Integrated metabolomic and transcriptomic analyses reveal distinct flavonoid biosynthetic pathways underlying petal color diversity in Meconopsis

Introduction Flower color is a key ornamental and ecological trait that influences both aesthetic appeal and pollinator interactions. Although the biosynthetic and regulatory mechanisms of floral pigmentation are well characterized in several model species, they remain poorly understood in Meconopsis , an alpine genus renowned for its striking color diversity. Elucidating the molecular basis of petal coloration is crucial for the genetic improvement and conservation of this unique ornamental resource. Methods Here, we combined metabolomic and transcriptomic analyses to investigate the molecular mechanisms underlying flower coloration in three Meconopsis species— M. balangensis (blue), M. punicea (red), and M. integrifolia (yellow)—using M. argemonantha (white) as a control. Results Metabolite profiling revealed strong correlations between color parameters and pigment composition, particularly flavonoids and anthocyanins. Blue and red pigmentation were primarily attributed to cyanidin- and delphinidin-based anthocyanins, while yellow coloration resulted from quercetin derivatives. Transcriptome analysis identified key structural genes ( F3’H , DFR , ANS , UFGT , CHS , F3H , and FLS ) and regulatory transcription factors (MYB and bHLH) that collectively modulate flavonoid biosynthesis across species. Discussion Our findings demonstrate that divergence in the regulation of the flavonoid biosynthetic pathway drives color differentiation among Meconopsis species. This study provides new insight into the metabolic and transcriptional control of alpine flower coloration and establish a theoretical foundation for the molecular breeding of novel Meconopsis cultivars.