Development of SSR markers on the basis of the Panax notoginseng transcriptome for agronomic and biochemical trait association analyses

Panax notoginseng (Burk.) F.H. Chen (Araliaceae) is a precious medicinal plant, but little is known about the mechanism underlying the inheritance of its important agronomic and biochemical traits. The development of effective molecular markers and the characterization of genes associated with agronomic and biochemical traits are critical for P. notoginseng genetic analyses and breeding. In this study, 41 pairs of primers for polymorphic simple sequence repeats (SSRs) were developed according to the P. notoginseng transcriptome. Among them, 18 SSR markers can be used to reveal the rich genetic diversity among four wild Panax stipuleanatus populations. In addition, 20 significant correlations between 15 SSR locus and 14 agronomic and biochemical traits were identified using mixed linear models. It is worth noting that P19-FAM loci is significantly correlated with the content of P. notoginseng saponin R1 in rhizomes and tuberous roots, and the corresponding unigene sequence of P19-FAM loci is a dof zinc finger protein-encoding gene (PnDof1). Moreover, the PnDof1 protein was localized in the plant cell nucleus, and transgenic PnDof1-overexpressing P. notoginseng cells had higher notoginsenoside R1 and ginsenoside (Rg1, Re, Rb1, and Rd) contents than non-transgenic cells. Some P. notoginseng saponin (PNS) biosynthesis-related genes were significantly up-regulated in the PnDof1-overexpressing transgenic cells. The transcriptome SSR markers developed in this study are useful for the genetic analysis of Panax germplasm resources as well as for molecular breeding. The PnDof1 gene may encode a transcription factor that regulates PNS biosynthesis in P. notoginseng.