Ecotype-specific phenolic acid accumulation and root softness in Salvia miltiorrhiza are driven by environmental and genetic factors

Abstract

Salvia miltiorrhiza Bunge, a renowned medicinal herb in traditional Chinese medicine, displays distinctive root texture and high phenolic acid content, traits influenced by genetic and environmental factors. However, the underlying regulatory networks remain unclear. Here, we performed multi-omics analyses on ecotypes from four major Chinese regions, focusing on environmental impacts on root structure, phenolic acid accumulation and lignin composition. Lower temperatures and increased UV-B radiation were associated with elevated rosmarinic acid (RA) and salvianolic acid B (SAB) levels, particularly in the Sichuan ecotype. Structural models indicated that the radial arrangement of xylem conduits contributes to greater root hardness. Genomic assembly and comparative analysis of the Sichuan ecotype revealed a unique phenolic acid metabolism gene cluster, including SmWRKY40, a WRKY transcription factor essential for RA and SAB biosynthesis. Overexpression of SmWRKY40 enhanced phenolic acid levels and lignin content, whereas its knockout reduced root hardness. Integrating high-throughput (DNA affinity purification sequencing) and point-to-point (Yeast One-Hybrid, Dual-Luciferase and Electrophoretic Mobility Shift Assay) protein-DNA interaction detection platform further identified SmWRKY40 binding sites across ecotypes, revealing specific regulatory networks. Our findings provide insights into the molecular basis of root texture and bioactive compound accumulation, advancing breeding strategies for quality improvement in S. miltiorrhiza.

Keywords: S. miltiorrhiza; evolution; genetic and environmental factors; multi‐omics analysis; phenolic acid metabolism.

Figure 1

The Component accumulation, morphology, anatomy and environmental correlation of roots of S. miltiorrhiza with different ecotypes. (a) Morphological characteristics and geographical distribution of S. miltiorrhiza in Sichuan, Shaanxi, Henan and Shandong provinces. (b) Morphological characteristics of mature root strips of S. miltiorrhiza with different ecotypes. (c) Daily average temperature heatmap of different S. miltiorrhiza‐producing regions in China during the root maturation period. (d) Correlation analysis between rosmarinic acid, salvianolic acid B, lignin content and environmental factors. (e) Root diameter, hardness, total lignin content, rosmarinic acid content, salvianolic acid B content. and correlation analysis between phenotype and components. Data show the arithmetic mean ± SD from 3 biological replicates (Sm.SC, n = 27; Sm.SX, n = 10; Sm.HN, n = 20; Sm.SD, n = 23; plants each). Different letters indicate significant differences at P < 0.05 (one‐way ANOVA, Tukey's posttest). (f) Paraffin sectioning and scanning electron microscopy imaging of mature roots of ecological type S. miltiorrhiza in Sichuan and Shandong. The red lines highlight the arrangement of xylem cells, and the Black letters mark the areas of the xylem (Xy), cuticular (Ca) and phloem (Ph). (g) Mechanical simulation analysis of bending deformation and extrusion deformation of root strips with different lignocellulosic arrangements using 3D modelling. A total of 2 rounds (R1 and R2) of force application direction for 2 models (M1 and M2) were analysed. (h) The dynamic changes in action time and stress intensity during bending deformation and extrusion deformation processes were recorded separately. (i) Comparison of different lignin monomers and S/G ratio in the root of Sichuan and Shandong S. miltiorrhiza.

