Genome-Wide Identification of the NFYA Family and Its Expression in Response to Abiotic Stress in Taxodium Hybrid ‘Zhongshanshan’

Nuclear Factor Y, subunit A (NFYA) constitutes a family of transcription factors that play critical roles in plant growth, development and abiotic stress responses. Taxodium hybrid ‘Zhongshanshan’ (T. mucronatum × T. distichum) is a fast-growing tree species with high industrial value and remarkable flooding tolerance. However, the systematic characteristics and abiotic stress response patterns of the ThNFYA gene family remain unclear. In this study, a total of 11 ThNFYA genes were identified. The encoded proteins ranged from 67 to 372 amino acids in length, with predicted molecular weights between 16.84 and 40.12 kDa. Phylogenetic analysis classified plant NFYAs into four clades, with all ThNFYAs falling into clades I and IV. Expression profiling revealed tissue-specific patterns, with six members showing the highest transcript levels in the cambium. Multiple cis-acting elements associated with stress and hormone responses were detected in the promoter regions of ThNFYAs. Most ThNFYAs were differentially regulated under salt, drought, and flooding stresses. Notably, most clade IV members (ThNFYA3, ThNFYA4, and ThNFYA6-ThNFYA8) were downregulated in the wood under partial submergence. This indicates their potential role in modifying wood properties in response to flooding. Co-expression network analysis identified ThNFYA1 and ThNFYA8 as central hub genes in leaves under partial submergence. Overall, these results suggest that the ThNFYA family may serve as candidate regulators of development and stress adaptation in T. hybrid ‘Zhongshanshan’. This study provides valuable insights for further functional verification of ThNFYAs and lays a foundation for marker-assisted breeding of stress-tolerant varieties.