Development of a combined molecular diagnostic and DNA fingerprinting technique for rice bacteria pathogens in Africa

Abstract

A combined molecular diagnostic and DNA fingerprinting PCR technique for Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas oryzae pv. oryzicola (Xoc), Pseudomonas fuscovaginae (Pf) and Pseudomonas syringae pv. syringae (Pss) pathogens from rice has been developed in Africa by this study, using four primer pairs designed from Xoo (NC-007705.1), Xoc (NZ-AAQN01000001.1), Pf (AB021381.1) and Pss (NC-007005.1) complete genome sequence. Molecular PCR diagnostic showed that the presence of at least a band indicates positive detection of a bacterial pathogen and absence of a band indicates negative for no bacterial pathogen detected, while in the same PCR assay the presence of one or more band at different position revealed the DNA fingerprint of a bacterial pathogen. Out of 95 bacterial cultured isolates analyzed, 84 contained Xoo, 50 contained Xoc, 19 contained Pf and 16 contained Pss pathogens. DNA fingerprinting of the 84 Xoo pathogens revealed seven Xoo genotypes, four Xoc genotypes were identified from 50 Xoc pathogens and 19 Pf pathogens produced three Pf genotypes while 16 Pss pathogens formed three Pss genotypes. Development of a reliable molecular technique for Xoo, Xoc, Pf and Pss identification and differentiation is a prerequisite into understanding the genetics of Xoo, Xoc, Pf and Pss population structure in Africa and deployment of durable resistance cultivars. © 2010 Asian Network for Scientific Information.