Reaction of Rice Blast Pyricularia oryzae CAV. isolates on a set of improved rice varieties in Western Kenya indicator to presence of pathogenic strains

Rice (Oryza sativa L.) remains the most favoured grain for human consumption in the world. The yields in Kenya and many African countries are below the world averages. Rice blast disease has been registered as a major cause for reducing yields. Resistance which is a major control measure for blast has been found elusive as a result of variability over the years. Tackling the disease requires insight into the causative agent. The main objective of this work was to identify biological and molecular characteristics of the blast pathogen (Pyricularia oryzae Cav) and compare their relation with virulence on selected popular rice varieties at Kibos research centre Kisumu Kenya. Diseased leaf samples were collected from all rice growing areas of Kenyan Counties. The samples were used to develop cultures from which pathogen characterization was done. DNA extracted from the cultures was used for PCR amplification. Fingerprints were utilized to determine the diversity of Pyricularia oryzae Cav. Isolates. Rep-PCR analysis was done by using two primer sequences ITS1 and ITS4 from ITS regions. The ITS region sequence reads from the sequencer were edited by Chromas Lite and sequences generated using BioEdit version ver. 7. Selected Kenyan varieties were screened for resistance to the disease using inoculum from eight isolates that showed morphological differences. Data analysis was by ANOVA using the general linear model (GLM) of the SAS system for windows. Studies on morphological character of the eight different isolates of P. oryzae revealed variation with respect to colony color, diameter, and morphology. Conidia shape, length and septations. Isolates were classified into three groups based on virulence viz. severely pathogenic PG-I, rating between 2-1.1, highly virulent to moderately virulent PG-II, rating 1.2-1.3 and low virulent PG-III, rating < 0.9, mildly pathogenic. The culture strains that were sequenced clustered into four haplo groups (HGs), that is HG1 for isolate 4, HG2 for isolate 6, HG3 for isolate 7a and HG4 for isolate 7b. The new isolates’ sequences were submitted to the NCBI GenBank database and the accession numbers assigned as, Pyricularia oryzae KY275366, Pyricularia oryzae KY275367 and Pyricularia oryzae KY275368. The result of the present study demonstrates that there is a certain level of genetic diversity among isolates of P. oryzae from various regions of Kenya. Virulence tests revealed that these isolates expressed different level of virulence. Groups PGI, Isolates 1,6 and 7 the highly virulent types produced a characteristic deep yellow metabolite, the least virulent PGIII isolates 8 and 4 had no visible yellow metabolite. A characteristic oily metabolite was noticed on isolate 5 which ranged in the PG II Group. The general heterogeneity was confirmed in the country shown by the genetic variability among isolates thus a recommendation for further studies using second generation analysis which may reveal presence of new strains. A study into Gene silencing may help deal with secondary metabolites in the effort to tackle disease virulence. Gene silencing technology has proven to be an effective tool for next generation of plant genomics.