Genome editing of an African elite rice variety confers resistance against endemic and emergingXanthomonas oryzaepv.oryzaestrains

Bacterial leaf blight (BB) of rice, caused byXanthomonas oryzaepv.oryzae(Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses ofXoocollections from Asia, Africa and the Americas demonstrated surprising continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemicXoo, carry Asian-type TAL effectors targeting the sucrose transporterSWEET11aand suppressingXa1. Phylogenomics clustered these strains withXoostrains from China. African rice varieties do not carry suitable resistance genes. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit six TALe-binding elements in threeSWEETpromoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains ofXoo, including strains recently discovered in Tanzania. This strategy could help to protect global rice crops from BB pandemics.