The KH Gene Family in Tomato (Solanum lycopersicum): Genomic Expansion, Structural Basis of RNA Binding, and Haplotype Variation Associated with Fruit Weight

The K-homology (KH) domain is a crucial RNA-binding motif central to post-transcriptional regulation. However, its corresponding gene family remains poorly characterized in tomato (Solanum lycopersicum), a key model species for studying fleshy fruit development. Here, we performed a genome-wide identification and comprehensive characterization of 47 SlKH genes in S. lycopersicum. Phylogenetic and synteny analyses indicated that the gene family expanded mainly through segmental duplications. While the core RNA-binding GXXG loop has evolved under strict purifying selection, specific orthologs, such as the SlKH3/AtKH6 pair (Ka/Ks = 1.78), exhibited putative signatures of positive selection. Haplotype variations in SlKH47, SlKH43, and SlKH35 are associated with significant differences in fruit weight, revealing their potential roles in crop domestication. Furthermore, expression profiling revealed distinct spatiotemporal patterns, highlighting several members that are significantly upregulated during fruit ripening. Structural modeling with AlphaFold 3 provided predictive insights into how the conserved GXXG motif mediates RNA recognition. This study provides a comprehensive genomic resource and foundational insights into the evolutionary and functional significance of KH proteins in S. lycopersicum development and breeding.