J Integr Plant Biol

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  • 收稿日期:2025-05-28 接受日期:2025-09-02

Natural variation in GmMET, an S-adenosyl- l-methionine-dependent methyltransferase gene, influences seed protein content in soybean

Limin Hu1†, Chengyijun Guo1†, Minghao Sun1,2†, Chaoge Ning1, Siming Wei1, Hui Li1, Huilin Tian1, Chang Xu1, Shuanzhe Li1, Xue Han1, Xu Le1, Mingliang Yang1, Hongwei Jiang3, Hongmei Qiu3, Qingshan Chen1* and Zhaoming Qi1*   

  1. 1. National Key Laboratory of Smart Farm Technology and Systems, National Research Center of Soybean Engineering andTechnology, Northeast Agricultural University, Harbin 150030, China

    2. Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China

    3. Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Soybean Engineering Center, Changchun 130033, China

    †These authors contributed equally to this work.

    *Correspondences: Qingshan Chen (qshchen@126.com); Zhaoming Qi (qizhaoming1860@126.com, Dr. Qi is fully responsible for thedistribution of all materials associated with this article)

  • Received:2025-05-28 Accepted:2025-09-02
  • Supported by:
    This research was funded by the National Natural Science Foundation of China (32301785, 32472108, 32201755), the Hainan Seed Industry Laboratory and China National Seed Group (B23YQ1503), the National Key R&D Program of China (2021YFD1201103, 2023ZD0403201‐03), the Natural Science Foundation of Heilongjiang Province of China (LH2024C004),the Heilongjiang Postdoctoral Science Foundation (LBH‐Z23011), and the China Agriculture Research System (CARS‐04‐PS15).

Abstract: Soybean is one of the most economically important crops worldwide and a valuable source of protein for human consumption and animal feed. The use of wild soybean accessions as a source of new alleles for improvement of soybean quality remains challenging owing to linkage drag. Here, using segregating populations derived from a set of wild soybean chromosome segment substitution lines, we fine-mapped quantitative trait loci (QTLs) (qPC-06-1) for seed protein content to a 48.8-Kb interval on chromosome 6. A gene encoding an S-adenosyl- L-methionine-dependent methyltransferase (GmMET) was determined to be the causal gene underlying the qPC-06-1 locus. Three single-nucleotide polymorphism/insertion-deletion markers (SNPs/InDels) in the coding region were found to modulate the methyltransferase activity of different GmMET alleles, thereby influencing seed protein content. Transgenic and multi-omics analyses provided preliminary evidence for the pathways through which GmMET influences seed protein content and exerts pleiotropic effects on seed oil content, oil composition, and related traits. Additional analyses showed that an elite GmMET allele was under selection during soybean domestication and improvement and is now widespread in modern cultivars, particularly in southern China. Our findings thus reveal that a methyltransferase gene affects the protein content of soybean seeds, providing a foundation for the continued development of high-protein soybean cultivars.

Key words: chromosome segment substitution lines, methyl-transferase, seed protein content, soybean

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