Assessing the Genetic Diversity of <i>Alternaria Bataticola</i> in South Africa using Molecular Markers

Authors

  • J. Chalwe Department of Biotechnology, Vaal University of Technology Private Bag X021, Vanderbijlpark
  • P. Adebola Department of Biotechnology, Vaal University of Technology Private Bag X021, Vanderbijlpark
  • M. Pillay Africa Rice Center (AfricaRice), Abidjan, Cote d’Ivoire

DOI:

https://doi.org/10.24203/ajas.v5i2.4367

Keywords:

Alternaria bataticola, sweetpotato, genetic diversity, RAPD, ITS2, secondary structure prediction

Abstract

Sweetpotato (Ipomoea batatas) an economically important food crop is affected by viral and fungal diseases. The most important fungal disease is Alternaria blight caused by Alternaria bataticola. Alternaria blight can be controlled using fungicides and cultural practices in the short-term. A sustainable control measure is the development of resistant sweetpotato cultivars. A prerequisite to this approach is the knowledge of the genetic diversity of this fungal pathogen. This study assessed the genetic diversity of A. bataticola in South Africa using RAPD analysis, DNA sequencing and secondary structures of the ITS2 region. Samples were collected from 25 different localities and the pathogen was identified in the laboratory. Both RAPD and ITS2 sequence data showed that there is high levels of genetic diversity among the isolates of A. bataticola. Although the dendrograms generated from the RAPD and ITS2 sequences clustered some isolates according to their place of origin, the majority of isolates did not group according to their geographic origins. The predicted ITS2 secondary structure models were variable ranging from simple to complex. The unique secondary structures of each isolate can be used to identify and distinguish each of the isolates used in this study. 

 

References

Prakash CS, “Sweet Potato Biotechnology: Progress and Potentialâ€, Biotechnology and

Development Monitor, vol. 18, pp. 1819-1822, 1994.

Hu J, Nakatani M, Lalusin AG, Kuranaichi T, Fajimura T, “Genetic analysis of Sweetpotato and wild relatives using inter-simple sequence repeats (ISSRs)â€, Breeding Science, vol. 53. no. 4, pp. 297-304, 2003.

FAO Statistics, “ERS, 2010; Statistics Divisionâ€. Food and Agriculture Organization of the United Nations, 2012.

Clark CA, Hoy MW, “Effects of common viruses on yield and quality of Beauregard sweetpotato in Louisianaâ€, Plant Disease, vol. 90, no. 1, pp. 83-88, 2006.

Adebola PO, Lane CR, Smith JJ, “Molecular characterisation of Alternaria species of sweet potato and development of a host resistance screening protocolâ€. IN Bruce T, Foyer C, Halford N, Keys A, Kunert K, Lawlor D, Parry M, Russell G, (Eds.) Agriculture: Africa's "engine for growth" - plant science and biotechnology hold the key. Aspects of Applied Biology 2Rothamsted Research, Harpenden, UK, 2009.

Lopes CA, Boiteux LS, “Leaf Spot and Stem Blight of Sweetpotato caused by Alternaria bataticola: A new record to South Americaâ€, Plant Disease Journal, pp. 1107-1109, 1994.

Skoglund LG, Smit NEJM, “Major Diseases and Pests of Sweetpotato in Eastern Africaâ€, International Potato Center (CIP) Peru, Lima, 1994.

Narayanin CD, Thompson AH, Slabbert MM, “First report of Alternaria blight of sweet potato caused by Alternaria bataticola in South Africaâ€, African Plant Protection, vol. 16, no. pp. 7-9, 2010.

Nath VS, Senthil M, Hegde VM, Jeeva ML, Misra RS, Veena SS, Raj M, “Genetic diversity of Phytophthora colocasiae isolates in India based on AFLP analysisâ€, Biotechology, vol. 3, pp. 297–305, 2013.

Leiminger L, Bahnweg G, Hausladen H, “Population genetics – consequences on early blight diseaseâ€, Twelfth EuroBlight workshop, vol. 1, pp. 1-8, 2010.

Benali S, Mohamed B, Eddine HJ, Neema C, “Advances of Molecular Markers Application in Plant Pathology Researchâ€, European Journal of Scientific Research, vol. 50, no. 1, pp. 110-123, 2011.

Capote N, Pastrana AM, Aguado A, Sánchez-Torres P, “Molecular Tools for Detection of Plant Pathogenic Fungi and Fungicide Resistanceâ€, In Cumagun CJ, ed. Plant Pathology, InTech, Croatia, pp. 151-203, 2012.

