Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo),

secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR–Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.



Figure 1: Distribution of SWEET-inducing TALes in Xoo strains.

Heat map indicates presence (gray) or absence of TALes shown or predicted to bind to SWEET promoters in fully sequenced Xoo genomes. Origin is indicated. TALes were grouped by DisTAL (Supplementary Fig. 1). Six groups containing previously characterized SWEET-inducing TALes are shown. A parsimony tree (top) that is based on whole-genome SNPs obtained using kSNP is shown, highlighting the two main Xoo lineages: XooS (Asia) and XooF (Africa). Six sublineages were defined for XooS, and are indicated in bold blue letters (a–f). Seventy-three percent of branches had support values over 0.9 as determined by FastreeMP implemented in kSNP3.