Comprehensive analysis of raffinose family oligosaccharide metabolism genes in Salix matsudana: Expression patterns and roles in abiotic stress adaptation

Raffinose family oligosaccharides (RFOs) are crucial regulators of abiotic stress tolerance in plants, yet the enzymes involved in RFO metabolism in willows remain underexplored. This study provides a comprehensive analysis of the genes involved in RFO metabolism in Salix matsudana , a species of significant ecological and economic value. We conducted genome-wide identification and expression analysis of genes encoding galactinol synthases (SmGolS), raffinose synthases (SmRS), beta-fructofuranosidases (SmBFLUCT), and alpha-galactosidases (SmAGAL). In total, 35 SmGolSs , 23 SmRSs , 10 SmBFLUCTs , and 9 SmAGALs were identified and characterized in terms of phylogenetic relationships, conserved motifs, and gene structures. Synteny analysis revealed gene duplication events that contributed to the expansion of these gene families. Comparative genomics demonstrated the evolutionary conservation and divergence of these genes across multiple species. Transcriptomic analysis under stress conditions identified differentially expressed genes (DEGs) associated with RFO metabolism, suggesting their role in stress tolerances. Notably, in response to submergence stress, SmRS9 and SmRS11 expression was upregulated in submergence-tolerant varieties, suggesting their involvement in the submergence response. Additionally, SmGolS17 and SmGolS28 were associated with ion binding, metabolic processes, and chloroplast functions, which are critical for submergence adaptation. This study provides a foundational understanding of RFO metabolism in willows and identifies candidate genes that may contribute to stress resilience. Synteny, evolutionary insights, and functional analysis of RFO metabolism genes in Salix matsudana . The Synteny and Evolutionary Analysis section presents the Ka, Ks, and Ka/Ks ratios across multiple species ( Salix matsudana , Arabidopsis thaliana , Oryza sativa , Populus trichocarpa , and Salix purpurea ), providing insights into gene duplication events and evolutionary pressures. The KEGG functional analysis section shows the involvement of these genes in various metabolic pathways, highlighting their roles in carbohydrate metabolism and other biochemical processes. ● The study identified 35 SmGolS , 23 SmRS , 10 SmBFLUCT , and 9 SmAGAL genes involved in raffinose family oligosaccharide metabolism in Salix matsudana . ● Phylogenetic and synteny analysis showed gene duplication events and evolutionary conservation, highlighting their role in willow stress resilience. ● Transcriptomic analysis under salt and submergence stress revealed these genes are crucial for enhancing willow's stress tolerance.