Storck R, “Nucleotide Composition of Nucleic Acids of Fungi II. Deoxyribonucleic Acidsâ€, Journal of Bacteriology, vol. 91, pp. 227-230, 1966.

Kakvan N, Zamanizadeh H, Morid B, Taheri H, Hajmansor S, “Study on pathogenic and genetic diversity of Alternaria alternata isolated from citrus hybrids of Iran, based on RAPD-PCR techniqueâ€, European Journal of Experimental Biology, vol. 2, pp. 570-576, 2012.

Sofi TA, Beig MA, Dar GH, Ahmad M, Hamid A, Ahangar FA, Padder B A, Shah MD, “Cultural, morphological, pathogenic and molecular characterization of Alternaria mali associated with Alternaria leaf blotch of appleâ€, African Journal of Biotechnology, vol. 12, pp. 370-381, 2013.

Tiwari K, Chittora M, “Assessment of genetic diversity and distribution of endophytic fungal communities of Alternaria solani isolates associated with the dominant Karanja plants in Sanganer Region of Rajasthanâ€, SpringerPlus, vol. 2, pp. 1-6, 2013.

Yao H, Song J, Liu C, Luo K, Han J, Li Y, Pang X, Xu H, Zhu Y, Chen PX, “Use of ITS2 Region as the Universal DNA Barcode for Plants and Animalsâ€, PLoS ONE, vol. 5, pp. 1-9, 2010.

Han J, Zhu Y, Chen X, Liao B, Yao H, Song J, Chen S, Meng F, “The Short ITS2 Sequence Serves as an Efficient Taxonomic Sequence Tag in Comparison with the Full-Length ITSâ€, BioMed Research International, vol. 13, pp. 1-7, 2013.

Osiru MO, Adipala E, Olanya OM, Kelly P, Lemaga B, Kapinga R, “Leaf Petiole and Stem Blight Disease of Sweet Potato Caused by Alternaria bataticola in Ugandaâ€, Plant Pathology Journal, vol. 7, pp. 118-119, 2008.

Shahin EA, Shepard JF, “An efficient technique for inducing profuse sporulation of Alternaria speciesâ€, Phytopathology, vol. 69, pp. 618-620, 1979.

Gonzalez-Mendoza D, Argumedo-Delira R, Morales-Trejo A, Pulido-Herrera A, Cervantes-Diaz L, Grimaldo-Juarez O, Alarcon A, “A rapid method for isolation of total DNA from pathogenic filamentous plant fungiâ€, Genetics and Molecular Research, vol. 9, pp. 162-166, 2010.

Nguluta M, Adebola P, Pillay M, “Genetic diversity analysis in South African taro (Colocasia esculenta) accessions using molecular tools, International Journal of Genetics and Molecular Biology (in press), 2016.

Rohlf FJ, “NTSYS-pc: Numerical taxonomy and multivariate analysis system, v. 2.0â€, United States of America, Setauket: Exeter Software, New York, 1998.

Gomes EA, Kasuya MCM, Barros EGD, Borges AC, Araújo EF, “Polymorphism in the internal transcribed spacer (ITS) of the ribosomal DNA of 26 isolates of ectomycorrhizal fungi†Genetics and Molecular Biology, vol. 25, pp. 477-483, 2002.

Konstantinova P, Bonants PJM, Van-Gent-Pelzer MPE, Van-Der-Zouwen P, Van-Den-Bulk R, “Development of specific primers for detection and identification of Alternaria spp. in carrot material by PCR and comparison with blotter and plating assaysâ€, Mycological Research, vol. 106, pp. 23-33, 2002.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, “MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods “, Molecular Biology and Evolution, vol. 28, pp. 2731-2739, 2011.

Tamura K, Nei M, “Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzeesâ€, Molecular Biology and Evolution, vol. 10, pp. 512-526, 1993.

Felsenstein J, “Confidence limits on phylogenies: An approach using the bootstrapâ€, Evolution, vol. 39, pp. 783-791, 1985.

Ding Y, Lawrence CE, “A statistical sampling algorithm for RNA secondary structure predictionâ€, Nucleic Acids Research, vol. 31, pp. 7280-7301, 2003.

David JC, “Alternaria bataticola. IMI Descriptions of Fungi and Bacteriaâ€, Mycopathologia, vol. 116, pp. 45-64, 1991.

Alajo A, “Distribution and characterization of sweetpotato Alternaria blight isolates in Ugandaâ€, Master Of Science Thesis, Kampala Makerere University, 2009.

