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ARS Home » Midwest Area » St. Paul, Minnesota » Cereal Disease Lab » Research » Publications at this Location » Publication #415762
Research Project: Surveillance, Pathogen Biology, and Host Resistance of Cereal Rusts

Location: Cereal Disease Lab

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

Author
item BRABHAM, HELEN - Sainsbury Laboratory
item HERNANDEZ-PINZON, INMACULADA - Sainsbury Laboratory
item YANAGIHARA, CHIZU - Kaneka Corporation
item ISHIKAWA, NORIKO - Kaneka Corporation
item KOMORI, TOSHIYUKI - Kaneka Corporation
item MATNY, OADI - University Of Minnesota
item HUBBARD, AMELIA - National Institute Of Agricultural Botany (NIAB)
item WITEK, KAMIL - Sainsbury Laboratory
item NUMAZAWA, HIRONOBU - Japan Tobacco International
item GREEN, PHON - Sainsbury Laboratory
item DREISEITL, ANTONÍN - Agrotest Fryo Ltd
item TAKEMORI, NOAKI - Sainsbury Laboratory
item KOMARI, TOSHIHIKO - Kaneka Corporation
item FREEDMAN, ROGER - The Gatsby Charitable Foundation
item STEFFENSON, BRIAN - University Of Minnesota
item VAN ESSE, PETER - Sainsbury Laboratory
item Moscou, Matthew

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 7/26/2024
Publication Date: 7/26/2024
Citation: Brabham, H.J., Hernandez-Pinzon, I., Yanagihara, C., Ishikawa, N., Komori, T., Matny, O.N., Hubbard, A., Witek, K., Numazawa, H., Green, P., Dreiseitl, A., Takemori, N., Komari, T., Freedman, R.P., Steffenson, B., Van Esse, P., Moscou, M.J. 2024. Discovery of functional NLRs using high expression level, high-throughput transformation, and large-scale phenotyping. bioRxiv. https://doi.org/10.1101/2024.06.25.599845.
DOI: https://doi.org/10.1101/2024.06.25.599845

Interpretive Summary: In agriculture, integrated disease/pest management is built on three pillars: (1) agricultural practice (i.e. crop rotation, planting density, mixed cropping), (2) chemical control (e.g. pesticides and fungicides), and (3) genetic resistance. The use of genetic resistance requires that plant breeders continuously integrate diverse sources of resistance, as plant pathogens can break resistance in the plants. The process of identifying new disease resistance genes typically involves screening diverse domesticated or wild species, generating crosses with elite crop accessions, identifying the location of resistance in the genome, and lastly, breeding this resistance into elite accessions. To accelerate this pipeline, we leveraged a high-throughput transformation system with a signature of functional resistance genes. Using this approach, we have mined resistance genes from 69 accessions belonging to 18 Pooideae species and identified 19 stem rust resistance genes.

Technical Abstract: Breeding crop species that are protected from pests and diseases is vital to achieving the sustainable agricultural systems needed for food security. Introducing functional resistance genes to enhance the plant immune system is an effective method of disease control, but identifying new immune receptors is time-consuming and resource intensive. We observed that functional immune receptors of the NLR class show an unexpected signature of high expression in uninfected plants across both monocot and dicot species. Here we show that this signature, combined with high throughput crop transformation, can be used to rapidly identify candidate functional NLRs from diverse wild plant species and validate pathogen resistance directly in crop plants. As a proof of concept, we generated a wheat transgenic library carrying 995 NLRs from 18 grass species. Screening the collection with the stem rust pathogen Puccinia graminis, which is a major threat to wheat production, we confirm 19 new resistance genes. This pipeline facilitates resistance gene discovery, unlocking a large gene pool of diverse and non-domesticated plant species and providing in-planta gene validation of disease resistance directly in crops.