Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains

Author:

Schepler-Luu Van12ORCID,Sciallano Coline3ORCID,Stiebner Melissa1ORCID,Ji Chonghui4,Boulard Gabriel3,Diallo Amadou3,Auguy Florence3,Char Si Nian4ORCID,Arra Yugander1ORCID,Schenstnyi Kyrylo1ORCID,Buchholzer Marcel1ORCID,Loo Eliza PI1ORCID,Bilaro Atugonza L5,Lihepanyama David5,Mkuya Mohammed6,Murori Rosemary7,Oliva Ricardo2,Cunnac Sebastien3,Yang Bing48ORCID,Szurek Boris3ORCID,Frommer Wolf B19ORCID

Affiliation:

1. Institute for Molecular Physiology, Heinrich Heine University Düsseldorf

2. International Rice Research Institute

3. Plant Health Institute of Montpellier (PHIM), Université Montpellier, IRD, CIRAD, INRAE, Institut Agro

4. Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri

5. Tanzania Agricultural Research Institute (TARI)-Uyole Centre

6. International Rice Research Institute, Eastern and Southern Africa Region

7. International Rice Research Institute (IRRI), Africa Regional Office

8. Donald Danforth Plant Science Center

9. Institute for Transformative Biomolecules, ITbM, Nagoya University

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.

Funder

Bill and Melinda Gates Foundation

Alexander von Humboldt-Stiftung

Deutsche Forschungsgemeinschaft

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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