Prasad SLM, Sujatha M, Chander Rao S, “Analysis of Cultural and Genetic Diversity in Alternaria helianthi and Determination of Pathogenic Variability Using Wild Helianthus Speciesâ€, Journal of Phytopathology, vol. 157, pp. 609-617, 2009.

Tiwari K, “Frequency Distribution and Assessment of Genetic Diversity of Novel Endophyte Alternaria alternata Accessions isolated from Pongamia pinnata L.â€, Pakistan Journal of Biological Sciences, vol. 16, pp. 1004-1009, 2013.

Kale SM, Pardeshi VC, Gurjar GS, Gupta VS, Gohokar RT, Ghorpade PB, Kadoo NY, “Inter - Simple Sequence Repeat Markers Reveal High Genetic Diversity among Alternaria alternata Isolates of Indian Originâ€, The Journal of Mycology and Plant Pathology, vol. 42, 2012.

Deng JX, Paul NC, Park MS, Yu SH, “Molecular characterization, morphology, and pathogenicity of Alternaria panax from araliaceous plants in Koreaâ€, Mycological Progress, vol. 12, pp. 383-396, 2013.

Valdés I, Rodríguez J, Jimenez P, “Alternaria species in the Bogotá plateau, Colombiaâ€, Phytopathology, 2013.

Tsuge T, Harimoto Y, Akimitsu K, Ohtani K, Kodama M, Akagi Y, Egusa M, Yamamoto M, Otani H, â€Host-selective toxins produced by the plant pathogenic fungus Alternaria alternateâ€, FEMS Microbiology Reviews, vol. 37, pp. 44-66, 2012.

Chowdappa P, Lakshmi MJ, Madhura S, “Matrix assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry for identification of plant pathogenic Alternaria speciesâ€, Phytoparasitica, vol. 41, pp. 169-179, 2013.

Laurie SM, “Sweetpotato cultivars. In Niederwieser, JG (Ed.) A guide to sweetpotato production in South Africa. ARC – Roodeplaat Vegetable and Ornamental Institute: CDP Printers, Pretoria, South Africa, 2004.

Kumar V, Haldar S, Pandey KK, Singh RP, Singh AK, Singh PC, “Cultural, morphological, pathogenic and molecular variability amongst tomato isolates of Alternaria solani in Indiaâ€, World Journal of Microbiology and Biotechnology, vol. 24, pp. 1003-1009, 2008.

Mello A, Napoli C, Murat C, Morin E, Marceddu G, Bonfante P, â€ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle groundsâ€, Mycologia, vol. 103, pp. 1184-1193, 2011.

Anginyah TJ, Narla RD, Carey EE, Njeru R, “Etiology, Effect of Soil pH and Sweetpotato Varietal Reaction to Alternaria Leaf Petoile and Stem Blight in Kenyaâ€, African Crop Science Journal, vol. 9, pp. 287-292, 2001.

Schultz J, Maisel S, Gerlach D, Muller T, Wolf M, “A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryotaâ€, RNA, vol. 11, pp. 361-364, 2005.

Landis FC, Gargas A, “Using ITS2 secondary structure to create species-specific oligonucleotide probes for fungiâ€, Mycologia, vol. 99, pp. 681-692, 2007.

Van Der Sande CA, Kwa M, Van Nues RW, Van Heerikhuzen H, Raue HA, Planta RJ, “Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNAâ€, Journal of Molecular Biology, vol. 223, pp. 899-910, 1992.

Cote CA, Peculis BA, “Role of the ITS2-proximal stem and evidence for indirect recognition of processing sites in pre-rRNA processing in yeastâ€, Nucleic Acids Research, vol. 29, pp. 2106-2116, 2001.

Majer D, Lewis BG, Mithen R, “Genetic variation among field isolates of

Pyrenopeziza brassicaeâ€, Plant Pathology, vol. 47, pp. 22-28, 1998.

Bock CH, Thralll PH, Burdon JJ, “Genetic structure of populations of Alternaria brassicicola suggests the occurrence of sexual recombinationâ€, Mycological Research, vol. 109, pp. 227-236, 2005.

Downloads

Published

2017-04-22

How to Cite

Chalwe, J., Adebola, P., & Pillay, M. (2017). Assessing the Genetic Diversity of <i>Alternaria Bataticola</i> in South Africa using Molecular Markers. Asian Journal of Applied Sciences, 5(2). https://doi.org/10.24203/ajas.v5i2.4367

Issue

Section

Articles