Systematic characterization and expression analysis of the NFY gene family reveal critical roles in pigment biosynthesis in pepper.

Fruit color, a primary quality affecting consumer and breeder preferences, depends on a coordinated regulation of numerous genes. Nuclear factor Y (NFY) is an evolutionarily conserved heterotrimeric transcription factor complex that plays crucial roles in diverse developmental processes in plants. However, little attention has been given to members of the large NFY gene family in the pepper (Capsicum annuum) genome. In this study, 43 CaNFY genes (15 CaNFYAs, 16 CaNFYBs, and 12 CaNFYCs) were identified. Their gene structure, genomic mapping, motif composition, phylogenetic relationships, and gene expression were investigated. Distinct expression patterns were detected during pericarp and placenta development. Expression data showed that CaNFY genes responded to light/dark transitions, different temperatures, and nitrogen starvation. Association analysis among 43 CaNFYs genes, pigment biosynthesis genes, and CaUBC, as well as CaUbox genes, revealed that CaNFYB9/15 and CaNFYC11 were positively correlated with chlorophyll biosynthetic gene CaCPOX, flavonoid biosynthetic gene CaF3H, and certain CaUBC and CaUbox genes. The results could provide a foundation for further cloning and functional analysis of CaNFY genes in fruit color formation in pepper.