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

Abstract

Bacterial leaf blight (BB) of rice, caused by <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>), threatens global food security and the livelihood of small-scale rice producers. Analyses of <i>Xoo</i> 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 <i>Xoo</i>, carry Asian-type TAL effectors targeting the sucrose transporter <i>SWEET11a</i> and iTALes suppressing <i>Xa1</i>. Phylogenomics clustered these strains with <i>Xoo</i> 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 <i>SWEET</i> promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of <i>Xoo</i>, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.