SCREENING TOMATO AND PEPPER GERMPLASM FOR RESISTANCE TO BEGOMOVIRUSES AND ROOT KNOT NEMATODES

Abstract

Tomato and pepper are among the most popular vegetable crops grown worldwide, owing to their nutritive value and diversified uses. In the few areas along the coast region where tomato and pepper are grown, production constraints such as diseases, pests, high cost of inputs and unsuitable varieties pose a major threat to tomato and pepper production. Root knot nematodes and Begomoviruses are among the most devastating pathogens since they reduce overall crop yields. The aim of this thesis was to determine Begomoviruses incidence and severity based on a diagnostic baseline survey, molecular characterization of Begomoviruses infecting tomato and pepper and the identification of resistance of tomato and pepper varieties to root knot nematodes-Begomoviruses disease complex under both screen house and field conditions. Generally, 16 farmers’ fields in the four counties showed viral disease symptoms; 10 growing tomato and 6 growing pepper. Begomoviruses incidence was generally moderate, averaging 51.7% and 65.2 % for tomato and pepper, respectively; while severity was 3.3 and 2.9 for tomato and pepper respectively. Lamu and Kwale counties recorded the highest and lowest disease in both crops respectively. Sequence analysis based on pairwise alignment the DNA-A partial genome of Begomoviruses isolates from coastal region showed significant variability amongst themselves but also considerable differences with previously published tomato Begomoviruses sequences from East Africa and neighbouring Indian Ocean islands. All the tomato and pepper isolates were found to be relatives of Tomato leaf curl Virus (ToLCV) strains. Phylogenetic analyses formed three distinct clades with one clade compised of xvii members from a putative new species. Two tomato varieties (AVTO 1211 and Kilele) and three pepper varieties (P1201232, PBC 384 and PBC 495) were found to be resistant to begomoviruses and root knot nematodes under both screen house and field conditions. The study concluded that there is a big diversity of Begomoviruses in the tomato and pepper production systems in the coastal region of Kenya. Besides, specific virus strains prevalent in the farmers’ fields were determined. Two varieties of tomato and two varieties of pepper showed resistance to both root knot nematodes and Begomoviruses infection and will contribute to increased tomato and pepper production in the coastal region.