Emergence of Bacterial Leaf Blight of Rice in Madagascar: A Recent Introduction from Asia

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight (BLB), a major rice disease causing up to 70% yield loss in Asia and West Africa. First described in Japan in 1884 and later reported in West Africa in the 1970s, BLB recently emerged in East Africa, with an epidemic reported in Tanzania in 2019. Remarkably, the disease was detected for the first time in Madagascar the same year, representing a serious threat to food security. To investigate the origin of BLB in Madagascar, we isolated 73 Xoo strains from symptomatic rice leaves collected between 2019 and 2023. MLVA genotyping revealed 19 haplotypes forming a single clonal complex, indicating low diversity and a likely recent introduction. In order to come up with disease control strategies, IRBB-based race-typing was achieved and identified four resistance genes (Xa8, xa13, Xa21, Xa23) that confer resistance to all Malagasy strains tested, while the 19 Malagasy varieties assessed were susceptible. The analysis of SWEET knock-out lines confirmed that Malagasy strains rely on the susceptibility gene OsSWEET11 for full virulence. Whole-genome sequencing and TALEs repertoire analyses of two strains allowed the identification of a PthXo1 ortholog predicted to induce OsSWEET11. SNP-based phylogenetic analyses clustered Malagasy strains within Asian lineages, most closely related to strains originated from India. Malagasy strains did not cluster with recently reported Tanzanian Xoo, suggesting independent introductions. Overall, our study demonstrates that BLB in Madagascar results from a recent and single introduction from Asia and identifies effective resistance genes for deployment.