Discovery of functional NLRs using expression level, high-throughput transformation and large-scale phenotyping

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Brabham, Helen J., Hernández-Pinzón, Inmaculada, Yanagihara, Chizu, Ishikawa, Noriko, Komori, Toshiyuki, Matny, Oadi N., Hubbard, Amelia, Witek, Kamil, Feist, Alexis, Numazawa, Hironobu, Green, Phon, Dreiseitl, Antonín, Takemori, Naoki, Komari, Toshihiko, Freedman, Roger P., Steffenson, Brian, van Esse, H. Peter and Moscou, Matthew J. (2025) Discovery of functional NLRs using expression level, high-throughput transformation and large-scale phenotyping. Nature Plants, 11 (10). pp. 2100-2114. ISSN 2055-026X

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Abstract

Protecting crops from diseases is vital for the sustainable agricultural systems that are needed for food security. Introducing functional resistance genes to enhance the plant immune system is highly effective for disease resistance, but identifying new immune receptors is resource intensive. We observed that functional immune receptors of the nucleotide-binding domain leucine-rich repeat (NLR) class show a signature of high expression in uninfected plants across both monocot and dicot species. Here, by exploiting this signature combined with high-throughput transformation, we generated a wheat transgenic array of 995 NLRs from diverse grass species to identify new resistance genes for wheat. Confirming this proof of concept, we identified new resistance genes against the stem rust pathogen Puccinia graminis f. sp. tritici and the leaf rust pathogen Puccinia triticina, both major threats to wheat production. This pipeline facilitates the rapid identification of candidate NLRs and provides in planta gene validation of resistance. The accelerated discovery of new NLRs from a large gene pool of diverse and non-domesticated plant species will enhance the development of disease-resistant crops.

Item Type: Article
Additional Information: Data availability: The whole-genome sequencing data from barley accessions CI 16147 and CI 16153 have been deposited in NCBI under BioProject PRJNA952654. The RNA-seq data for Arabidopsis thaliana, tomato and diverse Pooideae species have been deposited in NCBI under BioProjects PRJNA928100, PRJNA927036 and PRJNA913397, respectively. The GenBank identifiers for the transformation construct sequence for Mla7 under the Mla6 promoter/terminator and the native sequence are MZ555770 and OQ859100, respectively. The databases used for protein domain analysis include Pfam, Superfamily and ProSite. The raw data and uncropped images are available via figshare at https://doi.org/10.6084/m9.figshare.28680800.v1. Code availability: The scripts used for data analysis and figure preparation are available via figshare at https://doi.org/10.6084/m9.figshare.28680800.v1.
Faculty \ School: Faculty of Science > The Sainsbury Laboratory
Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 14 Nov 2025 14:30
Last Modified: 14 Nov 2025 20:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/100979
DOI: 10.1038/s41477-025-02110-w

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