Natural variation in <i>GmMET</i> , an <i>S</i> ‐adenosyl‐L‐methionine‐dependent methyltransferase gene, influences seed protein content in soybean

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.