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 surprising continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and suppressing Xa1. Phylogenomics clustered these strains with Xoo strains 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 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. This strategy could help to protect global rice crops from BB pandemics.

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.

Virulence of Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial leaf blight of rice, depends on induction of host SWEET sucrose efflux transporters. It remained unknown whether secreted sucrose serves bacterial nutrition or host defense. Here we identified the sux sucrose uptake/utilization locus of Xoo and demonstrate that it is necessary and sufficient for sucrose acquisition. Induction of sux genes during infection closely tracked induction of rice SWEET11a. sux mutants were defective in swimming, swarming, extracellular polysaccharide (EPS) production and biofilm formation. EPS synthesis in mutants was restored by the quorum-sensing factor DSF. Notably, transcripts for rate limiting steps in DSF production were unaffected by sucrose, transcripts of the DSF receptor were sucrose-inducible and increased during infection, indicating sensitization to DSF in response to sucrose supply. Sucrose induced the sigma factors transcripts for RpoN1 and RpoN2 that regulate swimming, EPS and virulence. Furthermore, in contrast to Xanthomonas axonopodis pv. manihotis, virulence of Xoo depended critically on sux gene function. Together, pathogen-induced sucrose efflux from host cells likely induces bacterial sigma factors and sensitizes quorum signaling necessary for biofilm formation and colonization of the xylem, serves as energy source for swimming against the xylem stream, and as nutrient for growth.Lay AbstractIf we want to efficiently protect plants against infections, we need to understand the disease mechanisms. Bacterial leaf blight is a major scourge for rice production in Asia and Africa. We had found that disease-causing bacteria use a set of keys, so-called TAL effectors, to switch on sugar transporter genes in rice leaves causing sucrose to be released around the bacteria. A key question was whether the sugars act primarily in activation of host defense, or serve as nutrients and signals for bacterial infection. Here we provide evidence that both the ability to attack as well as the growth of bacteria depend on sucrose uptake. We unravel a regulatory network including transcriptional regulators, quorum sensing, swimming, biofilm production and virulence that all depend on sucrose uptake. These discoveries may prove to be crucial for the development of strategies for protecting rice against this disease.

Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (O. glaberrima), however, introgression into O. sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single knockout mutants show neither substantial growth defects nor symptoms indicative of programmed cell death, possibly reflecting functional redundancy of the isoforms regarding other important functions. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits.

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