Genome-Wide Identification of NF-YA Transcription Factors in Strawberry and Their Responses to Salt Stress

Nuclear Factor Y (NF-Y) transcription factor family plays essential roles in plant growth, development, and abiotic stress responses. However, the NF-YA subfamily in cultivated strawberry (Fragaria × ananassa) has not been systematically characterized from a genome-wide range. In this study, 27 FaNF-YA genes were identified from the octoploid strawberry genome and classified into four phylogenetic groups. With bioinformatic methods, it was found that all FaNF-YA proteins contain a highly conserved CCAAT-binding domain, while their exon–intron structures and motif compositions vary among groups. Promoter cis-acting element analysis revealed various stress- and hormone-responsive motifs, including ABRE, MYB, MYC, and MeJA-responsive elements. With molecular biology methods, organ-specific expression profiling was generated and showed that FaNF-YA genes exhibit distinct spatial expression patterns, with extremely low transcript abundance in fruit. Under salt stress, several FaNF-YA groups (e.g., FaNF-YA14/16/18/22) were dramatically induced, which indicated their potential involvement in salt tolerance. Heterologous expression of FaNF-YA7 and FaNF-YA9 in yeast enhanced salt tolerance, and these two proteins did not exhibit transcription-activating activity in the yeast GAL4 system. This study provides a reference for understanding the roles of NF-YA genes in responses to abiotic stresses and potential targets for molecular breeding of stress-tolerant strawberry cultivars.