Natural variations in the promoter of OsSWEET13 and OsSWEET14 expand the range of resistance against Xanthomonas oryzae pv. oryzae

Abstract

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the major diseases that impact rice production in Asia. The bacteria use transcription activator-like effectors (TALEs) to hijack the host transcription machinery and activate key susceptibility (S) genes, specifically members of the SWEET sucrose uniporters through the recognition of effector-binding element (EBEs) in the promoter regions. However, natural variations in the EBEs that alter the binding affinity of TALEs usually prevent sufficient induction of SWEET genes, leading to resistance phenotypes. In this study, we identified candidate resistance alleles by mining a rice diversity panel for mutations in the promoter of OsSWEET13 and OsSWEET14, which are direct targets of three major TALEs PthXo2, PthXo3 and AvrXa7. We found natural variations at the EBE of both genes, which appeared to have emerged independently in at least three rice subspecies. For OsSWEET13, a 2-bp deletion at the 5th and 6th positions of the EBE, and a substitution at the 17th position appear to be sufficient to prevent activation by PthXo2. Similarly, a single nucleotide substitution at position 10 compromised the induction of OsSWEET14 by AvrXa7. These findings might increase our opportunities to reduce pathogen virulence by preventing the induction of SWEET transporters. Pyramiding variants along with other resistance genes may provide durable and broad-spectrum resistance to the disease.

Diagnostic kit for rice blight resistance

“…One A/G variant in the EBE for PthXo1 occurred at a frequency of 0.2% ( Supplementary Fig. 1 and Supplementary Table 2) 13,29 . Seven variations were found in the PthXo2 EBE at frequencies between 1.3% and 20.8% ( Supplementary Fig.…”

“…Seven variations were found in the PthXo2 EBE at frequencies between 1.3% and 20.8% ( Supplementary Fig. 2 and Supplementary Table 2) 29 . Notably, five variations were found at the TATA box of SWEET13 (TATATAAA, TATTTAAA, TATATATA, TATATAA and TATATAAAA), which overlap with the EBE.…”

“…In the PthXo3/AvrXa7 EBE, an insertion of one adenosine was found at a frequency of 7.7% ( Supplementary Fig. 3 and Supplementary Table 2) 29 . Lines CX371 and CX372 (or NERICA1 and NERICA2) carried a G/T variation in the TalC EBE and an 18-bp deletion spanning the PthXo3/AvrXa7 and TalF EBEs.…”

Resistance Genes and their Interactions with Bacterial Blight/Leaf Streak Pathogens (Xanthomonas oryzae) in Rice (Oryza sativa L.)—an Updated Review

“…The xa41 confers broad-spectrum resistance to 50% of the tested strains representing genetically distant groups isolated from different countries in Asia and Africa (Hutin et al 2015). In another study, in silico mining of OsSWEET13 and OsSWEET14 promoter polymorphisms in a diversity germplasm panel containing 3000 rice genome sequences and the Pakistani aromatic germplasm collection was conducted (Zaka et al 2018). Novel variations in the EBEs of OsSWEET13 and OsSWEET14 promoter regions were identified (Zaka et al 2018).…”

“…In another study, in silico mining of OsSWEET13 and OsSWEET14 promoter polymorphisms in a diversity germplasm panel containing 3000 rice genome sequences and the Pakistani aromatic germplasm collection was conducted (Zaka et al 2018). Novel variations in the EBEs of OsSWEET13 and OsSWEET14 promoter regions were identified (Zaka et al 2018).…”