Genome-Wide Identification and Comprehensive Analysis of Ubiquitin-Specific Protease Gene Family in Soybean ().

Deubiquitination plays a pivotal role in regulating plant responses to abiotic stress, growth, and development. Among the deubiquitinase (DUB) families, ubiquitin-specific proteases (UBPs) constitute the largest group. Despite this, limited research has been conducted on the functional characteristics of the gene family in soybean (). In this study, we identified 52 gene family members in soybean, all of which harbored UCH (ubiquitin C-terminal hydrolase) domains with short yet evolutionarily conserved Cys-box and His-box. These genes were phylogenetically classified into 14 distinct groups; genes within the same group shared analogous patterns of conserved domains and motifs. Moreover, a synteny analysis reveals that the family has undergone extensive gene duplication events and shares a close evolutionary relationship with . We conducted a focused analysis on , which is a gene exhibiting high expression levels in soybean seeds. Intriguingly, this gene exhibited several haplotypes in natural soybean varieties, with significant differences being observed in relation to seed traits, such as 100-seed weight, total fatty acid content, and protein content among different haplotypes. Collectively, the findings from this study provide a foundation for the functional characterization of genes, offering new insights into the regulatory network underlying seed development in soybean.