Department of Plant Pathology

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Browsing Department of Plant Pathology by browse.metadata.advisor "Beed, Fen"

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    Diversity and detection of Kenyan and Nigerian populations of Fusarium oxysporum f. sp. strigae
    (Stellenbosch : Stellenbosch University, 2017-12) De Klerk, Madelein; Viljoen, Altus; Mostert, Diane; Beed, Fen; Stellenbosch University. Faculty of AgriSciences. Dept. of Plant Pathology.
    ENGLISH ABSTRACT: The Genus Striga contains some of the most destructive plant-parasitic weed species in the world. These include S. hermonthica and S. asiatica, which attack important staple food crops in sub-Saharan Africa such as maize, sorghum and millet. Of the two, S. hermonthica is more devastating and can cause yield losses on average of 50% and, ultimately, land abandonment. The parasite produces up to 200 000 seeds per plant, which causes a rapid build-up of a seed bank in the soil. Germination of seeds happens after a ripening period and when strigolactones, exuded by the roots of susceptible hosts, are detected. After a haustorium connects to the host, it parasitizes the host for water and nutrients, and in effect stunts the development of the host plant. Striga infestations are difficult to manage due to its prolific nature and late emergence. The weed affects subsistence farmers most severely, as these growers have little access to, or the financial resources available, to control the pest with chemicals. Biological control, therefore, was proposed as a means of control, as this method can be integrated with existing farming practises, as its use would be safe to both the farmer and the environment. Fusarium oxysporum f. sp. strigae (Fos), a soil-borne fungal pathogen affecting Striga plants, was identified as a possible Biological Control Agent (BCA), as Fos was host specific and did not produce harmful secondary metabolites. Its population structure in Africa, and means to survive and disseminate in farmer fields, however, was unknown. The aims of this study, therefore, were to characterize Fos populations in two African countries, Kenya and Nigeria, and to develop molecular markers to rapidly and accurately identify the fungus. The diversity of Fos in Kenya and Nigeria was investigated by means of vegetative compatibility group analysis (VCGs) and phylogenetic analysis. VCG analysis showed that the Kenyan isolates consisted of a single VCG, and that the Nigerian isolates were divided into seven VCGs and eight SMV’s. A combined maximum likelihood tree of the translocation elongation factor (TEF) 1α and mitochondrial small sub-unit (MtSSU) gene areas revealed that Fos isolates from the two countries separated into two different clades. This suggested that there was two separate events of evolution, and that the Nigerian isolate group is older than the Kenyan group due to the greater number of VCGs present in Nigeria. Mating type analysis confirmed clonality within the Kenyan group, where all isolates in VCG 04708 contained only the MAT1-1 gene. However, a larger diversity was found in the Nigerian group, where both mating type idiomorphs were present in the different VCGs. Molecular markers that distinguish between the two Fos populations in Africa have been developed in this study. Primer-set Foxy2-F/R1 was developed form a single nucleotide polymorphism (SNP) in the TEF gene area, and primer set FK3-F/R from SNPs in the secreted-in-xylem 14 gene area. Both primer sets were tested against a collection of isolates that includes non-pathogenic F. oxysporum isolated from Striga, other Fusarium species associated with Striga, and other formae speciales of F. oxysporum. Sensitivity assays revealed that the Foxy2 primer only detected target Fos DNA at a concentration of 10 ng/μl in the presence of S. asiatica DNA. Primer-set FK3 on the other hand, could detect target Fos DNA at the low concentration of 0.1 ng/μl in the presence of S. asiatica DNA. The findings in this study suggest that pathogenicity evolved at two separate events in Fos. The molecular markers designed could compliment the primer-set designed by Zimmerman et al. (2015) to aid in diagnostics and monitoring of Fos after application as a BCA.