Genomic structural variation in an alpha/beta hydrolase triggers hybrid necrosis in wheat

Yaoqi Si, Huaizhi Zhang, Shengwei Ma, Shusong Zheng, Jianqing Niu, Shuiquan Tian, Xuejia Cui, Keyu Zhu, Xiaocui Yan, Qiao Lu, Zhimeng Zhang, Tingting Du, Ping Lu, Yongxing Chen, Qiuhong Wu, Jingzhong Xie, Guanghao Guo, Mengjun Gu, Huilan Wu, Yiwen Li, Chengguo Yuan, Zaifeng Li, Zhiyong Liu (), Lingli Dong (), Hong-Qing Ling () and Miaomiao Li ()
Additional contact information
Yaoqi Si: Chinese Academy of Sciences
Huaizhi Zhang: Chinese Academy of Sciences
Shengwei Ma: Yazhouwan National Laboratory
Shusong Zheng: Chinese Academy of Sciences
Jianqing Niu: Yazhouwan National Laboratory
Shuiquan Tian: Chinese Academy of Sciences
Xuejia Cui: Chinese Academy of Sciences
Keyu Zhu: Chinese Academy of Sciences
Xiaocui Yan: Hebei Agricultural University
Qiao Lu: Chinese Academy of Sciences
Zhimeng Zhang: Chinese Academy of Sciences
Tingting Du: Chinese Academy of Sciences
Ping Lu: Chinese Academy of Sciences
Yongxing Chen: Xianghu Laboratory
Qiuhong Wu: Xianghu Laboratory
Jingzhong Xie: Chinese Academy of Sciences
Guanghao Guo: Chinese Academy of Sciences
Mengjun Gu: Shandong University
Huilan Wu: Chinese Academy of Sciences
Yiwen Li: Chinese Academy of Sciences
Chengguo Yuan: Hebei Gaoyi Stock Seed Farm
Zaifeng Li: Hebei Agricultural University
Zhiyong Liu: Chinese Academy of Sciences
Lingli Dong: Chinese Academy of Sciences
Hong-Qing Ling: Chinese Academy of Sciences
Miaomiao Li: Chinese Academy of Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Hybrid necrosis, a century-old mystery in wheat, is caused by complementary genes Ne1 and Ne2. Ne2, encoding a nucleotide-binding leucine-rich repeat (NLR) immune receptor, has been cloned, yet Ne1 remains elusive. Here, we report that Ne1, which encodes an alpha/beta hydrolase (ABH) protein generated by structural variation, triggers hybrid necrosis with Ne2 by activating autoimmune responses. We further verify that not only allelic variation but also copy number variation (CNV) of Ne1 are pivotal for hybrid necrosis diversity in wheat. Ne1 likely originates from wild emmer wheat, potentially through duplication and ectopic recombination events. Unlike Ne2, which is frequently selected for rust resistance in wheat breeding, the lower prevalence of Ne1 in modern wheat cultivars is attributed to its association with hybrid necrosis. Altogether, these findings illuminate the co-evolution of the NLR/ABH gene pair in plant development and innate immunity, offering potential benefits for wheat breeding.

Date: 2025
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DOI: 10.1038/s41467-025-57750-5

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