Genome-Wide Characterization of Chrysanthemum indicum Nuclear Factor Y, Subunit C Gene Family Reveals the Roles of CiNF-YCs in Flowering Regulation

Nuclear Factor Y, Subunit C (NF-YC) transcription factors are conserved in most plants, and play essential roles in plant growth and development, especially in flowering regulation. Chrysanthemums are important commercial plants, and their market value is strongly impacted by flowering time. Until now, no details regarding the NF-YC family in the Chrysanthemum genus have been available. In this study, five NF-YC genes were cloned from Chrysanthemum indicum. Multiple alignments showed that CiNF-YCs had the highly conserved characteristic regions. Phylogenetic analyses identified a pair of paralogue NF-YC proteins in chrysanthemums. Gene structure and conserved motifs were also analyzed for functional understanding. According to the results of the expression experiments, CiNF-YC1 and CiNF-YC5 were mainly expressed in leaves or flowers, and their expression levels varied greatly from the seedling to flower bud differentiation stage. Arabidopsis overexpressing CiNF-YC1 and CiNF-YC3 showed significantly delayed flowering, accompanied by other morphological alterations. RT-qPCR analysis revealed that genes associated with photoperiod, vernalization, aging, and gibberellin pathways were downregulated in CiNF-YC1-OX lines, relative to the wild type, whereas in CiNF-YC3-OX lines, only SHORT VEGETATIVE PHASE (AtSVP), the key factor in the ambient temperature pathway, was upregulated. Taken together, these findings suggest that CiNF-YC1 and CiNF-YC3 negatively regulate flowering in Arabidopsis via different flowering pathways.