INCIDENCE AND DIVERSITY AMONG COFFEE LEAF RUST PATHOGEN ISOLATES (Hemileia vastatrix) FROM DIFFFERENT COFFEE GROWING COUNTIES OF KENYA

Abstract

Coffee leaf rust (CLR) is a fungal disease caused by Hemileia vastatrix. The pathogen is constantly evolving leading to rapid break down in resistance of once resistant coffee varieties. The disease affects Arabica coffee causing premature leaf fall, yield loss hence economic losses. In Kenya, CLR is the second most important disease after Coffee Berry Disease causing losses of up to 10-40%. The study will provide additional knowledge about the pathogen variability and differentiation that will be used to investigate the pathogen evolution and to design strategies for developing new varieties. The objectives of the study were to evaluate the disease intensity, pathogenicity and genetic diversity of CLR pathogen from coffee growing counties of Kenya. Purposeful and directional sampling methods were used to select factories and farms for disease scoring. The factories were used as the entry points from which four farms were picked through directional sampling. In each county, 120 farm units were randomly sampled. A total of seventy mature leaves were picked randomly from the selected coffee tree for disease scoring. Samples for studying pathogenicity and genetic diversity were collected from single coffee trees. The leaf samples infected with CLR pathogen were inspected for any contamination with mycophagous arthropods using a microscope. The isolates were inoculated on coffee leaf disks from different coffee genotypes. Eskes scale of 1-5 was used to score the ability to infect. DNA was extracted from the CLR pathogen spores using Diniz protocol with minor modifications using Mixed AlkylTriMethylammonium bromide (MATAB). Genetic diversity was determined using RAPD primers. Data was analyzed using EXLSTAT software 2014. Analysis of variance indicated highly significant variation (P<0.0001) in disease intensity among coffee growing counties of Kenya. UM2 had the highest disease intensity across all coffee growing counties. Kisii County had the highest disease intensity while Trans Nzoia County had the lowest disease intensity. Analysis of variance further revealed highly significant variation (P<0.0001) in pathogenicity among isolates from coffee growing counties of Kenya. Isolate 8 from Meru County was the most pathogenic on all the coffee genotypes (Mean score of 2.961). Mundo Novo was the most susceptible coffee genotype on all the CLR pathogen isolates (mean score of 3.953). No isolate sporulated on Ruiru 11, Robusta and HDT. RAPD primers revealed high genetic diversity (58%) among CLR pathogen isolates from coffee growing counties of Kenya. The number of bands produced per primer ranged from 5-14. There was dissimilarity among isolates from the same county and isolates from across the counties. Primer X-16 showed high polymorphism in CLR isolates. There is a relationship between genetic diversity and pathogenicity of CLR pathogen since both vary depending on the coffee growing County. Racetyping should be done in order to ascertain the races present in this CLR pathogen isolates