Genome-assisted identification of wheat leaf rust resistance gene Lr.ace-4A/Lr30

Jinwei Yang, Hongna Li, Mengyu Li, Rui Song, Tao Shen, Guiping Wang, Dong Xu, Ming Hao, Aolin Jia, Shams ur Rehman, Lei Hua, Yanyan Liang, Cheng Chi, Caixia Lan, Xing Wang Deng, Jorge Dubcovsky, Baoxing Song (), Xiaodong Wang () and Shisheng Chen ()
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Jinwei Yang: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Hongna Li: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Mengyu Li: Hebei Agricultural University
Rui Song: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Tao Shen: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Guiping Wang: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Dong Xu: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Ming Hao: Sichuan Agricultural University
Aolin Jia: Henan Agricultural University
Shams ur Rehman: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Lei Hua: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Yanyan Liang: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Cheng Chi: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Caixia Lan: Huazhong Agricultural University
Xing Wang Deng: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Jorge Dubcovsky: University of California
Baoxing Song: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Xiaodong Wang: Hebei Agricultural University
Shisheng Chen: Shandong Laboratory of Advanced Agriculture Sciences in Weifang

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Leaf rust is a devastating disease of wheat. Growing rust-resistant wheat varieties is the best strategy to mitigate this threat. Here, we generate a 10.51-gigabase chromosome-scale assembly of the durum wheat landrace PI 192051. Using mutagenesis and transcriptome sequencing, we identify the leaf rust resistance gene Lr.ace-4A within a recombination-sparse region of PI 192051 and demonstrate that Lr.ace-4A is identical to the previously designated Lr30 gene in hexaploid wheat. Lr.ace-4A/Lr30 encodes a non-canonical coiled-coil nucleotide-binding leucine-rich repeat receptor, featuring tandem nucleotide-binding domains. This gene is both necessary and sufficient to confer resistance to leaf rust, as demonstrated by CRISPR/Cas9-induced mutations and transgenic complementation. Lr.ace-4A provides near-immunity resistance in durum wheat, though its effectiveness is diminished in hexaploid wheat. Two amino acid polymorphisms differentiate the resistant and susceptible Lr.ace-4A haplotypes, with transgenic plants carrying either susceptible variant showing susceptibility. The cloning of Lr.ace-4A will accelerate its deployment in wheat breeding programs.

Date: 2025
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DOI: 10.1038/s41467-025-64428-5

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