Identification and Characterization of the CRY Gene Family Involved in Safflower Flavonoid Biosynthesis

The cryptochromes (CRYs) perceive blue light to regulate various developmental and metabolic events. However, the role of CRYs in flavonoid biosynthesis and flower pigmentation in safflower (Carthamus tinctorius L.) remains unknown. In this study, we determined flower color diversity among 485 safflower genotypes using the integrated CIELAB color space parameters and cluster analysis. On this basis, distinct colors were categorized into four groups, namely white (WW), yellow (YY), orange–red (OR), and yellow–red (YR). A genome-wide association study (GWAS) via 933,444 high-quality SNPs showed CtCRY2 as a flower color variation gene. Subsequently, genomic analysis identified three genes of the CRY family, including CtCRY1.1, CtCRY1.2, and CtCRY2. In silico analysis, such as gene structure, phylogeny and cis-acting elements, suggested CtCRY1.1 as a key candidate in pigment biosynthesis and was, therefore, selected for functional validation. Overexpression of CtCRY1.1 in Arabidopsis accumulated a high flavonoid content, particularly upregulating the expression of CHS, FLS, and ANS, proving its role as a positive regulator of flavonoid biosynthesis in safflower. These findings provide insights into the molecular mechanisms underlying flower color regulation in safflower and highlight CtCRY1.1 as a new target to enhance pigment-related traits in plants.