Analysis of Xanthomonas oryzae pv. oryzicola population in Mali and Burkina Faso reveals a high level of genetic and pathogenic diversity

Abstract

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv.oryzicola was first reported in Africa in the 1980s. Recently, a substantialreemergence of this disease was observed in West Africa. Samples werecollected at various sites in five and three different rice-growing regionsof Burkina Faso and Mali, respectively. Sixty-seven X. oryzae pv.oryzicola strains were isolated from cultivated and wild rice varieties and from weeds showing BLS symptoms. X. oryzae pv. oryzicola strains were evaluated for virulence on rice and showed high variation in lesion length on a susceptible cultivar. X. oryzae pv. oryzicola strains were further characterized by multilocus sequence analysis (MLSA) using six house keeping genes. Inferred dendrograms clearly indicated different groups among X. oryzae pv. oryzicola strains. Restriction fragment length polymorphism analysis using the transcriptional activator like effectoravrXa7 as probe resulted in the identification of 18 haplotypes. Polymerasechain reaction-based analyses of two conserved type III effector(T3E) genes (xopAJ and xopW) differentiated the strains into distinctgroups, with xopAJ not detected in most African X. oryzae pv. oryzicolastrains. XopAJ functionality was confirmed by leaf infiltration on‘Kitaake’ rice Rxo1 lines. Sequence analysis of xopW revealed fourgroups among X. oryzae pv. oryzicola strains. Distribution of 43 T3E genes shows variation in a subset of X. oryzae pv. oryzicola strains.Together, our results show that African X. oryzae pv. oryzicola strains are diverse and rapidly evolving, with a group endemic to Africa and anothe rone that may have evolved from an Asian strain.