Gene family expansion and contraction are key processes underlying functional innovation and genome evolution in plants, yet their roles in the horticultural plant white clover (Trifolium repens) remain poorly understood. In this study, we systematically investigated the association between lineage-specific whole-genome duplication (WGD) and short interspersed nuclear elements (SINEs) with gene family dynamics and stress-responsive transcription. Our results indicate that white clover underwent a lineage-specific WGD, which is associated with increased gene family expansion. SINE copy number was strongly correlated with the proportion of significantly expanded genes (r = 0.637, p = 0.0259, n = 12), but not with the proportion of significantly contracted genes. This result suggests a potential association between SINE insertions and gene family expansion. GO enrichment analyses indicated that expanded gene families are predominantly involved in metabolic processes, environmental stress responses, defense mechanisms, and floral organ development, whereas contracted gene families were mainly enriched in core housekeeping functions, such as ubiquitin-dependent protein catabolism and mitochondrial organization. Transcriptome analyses further showed that genes within expanded families were broadly upregulated under drought, cadmium, and cold stress, while generally upregulated in floral tissues compared with other organs. Collectively, these findings reveal the relationships among WGD, SINE elements, and gene family dynamics in environmental adaptation and flower development, providing a molecular framework for understanding adaptive regulation associated with gene family expansion.

Recent advances in plant genomics have characterized transposable elements (TEs) as key contributors to genome structure and gene regulation. This study focuses on the remarkably high abundance of short interspersed nuclear elements (SINEs) in the genus Trifolium. Using the allotetraploid horticultural plant white clover (Trifolium repens L.) as the study organism, we systematically investigate lineage-specific SINE amplification, genomic distribution, insertional preferences, and their regulatory effects on gene expression. Our analyses reveal that SINEs are significantly more abundant in Trifolium than in other angiosperms. Comparative genomic analyses further indicate that SINE accumulation is closely associated with polyploidization and domestication. Gene Ontology (GO) enrichment analyses demonstrate that SINEs are preferentially enriched in stress responsive genes. Expression analyses further showed that, within duplicated gene pairs, genes with SINE insertions in their upstream promoter regions exhibit significantly higher transcript levels compared with genes without such insertions. Under drought, cold, and cadmium stress, these SINE-associated genes exhibit upregulation, and our data analysis shows a strong correlation between the presence of SINE insertions and stress-induced upregulation of gene expression. This study demonstrates that SINE insertions in upstream promoter regions modulate transcriptional regulatory networks involved in stress responses, contributing to broad ecological adaptation in white clover.