Genetic Analysis of the Bacterial Leaf Streak Pathogen Responsible for Severe Rice Infections in Senegal and Identification of Sources of Resistance

Abstract

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a major bacterial disease affecting rice, wheat, triticale and Brassica crops. It was recently confirmed in Senegal with high incidence in rice fields. However, the precise Xoc strains responsible for the recent outbreaks remains unknown, and the sources of resistance to the growing disease pressure have yet to be identified. In this study, we tested the pathogenicity of Xoc strains collected from a 2023 epidemic in Senegal on Senegalese rice varieties and on near isogenic lines (NILs) specifically developed for a sister pathovar, Xanthomonas oryzae pv. oryzae (Xoo). We identified both local varieties and NILs resistant to 80% of the strains. However, neither NILs nor local varieties were resistant to S52-4-4, suggesting a significant mutation in this particular strain that poses a serious threat to rice production in Senegal. Comparative genomic and phylogenetic analysis revealed a close evolutionary relationship between S52-4-4 and pathogenic strains BLS256 and CFBP2286 from the Philippines and Malaysia respectively. Moreover, the detection of an equivalent number of TAL effectors in both S52-4-4 and BLS256 provided further evidence that both strains have a shared common ancestry. These findings, together with the available genomic sequence and characterisation of S52-4-4 in this study are useful for studying Xoc populations in Senegal and other countries. Nonetheless, S52-4-4 adaptation to all local cultivars grown in Senegal requires a prompt management response.