Genome-Wide Analysis of the FAR1/FHY3 (FRS) Gene Family and Expression Responses of PbFRS Genes to PEG-Induced Osmotic Stress, Light, and Shade in Phoebe bournei

Water availability and light conditions are among the most important environmental factors affecting tree growth and development. The FAR1/FHY3 (FRS) gene family consists of transposase-derived transcription factors that are widely involved in light signaling and responses to environmental stresses. Although FRS genes have been characterized in several plant species, a comprehensive analysis in P. bournei is still lacking. In this study, we performed the first comprehensive genome-wide analysis of the FRS gene family in P. bournei, including physicochemical characterization, chromosomal localization, phylogenetic analysis, gene structure and conserved motif analysis, protein structure prediction, promoter cis-element analysis, organ/tissue expression profiling, and RT-qPCR analysis under PEG-induced osmotic stress, full-light, and shade treatments. A total of 21 PbFRS genes were identified and found to be unevenly distributed across 11 chromosomes. Phylogenetic analysis, together with Arabidopsis thaliana and Zea mays FRS proteins, clustered the family members into five clades, including one P. bournei-specific clade, suggesting lineage-specific expansion and possible functional diversification. Structural analyses revealed both conserved and divergent features among PbFRS members. Promoter analysis identified diverse cis-acting elements related to light, temperature, hormones, and stress responses, suggesting that PbFRS genes may have diverse regulatory potentials in response to environmental signals. Organ/tissue expression profiling further revealed clear differences in expression patterns among family members. In addition, RT-qPCR analysis showed that several genes, including PbFRS9, PbFRS10, PbFRS12, PbFRS13, PbFRS16, and PbFRS18, exhibited transcriptional responses to PEG-induced osmotic stress, full-light, and shade treatments. These results indicate that these genes may serve as candidates for future functional studies, although their direct roles in stress tolerance require further validation. Overall, these results provide the first systematic overview of the PbFRS gene family and identify transcriptionally responsive candidate genes for future functional studies in P. bournei.