Distribution of Bacterial Leaf Streak (BLS) disease and genetic diversity of the causal pathogen xanthomonas oryzae pv. oryzicola in Uganda

Abstract

Bacterial leaf streak (BLS) disease is the third emerging rice production reported in many rice growing countries globally including Uganda in 2014. However, information on the extent of its spread and its pathogen, Xanthomonas oryzae pv oryzicola (Xoc) population structure in Uganda in lacking to guide decisions its management. This thesis sought to test the hypotheses that; bacterial leaf streak disease of rice is present in all the major rice growing districts of Uganda with varying levels of incidence and severity; that the population of Xanthomonas oryzae pv oryzicola (Xoc) causing bacterial leaf streak disease of rice in Uganda is genetically diverse; the Xoc variants are widely distributed in the different rice growing districts at varying levels; and Xoc variants in Uganda are genetically different from other known Xoc strains isolated from other countries and have high evolution frequencies. From the survey conducted in 15 rice-growing districts (May – October 2016), BLS disease was found in 11 of the 15 districts. Significant differences in disease incidence (P = 0.001) and severity (P = 0.0001) at 95% level of significance between the districts was observed. Highest BLS disease incidence of 47.2% was recorded in Bugiri, followed by Butaleja (36%). Bugiri district showed the highest mean BLS disease index score at 7.4, which significantly differed from those in the 11 other districts, except Butaleja, Rukungiri and Kanungu where the mean BLS disease index were not statistically different. Analysis of nucleotide sequences of gyrase sub unit B gene extracted from 53 Xoc isolates showed there is a genetic diversity within the population with mean inter population diversity 2.1478E008 ± -224.112 se) at P = 0.05. Three Xoc strains (UG_2, UG_3 and UG_4) have been identified in the country. The different Xoc strains have varying levels of distribution where UG_2 is present in all districts where BLS disease was present. UG_3 was found in six districts while UG_4 was isolated only in Nakaseke and Kayunga districts. An overalp of occurrence of the three strains within districts was observed with some districts having all the three strains while other districts had one or two of the three strains. Phylogenetic analysis showed that UG_2 is identical to 11 other Xoc variants previously isolated from six countries (Asia and Africa). UG_3 and UG_4 are unique Xoc variants that have never been isolated previously but have evolved much earlier than UG_2. Design of rice breeding approaches and management of BLS disease in Uganda should apply these facts. However, virulence characterization of Uganda’s Xoc strains coupled with gene pyramiding of effective R genes will contribute in the breeding for durable resistance against BLS disease in Uganda. In terms of hypotheses tested, the study concluded that BLS disease is present in most of the rice growing districts of Uganda with varying levels of incidences and severity between the districts; Uganda’s Xoc population is genetically diverse with three different strains, UG2, 3 and 4; the Xoc variants in Uganda are widely distributed in the different rice growing districts and some Ugandan Xoc strains are unique to Uganda.