Molecular characterization of Rhizoctonia Solani strains causing tomato (Lycopersicon Esculentum mill) damping-off and its management

Abstract

The objective of this study was to determine the genetic diversity among the Rhizoctonia solani strains causing damping off of tomato in Kenya and assess the efficacy of the disease control by nonchemical methods. Survey was conducted in the year 2002-2003 to determine the current status on the occurrence and distribution of Rhizoctonia damping- off and root rots of tomato in the 4 major tomato growing agro-ecological zones of Kenya. The genetic diversity of the damping off pathogens was evaluated from the 56 pathogenic Rhizoctonia solani isolates from infected tomato and rhizosphere soil using micro satellite technique. Efficacy of nonchemical control methods for damping off of tomato was evaluated by screening 7 tomato varieties grown in Kenya for resistance to the disease, assessment of antagonism between pathogenic R. solani and other soilborne pathogens on the disease control under greenhouse conditions, and field evaluation of the efficacy of various cultural practices on the disease management. The efficacy of the various cultural practices on the Rhizoctonia damping off of tomato control were compared with the conventional control methods such as chemical fumigation with Basamid and chemical seed treatment. The results of the survey indicated that the disease prevalence, incidence, severity and the number of pathogenic R. solani isolates recovered significantly (P:S0.05) varied with agroecological zones, season of production and the various crop production practices. The disease control was being hampered by lack of adequate information on causal agents, the disease epidemiological factors, and lack of cost-effective and sustainable control strategies. Laboratory isolation and characterization of soilborne fungal pathogens from infected plant and rhizosphere soil indicated that although R. solani was the most frequently isolated pathogen, other soilborne fungal pathogens such as Pythium, Fusarium and bacterial pathogens like Pseudomonas were also isolated. The various R. solani isolates differed on their morphological and cultural characteristics and pathogenicity on common tomato varieties. Molecular characterization of the 52 pathogenic Rhizoctonia solani isolates from the 4 agroecological zones using 7 micro satellite markers indicated a high genetic diversity among the Rhizoctonia solani causing damping off of tomato as indicated by high polymorphism, large number of alleles typed, high average heterozygosity, large variances of genetic distance and large number of molecular clusters generated. The deficiency of heterozygotes and lack of Hardy-weinberg equilibrium in 5 out of the 7 loci typed indicated a disquilibrium in group of populations from various agro-ecological zones implying low level of intermating within populations. However, the excess of average heterozygotes in the group of populations indicated high degree of gene flow between ecological zones probably due to efficient inoculum dispersal by run-offs and irrigation water. Evaluation of the efficacy of different management strategies in the control of Rhizoctonia damping off of tomato indicated that a potential exist for the disease control by microbial antagonism and cultural methods but not by use of resistant varieties. The efficacy of the disease control achieved by use of transplanting as opposed to direct seeding and raised beds + watering every 2 days compared favourably to the disease control by conventional strategies such as chemical fumigation with Basamid and chemical seed dressing with Gaucho 390 FS MT. The antagonism in causing Rhizoctonia damping off of tomato observed between pathogenic R. solani and nonpathogenic multinucleate R. solani and binucleate R. solani under greenhouse conditions implied a potential for the biocontrol of the disease by microbial antagonism. On the other hand, the positive synergism in causing Rhizoctonia damping off of tomato observed between pathogenic R. solani and pathogenic Pythium and Fusarium isolates implied the need to employ control measures that also suppresses Fusarium and Pythiuum for effective control of Rhizoctonia damping off of tomato. The high genetic diversity among R. solani isolates could have a bearing on their wide host range and virulence levels, all of which influence the efficacy of the disease control methods. Future research should aim at race typing of the different isolates to evaluate their virulence on different host cultivars and evaluate the response of each isolate to various control methods. The effective disease control by microbial antagonism and cultural methods demonstrated in this study will form part of a sustainable cost-effective disease control strategy especially for smallholder resource poor vegetable farmers in Kenya and be part of integrated pest management systems.