiphe graminis f.sp. hordei) infection (abstract). In: Kema GHJ, Niks RE, Daamen RA, editors. Proceedings of the Ninth European and Mediterranean Cereal Rusts and Powdery Mildew Conference; 1996 Sept 2–6; Wageningen, the Netherlands.
Ijaz, S. Sadaqat, H. A. and Khan, M. N. 2012. A review of the impact of charcoal rot (Macrophomina phaseolina) on sunflower. Journal of Agricultural Science, pp. 1- 6.
Jana, T., Sharma, T. R. and Singh, N. K. 2005a. SSR-based detection of genetic variability in the charcoal root rot pathogen Macrophomina phaseolina. Mycological Research, 109: 81−86.
Jana, T., Singh, N., Koundal, K. and Sharma, T. 2005b. Genetic differentiation of charcoal rot pathogen, Macrophomina phaseolina, into specific groups using URP-PCR. Canadian Journal of Microbiology, 51: 159−164.
Kang, H. W., Park, D. S., Par, Y. J. , You, C. H., Lee, B. M., Eun, M. Y. and Go, S. J. 2002. Fingerprinting of diverse genomes using PCR with universal rice primers generated from repetitive sequence of Korean weedy rice. Molecules and Cells, 13: 281-287.
Kendrick, B. 1992. The Fifth Kingdom. 2d ed. Waterloo, Ontario, Canada: Mycologue Publication, Focus Information Group Inc.
Khan, A. N., Shair, F., Malik, K., Hayat, Z., Khan, M. A., Hafeez, F. Y. and Hassan, M. N. 2017. Molecular Identification and Genetic Characterization of Macrophomina phaseolina Strains Causing Pathogenicity on Sunflower and Chickpea. Frontiers in Microbiology, 8: 1-11
Kohn, L. M. 1995. The clonal dynamic in wild and agricultural plant pathogen populations. Canadian Journal of Botany, 73: S1231-S140.
Lee, S. B. and Taylor, J. W. 1990. Isolation of DNA from fungal mycelia and single spores. PCR Protocols: a guide to methods and applications. In: Innis MA, Gelfand DH, Sinsky JJ. White TJ, editors. London: Academic Press. p. 282−287.
Linhai, W., Yanxin, Z., Donghua, L., Junbin, H., Wenliang, W., LvHaixia, L. and Xiurong Z. 2011. Variations in the isolates of Macrophomina phaseolina from sesame in China based on amplified fragment length polymorphism (AFLP) and pathogenicity. African journal of microbiology research, 5: 5584-5590.
Lynch, M. A. and Walsh, J. B. 1998. Genetics and analysis of quantitative traits. Sunderland: Sinauer Assocs., Inc.
Mahdizadeh, V., Safaie, N. and Mohamadi-Goltapeh, E. 2011. Diversity of Macrophomina phaseolina Based on Morphological and Genotypic Characteristics in Iran. Plant Pathology Journal, 27: 128-137.
Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209–220.
Mayek-Perez, N., Lpez-Castaeda, C., Gonzglez-Chavira, M., Garcia-Espinosa, R., Acosta-Gallegos, J., de la Vega, O. M. and Simpson, J. 2001. Variability of Mexican isolates of Macrophomina phaseolina based on pathogenesis and AFLP genotype. Physiological and Molecular Plant Pathology, 59: 257−264.
Menzies, J. G., Bakkeren, G., Matheson, F., Procunier, J. D. and Woods, S. 2003. Use of inter-simple sequence repeats and amplified fragment length polymorphisms to analyze genetic relationships among small grain-infecting species of Ustilago. Phytopathology. 93: 167–175.
Miao, V. P, Covert, S. F. and VanEtten, H. D. 1991. A fungal gene for antibiotic resistance on a dispensable ("B") chromosome. Science. 254: 1773–1776.
Mihail, J. D. and Taylor, S. J. 1995. Interpreting variability among isolates for Macrophomina phaseolina in pathogenicity, pycnidium production and chlorate utilization. Canadian Journal of Botany, 73: 1596–1603.
Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA. 70:3321–3323.
Peakall, R. and Smouse, P. E. 2006. GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes. 6:288–295.
Pecina, V., Alvarado, M. J., Alanis, H. W., Almaraz, R. T. and Vandemark, G. J. 2000 Detection of double-stranded RNA in Macrophomina phaseolina. Mycologia, 92: 900–907.
Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J. and Tingey, S. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsattlite) markers for germplasm analysis. Molecular Breeding, 3: 225–238.
Purkayastha, S., Kaur, B., Arora, P., Bisyer, I., Dilbaghi, N. and Chaudhury, A. 2008. Molecular genotyping of Macrophomina phaseolina isolates: comparison of microsatellite primed PCR and repetitive element sequence-based PCR. Journal of Phytopathology, 156: 372−381.
Radwan, N. A. M. 2000. Implication of certain physical and chemical treatments to improve diseases resistance of barley to powdery mildew. Ph.D. Thesis, Cairo University.
Reyes-Franco, M. C., Hernandez-Delgado, S., Beas-Fernandez, R., Medina-Fernandez, M., Simpson, J. and Mayek-Perez, N. 2006. Pathogenic and genetic variability within Macrophomina phaseolina from Mexico and other countries. Journal of Phytopathology, 154: 447−453.
Rholf, F. J. 2000. NTSYS-pc Numerical taxonomy and multivariate system version 2.1. Exeter publishing, Setauket.
Safaie, N., Alizadeh, A., Saidi, A., Rahimian, H. and Adam, G. 2005. Molecular characterization and genetic diversity among Iranian populations of Fusarium graminearum, the causal agent of wheat head blight. Iran. Journal of Plant Pathology, 41:171−189.
Sanchez, s., Chamorro, M., Henriquez, J., Grez, J., Díaz, I., Santos, B. D. L. and Gambardella, M. 2017. Genetic and biological characterization of Macrophomina phaseolina (Tassi) Goid. causing crown and root rot of strawberry. Chilean journal of agricultural research, 77 (4): 325-331
Slatkin, M. and Barton, N. H. 1989. A comparison of three indirect methods for estimating average levels of gene flow. Evolution, 43:1349–1368.
Trigiano, R. N, Windham, M. T. and Windham, A. S. 2008. Plant pathology: concepts and laboratory exercises. 2nd ed. Boca Raton (FL): CRC Press.
Yeh, F. C, Boyle, T. J. B., Ye, Y. Z. and Xiyan, J. M. 1999. POPGENE version 1.32. Microsoft Window-based freeware for population genetics analysis. University of Alberta and Center for International Forestry Research. (Last accessed March 2005).
Zietkiewicz, E., Rafalski, A. and Labuda, D. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20:176–183.