Epidemiology and Molecular Identification of Bacterial Blight (Xanthomonas oryzae pv. oryzae) Strains in Lowland Rice Ecosystems of Uganda

African Journal of Agriculture | Vol. 13, No. 8, August 2026 | pp. 098–105

DOI: 10.46882/2026/AJA/000746

Article Type: Original Research Article

Title: Epidemiology and Molecular Identification of Bacterial Blight (Xanthomonas oryzae pv. oryzae) Strains in Lowland Rice Ecosystems of Uganda

Names of Authors: Godfrey M. Kasenge¹, Proscovia R. Namugga¹, Moses W. Kibwika²

Authors’ Affiliations: ¹National Agricultural Research Organisation (NARO), National Crops Resources Research Institute, Namulonge, Uganda; ²School of Agricultural Sciences, Makerere University, Kampala, Uganda

Abstract: Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is an escalating biotic threat to lowland rice (Oryza sativa L.) schemes in East Africa. Effective breeding initiatives require a systematic mapping of disease distribution and the molecular diversity of circulating bacterial strains. A diagnostic field survey was executed across 80 irrigated and rainfed lowland rice blocks in eastern and northern Uganda. Disease incidence and severity scores were gathered alongside 120 symptomatic leaf samples. Pathogens were isolated using nutrient agar media, verified via polymerase chain reaction (PCR) using Xoo-specific primers (TXT9A and TXT9B), and genotyped using repetitive sequence-based PCR (rep-PCR). The field survey revealed an average BLB incidence of 54.6%, with the highest severity recorded in the Doho Irrigation Scheme (score of 4.2 on a 1-to-9 scale). PCR amplification confirmed the presence of Xoo in 84.0% of the symptomatic samples. The rep-PCR cluster analysis grouped the isolated strains into three distinct genomic lineages (Lineage I, II, and III). Lineage I was dominant in eastern Uganda and displayed high virulence when inoculated back onto the susceptible local cultivar 'Komboka' under greenhouse conditions. The widespread distribution of highly virulent Xoo strains underscores the urgency of screening regional germplasm pools for durable resistance genes like Xa21.

Keywords: Xanthomonas oryzae, Polymerase chain reaction, Disease severity, Genetic lineage, Lowland rice, Virulence mapping

Manuscript Timeline: Received: May 20, 2026; Revised: June 26, 2026; Accepted: July 20, 2026; Published: August 30, 2026

Citation: Kasenge, G. M., Namugga, P. R., & Kibwika, M. W. (2026). Epidemiology and Molecular Identification of Bacterial Blight (Xanthomonas oryzae pv. oryzae) Strains in Lowland Rice Ecosystems of Uganda. African Journal of Agriculture, 13(8), 098–105. DOI: 10.46882/2026/AJA/000746

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