Figure 2

Genome assembly, comparative genomics, population variation and gene cluster mining based on Sichuan S. miltiorrhiza. (a) Collinearity circos plot of the genomic features of S. miltiorrhiza from Sichuan, Shaanxi and Shandong. (b) The phylogenetic tree was constructed using 2211 single‐copy genes from 6 Labiaceae species. All branches in the tree had posterior probabilities exceeding 0.99. Pie charts and the corresponding numbers represent the expansion and reduction of gene families. (c) Distribution of synonymous substitution rates (Ks) for paired syntenic paralogs was analysed in S. miltiorrhiza of 3 ecotypes and three other plants. (d) Synteny maps were generated to compare S. miltiorrhiza from Sichuan, Shaanxi, Shandong, S. bowleyana, S. hispanic and S. baicalensis. Light grey lines represent synteny blocks. The colours of connecting lines indicate representative metabolic modules with a high degree of evolutionary conservation. Red lines indicate rosmarinic acid synthase (RAS) gene. Blue lines indicate the BAHD acyltransferase genes. (e) Volcano plot drawn from RNA‐seq differentially expressed gene (Fold Change > 2, P < 0.05) data set from mature roots of Sichuan and Shandong S. miltiorrhiza. (f) Heatmap of differentially expressed gene sets derived from tyrosine and phenylalanine metabolic pathway. (g) Gene expression data were mapped to metabolic pathways, with red modules indicating up‐regulated pathways and blue modules indicating down‐regulated pathways. *P < 0.05; **P < 0.01. (h) Among the co‐expression networks formed between tyrosine and phenylalanine metabolic pathway genes and transcription factors, the WRKY TFs have the highest network flux. (i) Neighbour‐joining tree of 30 S. miltiorrhiza germplasms, including 10 high phenolic acid, 15 middle phenolic acid and 5 low phenolic acid accumulation germplasms. Branch colours indicate different groups. (j) Highly divergent genomic regions between different germplasm. The horizontal dashed line indicates the top 5% of Fst and the marked by the letter indicate gene cluster in the highly divergent regions of the phenolic acid metabolism pathways. (k) A key gene cluster of lignin synthase CCRs and HCTs tandem repeating phenolic acids upstream and downstream centred on transcription factor gene SmWRKY40 was identified within the selected clearance interval. (l) Haploid analysis of promoters and coding regions of several genes in gene clusters. The same colour represents the same haplotype.

Figure 3

SmWRKY40 promote root development and improve the accumulation of rosemic acid, salvianolic acid B and total lignin. (a, b) S. miltiorrhiza hairy root with overexpression (a) and knockout (b) of the SmWRKY40 gene. CC, CRISPR‐Cas9; EV, Empty vector; OE, overexpression. (c) Transgenic PCR identification and sequencing validation of CRISPR‐Cas9 mediated gene editing sites. (d) Roseminic acid and salvianolic acid B content in hairy roots by HPLC. (e) Analysis of rosmarinic acid, salvianolic acid B and total phenolic acid in hairy roots. (f, g) Overexpression and knockout of the dissected structure of hairy roots, and observation of the effects of SmWRKY40 on the development of hairy root xylem using toluidine blue staining (f) and scanning electron microscopy (g), respectively. (h) Analysis of the phenotype and lignin content performed on hairy roots. (i) Comparison of phenotypes between transgenic Arabidopsis with heterologous expression of SmWRKY40 and after supplementation with SmWRKY40 in atwrky40 mutant. (j) Phenotypic statistics and lignin content determination of Arabidopsis roots. (k) Histochemical stain of transgenic Arabidopsis with heterologous expression of SmWRKY40 and after supplementation with SmWRKY40 in atwrky40 mutant. (l) Three kinds of lignin monomer components were quantitatively detected by GC–MS. All data show the arithmetic mean ± SD from 3 biological replicates. Different letters indicate significant differences at P < 0.05 (one‐way ANOVA, Tukey's posttest). *P < 0.05; **P < 0.01; ***P < 0.001.

Figure 4

DAP‐seq identify SmWRKY40 diverged on the transcriptional regulation of rosmarinic acid and lignin biosynthesis pathway in different ecotypes of S. miltiorrhiza. (a) Distribution of candidate SmWRKY40‐binding regions across 2 sets of S. miltiorrhiza reference genomes (Sichuan and Shandong ecotypes) as determined by DAP‐seq. (b) Motif analysis using HMMER to identify core motifs enriched within the experimentally determined (by DAP‐seq) SmWRKY40‐binding regions. (c) Distribution of binding regions enriched at the transcription start site (TSS). (d) Functional enrichment of target genes bound to the promoter region by SmWRKY40. (e) Displayed the binding sites of SmWRKY40 in the promoter region of the genes involved in the tyrosine and phenylalanine metabolism pathways of S. miltiorrhiza in Sichuan (red peaks) and Shandong (yellow peaks). Grey peaks represent Input. (f–h) Protein‐DNA interactions were investigated through Daul‐LUC (f), Yeast one‐hybrid assay (g) and EMSA (h).

