Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains
- Heinrich Heine University Düsseldorf, Germany
- Université Montpellier, France
- University of Missouri, United States
- Tanzania Agricultural Research Institute (TARI)-Uyole Centre, United Republic of Tanzania
- International Rice Research Institute, Kenya
- World Vegetable Center, Taiwan
Abstract
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.
Data availability
All data supporting the results are available in the main text or supplementary materials. All data that support the findings of this study were included in the manuscript; raw data are available at Dryad (https://doi.org/10.5061/dryad.xpnvx0kk3; Summary of raw data files deposited at dryad is provided in Source_data_overview deposited raw data @dryad). Sequencing data for strains from this study have been deposited in the NCBI Sequence Read Archive (SRA) database (Accession codes for iTz strains are provided in Supplementary File 2 - Tabs 1 and 2). Source data have deposited at Dryad. Materials will be made available under MTA.
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Raw DataDryad Digital Repository, doi:10.5061/dryad.xpnvx0kk3.
Article and author information
Author details
Funding
Bill and Melinda Gates Foundation (OPP1155704)
- Wolf B Frommer
Alexander von Humboldt-Stiftung (Professorship)
- Wolf B Frommer
Deutsche Forschungsgemeinschaft (EXC-2048/1 - project ID 390686111)
- Wolf B Frommer
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2023, Schepler-Luu et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains
eLife 12:e84864.
https://doi.org/10.7554/eLife.84864
Further reading
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- Microbiology and Infectious Disease
Influenza A virus transcribes viral mRNAs from the eight segmented viral genome when it infects. The kinetics of viral transcription, nuclear export of viral transcripts, and their potential variation between the eight segments are poorly characterised. Here, we introduce a statistical framework for estimating the nuclear export rate of each segment from a snapshot of in situ mRNA localisation. This exploits the cell-to-cell variation at a single time point observed by an imaging-based in situ transcriptome assay. Using our model, we revealed the variation in the mRNA nuclear export rate of the eight viral segments. Notably, the two influenza viral antigens hemagglutinin and neuraminidase were the slowest segments in the nuclear export, suggesting the possibility that influenza A virus uses the nuclear retention of viral transcripts to delay the expression of antigenic molecules. Our framework presented in this study can be widely used for investigating the nuclear retention of nascent transcripts produced in a transcription burst.
