DNA SeqUeNCINg ANAlySIS Of AfRICAN Xanthomonas oryzae pv. oryzae vIRUleNCe geNe (aXaVrg) DNA MARkeR

Global rice production is constrained by bacterial leaf blight (BLB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo). BLB disease incidence in West Africa was between 70–85% and yield loss in farmers’ fields was in the range of 50–90% from 2005 to 2010. In the present study, African Xoo virulence gene OPP-172000 DNA marker was identified and purified using randomly amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) products from 50 Xoo isolates. Genomic DNA of 50 Xoo isolates were analyzed using OPP-17 primer in RAPD-PCR during which African Xoo virulence gene OPP-172000 DNA marker was identified, purified, cloned, and sequenced. Cloning and DNA sequencing of African Xoo virulence gene OPP-172000 DNA generated a 1953 bp nucleotide sequence consequently tagged as AXaVrg-1953. BLAST homologous analysis of the AXaVrg-1953 sequence provides comprehensive identification of the type II secretion genes and secreted proteins, type III secretion genes and secreted proteins in African Xoo virulence gene. Phylogenetic unweighted pairgroup method arithmetic (UPGMA) analysis revealed the African AXaVrg-1953 sequence was distinct from the other Xoo virulence gene sequences from China, Japan, Korea, Germany, and the United States. This information is potentially useful for effective management of BLB disease in West Africa. Bacterial leaf blight, Operon primer, RAPD-PCR products, Xoo virulence gene DNA marker, cloning, Secreted proteins, BLAST, West Afric

Molecular Characterization and DNA Fingerprinting of Xanthomonas oryzae pv. oryzae Isolates from Climate Change Prone Areas in East Africa

Genomic DNA fingerprinting is a useful tool for effective and reliable identification and differentiation of Xanthomonas oryzae pv. oryzae (Xoo) pathogen from rice. The study aimed to conduct molecular characterization and DNA fingerprinting of 23 Xoo isolates from East Africa and two Xoo isolates from IRRI (Philippines) as control. PCR analysis was carryout on genomic DNA of 25 Xoo isolates using 6 Xoo specific primer pairs. Cluster analyses of genetic data obtained from 25 Xoo DNA fingerprints revealed two major genotypes (GrpA and GrpB) among the 25 Xoo isolates. GrpA has three subgroups (GrpA1; GrpA2; GrpA3) and GrpB (GrpB1; GrpB2; GrpB3). GrpA genotype consists of 20 Xoo isolates from Uganda, Rwanda and Philippines while GrpB genotype has 5 Xoo isolates from Rwanda. Some Xoo isolates were identical (PX-1, PX-2; UX621, RX2101; RX554, UX623, RX4113; UX211, UX213, UX214, RX4112, UX215). The emergence of subgroup genotypes could possibly be due to mutations and interactions among isolates and strains in host cells. Some Xoo isolates from Rwanda and Uganda were identical suggesting possible pathogen migration between these countries and long-term survival. Durable resistance rice cultivars would need to overcome both GrpA and GrpB Xoo genotypes in order to survive after their deployment into different rice ecologies in East Afric