GENETIC LOCI FOR RESISTANCE TO BLAST (Pyricularia oryzae) POPULATIONS IN IRRIGATED RICE IN KENYA

Abstract

Rice (Oryza sativa) is the third most important food crop after maize and wheat in Kenya. Blast (Pyricularia oryzae) is one of the most destructive and widespread diseases of rice in Kenya but minimal research attention have been given to this disease. Differential lines and recombinant inbred lines (RILs) were grown under irrigation in Mwea, West Kano and Gamba to characterize virulence spectrum of blast populations; identify resistance genes and quantitative trait loci (QTL) that confer adaptability to the local agricultural conditions. RILs were genotyped using single nucleotide polymorphisms (SNP) markers. Virulence spectrum of blast populations in irrigated ecosystems in Kenya varied significantly within and across the locations. West Kano had 68.63% of rice differential lines susceptible to blast population, followed by 49.02% in Mwea and 40.02% in Gamba. Some rice differential lines carrying the same genes from different donors showed different reaction to blast population, suggesting that background effects of the donor varieties had a role in the susceptibility as well as resistance of the lines. Environment had a significant effect on the expression of genes. Further, some rice differential lines in different genetic background showed varied response to blast population at each location and across the locations. Lines with Pik-s, Pik-p, Pik-h, Piz-5, Piz, Pit, Pish Pi1, Pi5 (t), Pi12 (t), Pik-m, Pita-2, Pib and Pik were resistant to blast population. IRBLzt-IR56 [CO] carrying Piz-t gene showed resistance to blast across the locations. Reaction of RILs to blast differed significantly within and across the locations. Linkage map was constructed with 2416 polymorphic SNP markers and QTL declared at logarithm of odds (LOD) score of 3.0. Genetic map had a total distance of 1526.8 cM with an average distance of 0.63 cM between adjacent markers, and covered 95.48% (364.73 cM) of the rice genome. Eighteen QTL on on chromosomes 1, 2, 3, 4, 5, 6, 8, 9 and 11 with variable effects co-segregated with blast resistance. Most QTL mapped to the genomic regions where blast resistance genes have been observed, suggesting that QTL in this study may be identical or allelic to the specific resistance genes described previously. Eight QTL namely; qrbr-1-4, qrbr-4-1, qrbr-4-2, qrbr-4-3, qrbr-4-4, qrbr-5, qrbr-8-2 and qrbr-9-2 mapped to QTL for agronomic traits and bacterial blight and sheath blight. Such corresponding locations suggest that some of the genes underlying QTL are commonly involved in the defense response against pathogens and may be linked to other traits of agricultural value. Most promising R genes and QTL observed in this study would be introgressed into preferred yet susceptible rice varieties in Kenya. Characterization of R gene(s) in BW196 and QTL that confer resistance to multiple diseases and agronomic traits is required for inclusion in breeding programs