Figure 5

Comparison of the subcellular localization and kinetic characteristics of the RAS enzymes for the different haplotypes. (a) Subcellular localization of SmWRKY40. Green fluorescence (GFP) represents the RAS^146C and RAS^146G recombinant protein, and red fluorescence (RFP) represents the nuclear marker. The superimposed images show yellow fluorescence. (b) Purified pET28a‐RAS (146C and 146G) recombinant plasmid was introduced in the E. coli expression system, induced at 0.2 μM iptg and purified protein obtained through a Ni chromatography column. (c) Molecular docking simulations and enzymatic reaction mechanism of caffeoyl‐CoA and quinic acid with RAS proteins. (d) Molecular docking simulations and enzymatic reaction mechanism of caffeoyl‐CoA and danshensu with RAS proteins. (e) High‐performance liquid chromatography (HPLC) showing the formation of rosmarinci acid during in vitro enzyme assays with recombinant RAS^146C and RAS^146G using caffeoyl‐CoA and danshensu as substrates, compared to an authentic standard of corresponding compounds. (f) High‐performance liquid chromatography (HPLC) showing the formation of rosmarinci acid during in vitro enzyme assays with recombinant RAS^146C and RAS^146G using caffeoyl‐CoA and danshensu as substrates, compared to an authentic standard of corresponding compounds. (g, h) Michaelis–Menten curves of RAS catalysing the enzymatic reaction of caffeyl quinic acid (g) and rosmarinci acid (h) pathways.

Figure 6

Phenotypic, compositional and histological comparison of two RAS haplotypes transgenic in hairy roots. (a) Two RAS haplotypes transgenic in hairy roots. (b) Phenotypic statistics of the transgenic hairy roots. (c) Comparison of substrate and products of rosmarinic acid and lignin pathway in transgenic hairy roots. (d) SEM imaging of the transgenic hairy roots. (e) Statistics on hardness, cell wall thickness, cell cross‐sectional area and cell number of transgenic hairy roots. All data show the arithmetic mean ± SD from 3 biological replicates. Different letters indicate significant differences at P < 0.05 (one‐way ANOVA, Tukey's posttest).

Figure 7

The replacement phenotypes of two haplotypes of SmRAS in Arabidopsis athct2 mutants. (a, b) Phenotypic comparison of 6‐week and 10‐week seedling ages in Arabidopsis with different genotypes. (c–f) Statistics on total biomass, plant height, total lignin content in roots and number of lateral branches in aboveground parts of different genotypes of Arabidopsis plants at 10 weeks of seedling age. (g) Histochemical staining of roots in Arabidopsis plants with different genotypes. (h) Quantitative detection of three lignin monomer components in the roots of different genotypes of Arabidopsis plants using GC–MS. All data show the arithmetic mean ± SD from 3 biological replicates. Different letters indicate significant differences at P < 0.05 (one‐way ANOVA, Tukey's posttest).

Figure 8

Heterologous expression validates the biological functions of SmWRKY40 and SmRASs in response to UV‐B exposure. (a) Plate growth phenotype of wild‐type (col‐0), OE‐SmWRKY40, atwrky40 mutant and SmWRKY40 complemented atwrky40 mutant A. thaliana under UV‐B exposure. The fluorescence intensity reflects the chlorophyll fluorescence in the plant leaves, and the stronger the fluorescence intensity the higher the plant's biological activity. (b) Root length of different genotypes of Arabidopsis under UV‐B exposure. (c) Phenotypes of different genotypes of Arabidopsis under UV‐B exposure. (d) Germination rate statistics of Arabidopsis under UV‐B exposure for different genotypes. (e) Carotenoid and chlorophyll content of different genotypes of Arabidopsis under UV‐B exposure. (f) Phenotypic statistics and antioxidant physiology assays of different genotypes of Arabidopsis under UV‐B exposure. (g) Growth status of yeast transferred with pYES2 vector, pYES2‐SmWRKY40, pYES2‐RAS ^146C and pYES2‐RAS ^146G on plates under UV‐B exposure. (h) Growth curves of yeast with different genotypes under UV‐B exposure. (i) Antioxidant physiological detection of yeast with different genotypes under UV‐B exposure. All data show the arithmetic mean ± SD from the three biological replicates. Different letters indicate significant differences at P < 0.05 (one‐way ANOVA, Tukey's posttest).