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DEVELOPMENT OF A MULTIPLEXED PRIME EDITING CONSTRUCT TO DISRUPT THE OsSWEET EFFECTOR BINDING ELEMENTS FOR ENHANCED BACTERIAL BLIGHT RESISTANCE IN RICE (Oryza sativa L.)
* 1 , 1 , 2
1  Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
2  Plant Breeding, Genetics, and Biochemistry Division, International Rice Research Institute, Los Baños, Laguna 4031, Philippines
Academic Editor: Rodomiro Ortiz

Abstract:

Rice (Oryza sativa L.) remains vulnerable to bacterial blight, a major yield-limiting disease caused by Xanthomonas oryzae pv. oryzae (Xoo). This pathogen delivers transcription activator-like effectors (TALEs) that bind to effector-binding elements (EBEs) in the promoters of host susceptibility (S) OsSWEET genes. Deletions were made to disrupt these EBEs. A multiplexed prime-editing construct was designed to target four critical EBEs with deletions: 13 bp for PthXo1 (OsSWEET11), 10 bp for PthXo2 (OsSWEET13), and two EBEs in OsSWEET14 (11 bp for TalC and 24 bp for the shared site of PthXo3/AvrXa7/TalF). The deletions were based on previously validated resistance alleles and optimized to expand TALE resistance. Engineered pegRNAs (epegRNAs) were designed based on previously validated edits and incorporated with new deletions to broaden effector resistance. Each pegRNA included a primer-binding site (PBS), a reverse transcription (RT) template, and a paired nicking guide RNA (ngRNA) for PE3-mediated editing. The epegRNA–ngRNA cassettes were individually cloned into entry vectors using Golden Gate assembly. Colony PCR confirmed insert sizes of 986 bp for pegRNA scaffolds, and 347 bp (PL25025), 351 bp (PL25026), 355 bp (PL25027), and 348 bp (PL25028) for assembled modules. Sanger sequencing validated 100% identity and error-free constructs. All four verified cassettes were assembled into a single binary transformation vector (PL25034) using Multi-site Gateway recombination. LR product confirmation via colony PCR showed the expected 1,580 bp amplicons. Restriction digestion of PL25034 using Mlu I produced five distinct bands at 7,617 bp, 5,870 bp, 3,006 bp, 1,140 bp, and ~750 bp, consistent with the expected number of fragments generated. The final construct was transformed into Escherichia coli TOP10, yielding over 1,000 colonies per plate. Positive clones were archived in 15% glycerol stocks for long-term storage. This study provides foundational groundwork for modular, multiplexed prime editing of OsSWEET EBEs, advancing efforts to develop broad-spectrum, bacterial blight-resistant rice through precise promoter editing.

Keywords: rice; prime editing; OsSWEET; bacterial blight; TALE; effector binding elements

 
 
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