Genome-wide Analysis and Identification of Nuclear Factor Y (NF-Y) Gene Family in Camelina (Camelina sativa)

Abstract The transcription factor family known as Nuclear Factor Y (NF-Y) is essential for regulating plant growth and stress reactions. This investigation carried out a thorough genome-wide examination of the NF-Y gene family in Camelina sativa, a hexaploid oilseed crop valued for its environmental resiliency and bioenergy potential. Using bioinformatics techniques, 73 CsNF-Y genes were found, comprising 28 NF-YA, 15 NF-YB, and 30 NF-YC subunits, a considerable growth compared to Arabidopsis thaliana’s 36 NF-Y genes, possibly driven by C. sativa’s triplicated genome. Structural analyses revealed various physicochemical features, conserved domains, and exon-intron organizations, indicating functional specialization. Phylogenetic analysis indicated evolutionary conservation with A. thaliana and Oryza sativa, whereas synteny analysis verified substantial genomic conservation with A. thaliana, suggesting orthologous links. Cis-regulatory element (CRE) analysis identified stress-responsive (e.g., MYB-binding sites), light-responsive (e.g., G-Box), and hormone-responsive elements, particularly enriched in NF-YC promoters, emphasizing their significance in salinity tolerance. Gene ontology research showed functions in transcriptional control, photomorphogenesis, and somatic embryogenesis, crucial for seed formation. RNA-seq data (GSE102422) indicated tissue-specific expression, with genes including CsNF-YA01 and CsNF-YC15 significantly upregulated in roots during salt stress (5 to 60 CPM), confirming their relevance in osmotic and ionic stress responses. Subcellular localization analysis showed 79% nuclear localization, with NF-YC genes like CsNF-YC06 and CsNF-YC07 also predicted in plastids and chloroplasts, suggesting novel organellar functions. These findings elucidate the structural, evolutionary, and regulatory complexity of CsNF-Y genes, highlighting their potential for enhancing C. sativa’s stress tolerance and agronomic traits through targeted genetic approaches.