Whole-genome identification and expression analysis of the nuclear factor Y gene family in response to drought and salt stresses in Helianthus annuus L․

• Identified and classified 56 NF-Y genes in sunflower. • Revealed structural diversity and evolutionary relationships of NF-Y genes. • Several NF-Y genes respond strongly to drought and salt stresses. • The identified candidate genes facilitate marker-assisted breeding for stress-resilient sunflower varieties. The nuclear factor Y (NF-Y) family represents a key group of transcription factors that function as heterotrimeric complexes formed by NF-YA, NF-YB, and NF-YC subunits. These regulatory proteins play critical roles in modulating plant growth, developmental processes, and stress responses. Sunflower ( Helianthus annuus L.) is ranked as the world's fourth most important oilseed crop. However, the genome-wide characteristics and evolution of the NF-Y gene family in sunflower have yet to be characterized. In this study, we identified 56 sunflower NF-Y genes ( HaNF-Ys ), including 13 HaNF-YA , 27 HaNF-YB , and 16 HaNF-YC genes. Evolutionary analysis revealed four orthologous gene pairs between sunflower and Arabidopsis thaliana , as well as 11 pairs of paralogous genes within sunflower (3 pairs of HaNF-YAs , 6 pairs of HaNF-YBs , and 2 pairs of HaNF-YCs ). HaNF-Ys within the same subfamily exhibited similar motifs, conserved domains, and gene structure distributions. Promoter regions of the HaNF-Y genes contain various cis-acting elements implicated in responses to light, hormones, growth, development, and stress. The HaNF-Y genes were unevenly distributed on sunflower chromosomes. The identification of fourteen gene duplication events among the 56 HaNF-Y genes suggests a genetic basis for the family's expansion and the consequent improvement in plant adaptability. Interspecies synteny analysis indicated that sunflower has a closer relationship with dicot species compared to monocotyledons. Based on the protein-protein interaction network, putative hub NF-Y proteins in sunflower were identified. It was found that the HaNF-YB subfamily exhibited higher connectivity compared to the HaNF-YA subfamily, while the HaNF-YC subfamily had the weakest connectivity among the three. HaNF-Ys displayed organ-specific expression patterns at different developmental stages of sunflower. RNA-seq analysis revealed that HaNF-YA2, HaNF-YA5, HaNF-YA7, HaNF-YB9 , and HaNF-YB12 exhibited notable expression changes in response to drought and salt stresses. qRT-PCR results further confirmed significant expression changes in HaNF-YA5, HaNF-YA7, HaNF-YB4 , and HaNF-YC8 under salt stress, and the specific induction of HaNF-YA5, HaNF-YA7, HaNF-YA12, HaNF-YB4, HaNF-YB5, HaNF-YB6 , and HaNF-YB8 under drought stress. Our comprehensive analysis of the HaNF-Y gene family reveals its features and potential regulatory roles, forming a basis for subsequent studies on the evolution and diverse biological functions of NF-Y members.