Polyploidy-driven expansion and regulatory diversification of the Kelch repeat F-box gene family in sweetpotato

BACKGROUND: Kelch repeat F-box (KFB) proteins are substrate-recognition components of SCF (SKP1-CULLIN1-F-box) E3 ubiquitin ligases and play important roles in protein turnover, specialized metabolism, and stress responses in plants. However, the evolutionary history of the KFB gene family across different ploidy levels remains unclear in sweetpotato (Ipomoea batatas), an important polyploid crop. Here, we tested the hypothesis that KFB genes in sweetpotato and its relatives underwent expansion and transcriptional diversification during polyploid evolution while retaining the conserved structural framework required for SCF-mediated proteolysis. RESULTS: We performed a cross-ploidy comparative analysis of the KFB gene family in four Ipomoea species representing three ploidy levels: diploid I. trifida and I. triloba, tetraploid I. tabascana, and hexaploid cultivated sweetpotato (I. batatas). We identified 24, 27, 16, and 102 KFB genes in these species, respectively. The marked expansion in hexaploid sweetpotato, together with the reduced KFB repertoire in tetraploid I. tabascana, indicates that KFB family size does not scale linearly with ploidy and instead reflects lineage-specific retention and loss in gene family evolution. Segmental duplication was the predominant mode associated with KFB expansion, whereas tandem duplication was not detected. Most duplicated gene pairs had Ka/Ks ratios below 1, indicating strong purifying selection on retained copies. Despite substantial variation in copy number, KFB proteins retained conserved F-box/Kelch domain organization, with moderate variation in motif composition and gene structure. Transcriptome profiling, co-expression analysis, and qRT-PCR further revealed substantial tissue-, stress-, and hormone-responsive expression divergence among KFB genes. CONCLUSIONS: These findings establish an evolutionary framework for KFB family diversification in Ipomoea and show that expansion of the KFB family in sweetpotato is shaped not only by genome multiplication, but also by lineage-specific gene retention, loss, and regulatory divergence. The identified KFB candidates provide a useful foundation for future functional studies of stress adaptation and metabolic regulation in sweetpotato.