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

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