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

## TL;DR

This study identifies 52 UBP genes in soybean and explores their role in seed development and traits like weight and nutrient content.

## Contribution

The first comprehensive analysis of the UBP gene family in soybean, revealing their evolutionary patterns and functional diversity.

## Key findings

- 52 UBP genes were identified in soybean, grouped into 14 phylogenetic clusters with conserved domains.
- GmUBP7 shows significant haplotype variation linked to seed weight, fatty acid, and protein content in natural soybean varieties.
- Gene duplication and synteny suggest a close evolutionary relationship between soybean and Arabidopsis UBP genes.

## Abstract

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 UBP gene family in soybean (Glycine max). In this study, we identified 52 UBP 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; GmUBP genes within the same group shared analogous patterns of conserved domains and motifs. Moreover, a synteny analysis reveals that the GmUBP family has undergone extensive gene duplication events and shares a close evolutionary relationship with Arabidopsis thaliana. We conducted a focused analysis on GmUBP7, 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 GmUBP genes, offering new insights into the regulatory network underlying seed development in soybean.