Genome-Wide Analysis Reveals the Roles of FAR1/FHY3 Genes in Fragaria × ananassa Under Abiotic/Biotic Stresses and Highlights Their Potential Functions in Anthocyanin Biosynthesis During Fruit Development

FAR1/FHY3 transcription factors are key regulators of plant growth and development, but their identification and functions in strawberries (Fragaria × ananassa) remain largely unexplored. In this study, 47 FaFAR1/FHY3 genes in cultivated strawberries were systematically identified, which were categorized into six subfamilies and randomly distributed across 15 chromosomes, with segmental duplication as the main driver of the expansion of this gene family. Integration of phylogenetic relationships, gene structure, and conserved motif composition uncovered distinct divergences among the subfamilies. A cis-acting element analysis of promoters and gene expression profiles showed that these genes responded to various abiotic and biotic stresses, phytohormones, and far-red light signals, with FaFAR1-7 and FaFAR1-44 strongly responding to multiple stresses, including temperature, drought, and pathogen infection. Additionally, FaFAR1-12 and FaFAR1-18 exhibited positive correlations with anthocyanin accumulation and the expression of key anthocyanin biosynthesis genes during fruit development. Dual-luciferase reporter assays further confirmed that FaFAR1-12 and FaFAR1-18 significantly activated the promoters of key structural genes related to anthocyanin biosynthesis, indicating that these two TFs exert vital regulatory functions in anthocyanin accumulation during strawberry fruit development. This study comprehensively identifies and characterizes the FaFAR1/FHY3 genes in cultivated strawberries, laying a foundation for their functional analysis and for screening out the key regulatory genes for strawberry fruit quality improvement.