The formation of high-quality Chinese medicinal materials is a micro-evolutionary process of multiple genes involving quantitative inheritance under environmental stress. Atractylodes lancea is a traditionally used medicinal plant in China that is broadly distributed and possesses a considerable amount of essential oils. However, to date, limited research has been conducted to characterize the genetics and metabolites of A. lancea shaped by natural variation. Hence, we assembled a high-quality genome of A. lancea, featuring a contig N50 of 1.18 Mb. We further integrated population resequencing of A. lancea and conducted analyses to characterize its genetic diversity, population evolution, and rewiring of volatile metabolites. The natural variation effect exerted significant pressure on A. lancea from different geographic locations, resulting in genetic differentiation among three groups. Correlation analysis of metabolites in A. lancea revealed significant natural variations of terpenoids, heterocyclic compounds, ketones, and esters. We also found that 427 metabolites displayed noteworthy divergence due to directional selection. Additionally, our genome-wide association studies on the metabolome for medicinal quality traits identified several candidate genes, such as AlZFP706 and AlAAHY1, exhibiting significant correlations with atractylodin and hinesol levels, respectively. Overall, this study provides an intricate genomic resource for A. lancea, thereby expanding our understanding of the effect of natural variation on metabolites and facilitating the genetic improvement of its medicinal properties.

Fagopyrum dibotrys, being native to southwest China, is widely distributed in Yunnan, Guizhou Provinces and Chongqing City. However, the quality of medicinal materials growing in different origins varies greatly, and cannot meet the market demand for high-quality F. dibotrys. In this study, 648 metabolites were identified, and phenolic compounds of F. dibotrys from different origins were clearly separated by principal component analysis (PCA). Our results suggested that the medicinal differences of F. dibotrys from different origins can be elucidated via the variations in the abundance of the phenolic and flavonoid compounds. We found that the epicatechin, total flavonoids and total tannin content in Yunnan Qujing (YQ) and Yunnan Kunming (YK) were higher than those in Chongqing Shizhu (CS), Chongqing Fuling (CF) and Guizhou Bijie (GB), suggesting that Yunnan Province can be considered as one of the areas that produce high-quality medicinal materials. Additionally, 1,6-di-O-galloyl-β-D-glucose, 2,3-di-O-galloyl-D-glucose and gallic acid could be used as ideal marker compounds for the quality control of F. dibotrys from different origins caused by metabolites, and the F. dibotrys planted in Yunnan Province is well worth exploiting.

The rhizome of Atractylodes lancea (Thunb.) DC. is a traditional Chinese medicine used extensively owing to its antimicrobial properties. It is utilized to treat nyctalopia and problems related to the gastrointestinal tract. However, its yield is limited because of its endangered status, long growth period, and restricted reproductive ability. Ancillary approaches have not been established to ensure sustainable resource utilization by applying efficient plant regeneration technologies and producing bioactive metabolites via genome editing. This study reports the effects of explants, hormones, and culture conditions on embryogenic callus induction, plant regeneration, adventitious and hairy root cultivation, and essential oil production. Embryogenic calli were successfully induced in MS and 2.0 mg/L 2,4-D and 1.0 mg/L NAA and 1/2MS medium supplemented with 4.0 mg/L 6-BA and 0.4 mg/L NAA, which were optimal for callus differentiation. Maximum proliferation (12-fold) of cluster buds was observed with a select combination of hormones [NAA (0.2 mg/L) and 6-BA (2.0 mg/L)]. “Efficient plant regeneration and bioactive metabolite production” can provide technical support for the protection and sustainable utilization of A. lancea germplasm resources in terms of resource preservation and new variety breeding, natural product production, and industrial breeding of medicinal plants.