Analysis wheat wild relatives Thinopyrum intermedium and Roegneria kamoji genomes reveal different polyploid evolution paths

Silong Sun (), Naixiu Che, Liyang Chen, Yongchao Hao, Yongchang Xu, Qingyang Chen, Wenyang Ge, Shuangshuang Qin, Wenxiu Zhang, Chunmei Dong, Jianqiang Li, Yuxin Liu, Fangfang Yan, Long Han, Zhangwei Liu, Liang Zhang, Chengzhi Jiang, Zujun Yang, Hongwei Wang () and Lingrang Kong ()
Additional contact information
Silong Sun: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Naixiu Che: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Liyang Chen: Smartgenomics Technology Institute
Yongchao Hao: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Yongchang Xu: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Qingyang Chen: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Wenyang Ge: Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy
Shuangshuang Qin: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Wenxiu Zhang: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Chunmei Dong: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Jianqiang Li: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Yuxin Liu: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Fangfang Yan: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Long Han: Tai’an Academy of Agricultural Sciences
Zhangwei Liu: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Liang Zhang: Shandong Agricultural University, College of Information Science and Engineering
Chengzhi Jiang: University of Electronic Science and Technology of China, Center for Informational Biology, School of Life Science and Technology
Zujun Yang: University of Electronic Science and Technology of China, Center for Informational Biology, School of Life Science and Technology
Hongwei Wang: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy
Lingrang Kong: Shandong Agricultural University, State Key Laboratory of Wheat Improvement, College of Agronomy

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Many wild relatives of wheat in the Triticeae tribe provide important genetic resources for crop improvement, but their complex, polyploid genomes shaped by hybridization remain poorly understood. Here, we assemble and analyze the genomes of Thinopyrum intermedium and Roegneria kamoji, two species commonly used in wheat hybridization. We show that Th. intermedium contains genomic contributions from Pseudoroegneria (St), Dasypyrum (V), and Aegilops (J), while R. kamoji contains subgenomes related to Pseudoroegneria (St), Dasypyrum (V-related “Y”), and Hordeum (H). Phylogenomic evidence indicates that both species underwent independent polyploidization events, with Pseudoroegneria serving as the original maternal donor. R. kamoji likely evolved from tetraploid Roegneria. We also identify two Fhb7 homologs in the St and H subgenomes of R. kamoji that enhance Fusarium head blight resistance in a dosage-dependent manner. These findings refine the understanding of Triticeae polyploid evolution and offer valuable genomic resources for wheat improvement and forage breeding.

Date: 2025
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DOI: 10.1038/s41467-025-63007-y

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