LAUSR

Background Xanthomonas oryzae ( Xo ) is one of the important pathogenic bacterial groups affecting rice production. Its pathovars Xanthomonas oryzae pv. oryzae ( Xoo ) and Xanthomonas oryzae pv. oryzicola ( Xoc ) cause bacterial blight and bacterial leaf streak in rice, respectively. Xo infects host plants by relying mainly on its transcription activator-like effectors (TALEs) that bind to host DNA targets, named effector binding elements (EBEs), and induce the expression of downstream major susceptibility genes. Blocking TALE binding to EBE could increase rice resistance to the corresponding Xo . Findings We used CRISPR/Cas9 to edit the EBEs of three major susceptibility genes ( OsSWEET11 , OsSWEET14 and OsSULTR3;6 ) in the rice varieties Guihong 1 and Zhonghua 11. Both varieties have a natural one-base mutation in the EBE of another major susceptibility gene ( OsSWEET13 ) which is not induced by the corresponding TALE. Two rice lines GT0105 (from Guihong 1) and ZT0918 (from Zhonghua 11) with target mutations and transgene-free were obtained and showed significantly enhanced resistance to the tested strains of Xoo and Xoc . Furthermore, under simulated field conditions, the morphology and other agronomic traits of GT0105 and ZT0918 were basically the same as those of the wild types. Conclusions In this study, we first reported that the engineering rice lines obtained by editing the promoters of susceptibility genes are resistant to Xoo and Xoc , and their original agronomic traits are not affected.