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Rapid Discovery of Functional NLRs Using the Signature of High Expression, High-Throughput Transformation, and Large-Scale Phenotyping

47 Pages Posted: 15 May 2023 Publication Status: Review Complete

See all articles by Helen Jane Brabham

Helen Jane Brabham

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL)

Inmaculada Hernández-Pinzón

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL)

Chizu Yanagihara

Japan Tobacco Inc - Plant Innovation Center

Noriko Ishikawa

Japan Tobacco Inc - Plant Innovation Center

Toshiyuki Komori

Japan Tobacco Inc - Plant Innovation Center

Oadi N. Matny

University of Minnesota - St. Paul - Department of Plant Pathology

Amelia Hubbard

National Institute of Agricultural Botany (NIAB) - NIAB, Cambridge

Kamil Witek

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL)

Hironobu Numazawa

Japan Tobacco Inc - Plant Innovation Center

Phon Green

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL)

Antonín Dreiseitl

Agrotest Fyto Ltd. - Department of Integrated Plant Protection

Naoki Takemori

Japan Tobacco Inc - Plant Innovation Center

Toshihiko Komari

Japan Tobacco Inc - Plant Innovation Center

Roger P. Freedman

2Blades Foundation

Brian Steffenson

University of Minnesota - St. Paul - Department of Plant Pathology

H. Peter van Esse

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL)

Matthew James Moscou

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL)

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Abstract

Breeding crop species that are safe from pests and diseases is vital to build sustainable food systems crucial for food security. An effective and environmentally friendly method of disease control is to enhance the plant immune system by introducing functional resistance genes. A major class of plant immune receptors are nucleotide-binding, leucine-rich repeat receptors (NLRs), however identifying NLRs for use in elite crop varieties is time-consuming and resource-intensive. Through analyses of copy number variation and expression data, we identify high expression as an overlooked molecular signature of functional NLRs. Combining this signature with high-throughput crop transformation, we developed an approach that enables rapid identification and in planta validation of NLRs from non-domesticated germplasm. Screening 995 NLRs from 18 grass species identified 19 new resistance genes against wheat stem rust, a critical threat to wheat production. This pipeline facilitates rapid resistance gene discovery from diverse plant species to generate disease-resistant crops.

Keywords: plant disease, plant immunity, genetics, nucleotide binding, leucine rich repeat receptor, NLR, plant biotechnology, trait discovery, gene expression, copy number variation, crop improvement, wheat, wheat stem rust

Suggested Citation

Brabham, Helen Jane and Hernández-Pinzón, Inmaculada and Yanagihara, Chizu and Ishikawa, Noriko and Komori, Toshiyuki and Matny, Oadi N. and Hubbard, Amelia and Witek, Kamil and Numazawa, Hironobu and Green, Phon and Dreiseitl, Antonín and Takemori, Naoki and Komari, Toshihiko and Freedman, Roger P. and Steffenson, Brian and van Esse, H. Peter and Moscou, Matthew James, Rapid Discovery of Functional NLRs Using the Signature of High Expression, High-Throughput Transformation, and Large-Scale Phenotyping. Available at SSRN: https://ssrn.com/abstract=4446759 or http://dx.doi.org/10.2139/ssrn.4446759
This version of the paper has not been formally peer reviewed.

Helen Jane Brabham

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL) ( email )

Inmaculada Hernández-Pinzón

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL) ( email )

Chizu Yanagihara

Japan Tobacco Inc - Plant Innovation Center ( email )

Noriko Ishikawa

Japan Tobacco Inc - Plant Innovation Center ( email )

Toshiyuki Komori

Japan Tobacco Inc - Plant Innovation Center ( email )

Oadi N. Matny

University of Minnesota - St. Paul - Department of Plant Pathology ( email )

Amelia Hubbard

National Institute of Agricultural Botany (NIAB) - NIAB, Cambridge ( email )

Kamil Witek

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL) ( email )

Hironobu Numazawa

Japan Tobacco Inc - Plant Innovation Center ( email )

Phon Green

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL) ( email )

Antonín Dreiseitl

Agrotest Fyto Ltd. - Department of Integrated Plant Protection ( email )

Naoki Takemori

Japan Tobacco Inc - Plant Innovation Center ( email )

Toshihiko Komari

Japan Tobacco Inc - Plant Innovation Center ( email )

Roger P. Freedman

2Blades Foundation ( email )

Brian Steffenson

University of Minnesota - St. Paul - Department of Plant Pathology ( email )

H. Peter Van Esse

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL) ( email )

Matthew James Moscou (Contact Author)

University of East Anglia (UEA) - The Sainsbury Laboratory (TSL) ( email )

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