Global identification and characterization of soybean TPR genes with expression analysis under photoperiod variations

TOPLESS/TOPLESS-RELATED (TPR) proteins are conserved transcriptional co-repressors vital for plant growth and development. However, the functions of soybean TPR (GmTPR) gene family members and their roles in photoperiod responses remain largely unexplored. In this study, we identified 12 TPR genes in the soybean genome, distributed across 11 chromosomes. Phylogenetic analysis classified GmTPRs into three subfamilies (Class I-III) by comparing them with Arabidopsis TPR proteins. Collinearity analysis revealed that 6 GmTPR genes are collinear with 3 AtTPR genes, resulting in 10 pairs of collinear genes, with no tandem duplications found. Analysis of physicochemical properties, motif composition, and gene structure indicated significant differences among GmTPR members. Subcellular localization confirmed that GmTPRs predominantly reside in the nucleus, suggesting regulatory functions. Additionally, analysis of cis-regulatory elements revealed significant enrichment of light-responsive elements in GmTPR promoters, indicating possible regulation by light. Tissue-specific expression analysis showed that GmTPR genes are mainly expressed in flowers and seeds. RNA-seq and RT-qPCR analyses revealed distinct expression patterns of GmTPRs between long and short photoperiods, highlighting their responsiveness to photoperiod changes. This study provides a comprehensive analysis of the GmTPR family, emphasizing their critical role in photoperiod responses.