Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.

Bacteria were sampled, and genome sequences were determined by whole genome sequencing.

Plasmids were sequenced (.dna).

Xanthomonas oryzae pv. oryzae strains from Tanzania were sequenced. 

Virulence of bacteria was evaluated using Kauffman clipping assays and lesion length was determined with images and Excel files (.csv).

PCR and qPCR were used for genotyping.

.dna – A DNA file is a data file created by GSL Biotech SnapGene, a molecular biology analysis application. It stores a DNA sequence and includes metadata, such as the author, a description of the sequence, and comments.

.csv – Excel or similar.

.fasta – text-based format for representing nucleotide sequences.