Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains

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.

Automated summary

Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), poses a threat to global food security and the livelihood of small-scale rice producers. Despite robust global rice trade, Xoo strains from different regions show complete continental segregation. Unprecedented BB outbreaks were discovered in Tanzania, caused by Xoo strains carrying Asian-type TAL effectors and iTAL effectors, unlike endemic African Xoo strains. In order to protect African rice production from this emerging threat, a hybrid CRISPR-Cas9/Cpf1 system was developed to edit TALe-binding elements in SWEET promoters. The edited lines displayed broad-spectrum resistance against Asian and African Xoo strains.