Transcriptome Dynamics Reveal the Potential Roles of Long Non-Coding RNAs in Regulating Flower Color of Safflowers (Carthamus tinctorius)

Safflower (Carthamus tinctorius L.) is an important medicinal plant widely used as a source of natural pigments. Flower color is a key trait affecting both ornamental and commercial value; however, the roles of long non-coding RNAs (lncRNAs) in safflower flower coloration remain largely unclear. In this study, strand-specific RNA sequencing was performed on three safflower varieties with distinct flower colors at different floral developmental stages. A total of 4851 lncRNAs were identified, including 940 natural antisense transcript (NAT) pairs. Among them, lncRNA MSTRG.28365 was identified as a natural antisense transcript paired with CtCHS.7, a chalcone synthase-like gene potentially involved in flavonoid biosynthesis. Expression analysis revealed that CtCHS.7 was highly expressed in the red-flowered variety, whereas MSTRG.28365 exhibited an opposite expression pattern, suggesting a potential regulatory association. Co-expression analysis further indicated that CtCHS.7 was associated with genes putatively involved in flavonoid modification, including UDP-glycosyltransferases and cytochrome P450 enzymes. Functional assays showed that the recombinant CtCHS.7 protein could catalyze the production of downstream flavonoid-related metabolites, although the detected product differed from canonical naringenin chalcone. These findings suggest that lncRNAs may participate in flower color variation and flavonoid biosynthesis-related processes in safflower. This study provides candidate regulatory elements for future functional validation of safflower flower coloration mechanisms.