Maina MwangiSteven RunoNuwamanya, Andrew2023-02-082023-02-082022http://ir-library.ku.ac.ke/handle/123456789/24702A Thesis Submitted in Partial Fulfilment of the Requirements for the Award of the Degree of Master of Science in Crop Protection (Plant Pathology Option) in the School of Agriculture and Environmental Sciences of Kenyatta University,October, 2022Early blight (EB) caused by Alternaria solani is ranked as one of the most important tomato diseases in Kenya and farmers predominantly rely on synthetic fungicides to control it. However, there have been reports about the declining efficacy of some fungicides against EB control. This study was carried out to (i) determine the occurrence, importance and current management practices for tomato EB in Kirinyaga, Kajiado and Kiambu counties, Kenya; (ii) characterize Alternaria solani tomato isolates from the selected counties by morphological features and sensitivity to two commonly used fungicide groups and (iii) determine occurrence and spatial distribution of resistance-associated mutations in A. solani isolates from the three counties. A baseline survey was carried out in 175 tomato fields in Kirinyaga (n=58), Kajiado (77) and Kiambu (40) counties, data was collected using semi-structured questionnaires and field observation. Tomato shoots showing typical EB symptoms were collected from surveyed fields (one per field) and carried to Kenyatta University Pathology Laboratory, where a total of 96 A. solani isolates were isolated. Results indicate that EB was highly prevalent (75-91%) in all regions and all farmers were controlling it by fungicide application. A total of 40 fungicide products, representing 20 active compounds, with varying resistance risk levels, were in use against EB. Most farmers (83%) were applying the fungicides at higher than the recommended doses. Most farmers (81%) reported declines in effectiveness of fungicides, especially strobilurins and triazoles. The Alternaria solani isolates were characterized based on cultural features, conidial morphology and sensitivity to two fungicides; azoxystrobin (a strobilurin) and difenoconazole (a triazole) in vitro by poisoned food technique. One way analysis of variance revealed that colony and conidial parameters of isolates did not differ significantly (at α=0.05) across the study counties. Isolates were considered resistant to the fungicide whenever their % Mycelial Growth Inhibition (%MGI) at manufacturer’s recommended dosage was below 50% and sensitive when above 50%. While all isolates were susceptible to Difenoconazole, majority of them (64%) were resistant to Azoxystrobin. Locations significantly differed in regard to sensitivity of isolates to fungicides with Kajiado and Kirinyaga isolates being least sensitive to Azoxystrobin and Difenoconazole, respectively. To determine the genetic basis of Azoxystrobin resistance, the cytochrome b gene (in all isolates) was PCR amplified, sequenced and analyzed for resistance-associated mutations at amino acid positions 129, 137 and 143. The F129L mutation was present in all Azoxystrobin resistant isolates plus 10 susceptible ones with MGI values close to the 50% threshold. Kajiado county had the highest percentage of mutated isolates (96.8%), followed by Kirinyaga (70%) and lastly Kiambu (40%). These findings indicate that Kenya’s A. solani populations have developed resistance to some fungicides by mutation. The study recommends that anti-fungicide resistance strategies should be applied, for more effective management of tomato early blight.enCharacterization and Fungicide SensitivityTomato IsolatesAlternaria Solani SorauerKajiadoKiambuKirinyagaKenyaThesis