A natural allelic variant of GmSW17.1 confers high 100-seed weight in soybean

Soybean (Glycine max) is an important and valuable crop, providing oil and proteins for both humans and animals. Seed weight is a key trait that determines soybean yields; however, the genes and mechanisms controlling seed weight remain poorly understood. Here, we used genome-wide association study (GWAS) and joint linkage mapping to identify a ubiquitin-specific protease, GmSW17.1, which regulates 100-seed weight in soybean. Two natural allelic variants of GmSW17.1 resulted in significantly different 100-seed weight, with GmSW17.1^T conferring heavier seeds. We used CRISPR/Cas9 technology to knock out GmSW17.1, resulting in lighter and smaller seeds; however, these mutants produced more seeds than the wild type, resulting in similar overall yields. Owing to the increased number of seeds, we determined that GmSW17.1 is highly transcribed in developing seeds, and its encoded protein physically interacts in the nucleus with GmSGF11, which plays a crucial role in the deubiquitinating pathway. Analysis of genomic sequences from more than 1714 soybean accessions suggested that the natural allele GmSW17.1^T was selected during the domestication and genetic improvement, resulting in its rapid expansion in cultivated soybean. These findings provide important insights into the role of GmSW17.1 in 100-seed weight and offer valuable clues for the molecular breeding of soybean.