Natural variation in histone demethylase GmLDL2 confers flowering time divergence for geographical expansion in soybean

Mengshi Liu, Yuan Fang, Jiacan Jiang, Huaizhen Chen, Bing Yang, Xiaomin Xu, Guoqiang Liu, Chen Ling, Zhicheng Dong, Cunyi Yang () and Yingxiang Wang ()
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Mengshi Liu: Guangzhou
Yuan Fang: Guangzhou
Jiacan Jiang: Guangzhou
Huaizhen Chen: Guangzhou
Bing Yang: Guangzhou
Xiaomin Xu: Guangzhou
Guoqiang Liu: Guangzhou
Chen Ling: Guangzhou
Zhicheng Dong: Guangzhou University
Cunyi Yang: Guangzhou
Yingxiang Wang: Guangzhou

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

Abstract: Abstract Flowering at the appropriate time is one of the critical traits to determine regional adaptation and yield of soybeans. Although several genes in regulating flowering time have been identified in soybeans, the epigenetic regulators are still largely unknown. Here, we identify an early flowering mutant (ef1) and clone the causal gene as lysine-specific demethylase like 2 (GmLDL2). Enzymatic activity assay shows that GmLDL2 has demethylase activity towards H3K4me1 and H3K4me2. Integrative ChIP-seq and RNA-seq analyses demonstrate that GmLDL2 directly inhibits the expression of GmFER, an ortholog of Arabidopsis FERONIA. Genetic analysis reveals that GmLDL2 regulates soybean flowering in a GmFER-dependent manner. Interestingly, both GmLDL2H1 and GmLDL2H2 haploids display distinct demethylase activity and likely facilitate the adaptation of soybeans to low- and high-latitude regions, respectively. Together, our findings reveal the GmLDL2-GmFER module in regulating soybean flowering and provide useful information for manipulating the regional adaptability of soybeans.

Date: 2025
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DOI: 10.1038/s41467-025-61328-6

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