QTL mapping and identification of candidate genes for anthocyanidin accumulation in Salvia miltiorrhiza flowers

Abstract Salvia miltiorrhiza Bunge is an ornamental plant known for its diverse flower colors, ranging from white to dark violet. To elucidate the regulatory mechanisms underlying flower color, we conducted QTL mapping and identified candidate genes involved in anthocyanidin accumulation. Total anthocyanidin content and six anthocyanidins in the corollas of S. miltiorrhiza were quantified using the pH differential method and HPLC, respectively. Composite interval mapping was employed to identify QTLs, followed by the identification of candidate genes based on stable QTL intervals across at least two different planting environments. These candidate genes were further validated through gene cloning and expression analysis. Anthocyanidin analysis in the F2 population revealed a positive correlation between total anthocyanidin content and flower color intensity. Notably, three major anthocyanidins of delphinidin (Dp), cyanidin (Cy), and petunidin (Pt) were detected in varying degrees of purple flowers, while no anthocyanidins were found in white flowers. In total, 33 QTLs associated with anthocyanidin content were identified, with two major QTLs located on linkage groups LG4 and LG5. Two candidate genes, CHS1 (a chalcone synthase) and TCP15 (a transcription factor), were identified in the genetic intervals of two major QTL sites, respectively. Preliminary verification experiments suggest that CHS1 may play a positive role in anthocyanidin biosynthesis, whereas TCP15 appears to potentially act as a negative regulator. This study provides a foundation for cloning genes controlling flower color and advances our understanding of the molecular mechanisms regulating flower color in S. miltiorrhiza.