Transcriptome analysis reveals changes in lignin and flavonoid biosynthesis in Serendipita indica colonized Tartary buckwheat

Abstract

Introduction: Tartary buckwheat (Fagopyrum tataricum Gaertn.), classified as a food and herbal medicinal crop, offers substantial nutritional benefits but suffers from poor yields and quality. Studies indicate that Serendipita indica positively impacts Tartary buckwheat's yield and quality, yet the underlying processes remain largely unexplored.

Methods: This study aimed to examine the genetic transcript of Tartary buckwheat in both colonized and uncolonized S. indica.

Results: It was discovered that the pathway for producing phenylpropanoids in Tartary buckwheat, both in colonized and uncolonized S. indica, both in colonized and uncolonized S. indica, was found to be enriched in KEGG (Kyoto Encyclopedia of Genes and Genomes). Genetic expression analysis of lignin and flavonoid biosynthesis pathways in colonized S. indica showed a comparison between lignin biosynthesis pathway genes in colonized S. indica and those in uncolonized S. indica in Tartary buckwheat. Research revealed a decrease in certain genes linked to lignin synthesis and an increase in others associated with flavonoid biosynthesis in both colonized and uncolonized S. indica Tartary buckwheat. Furthermore, research revealed a reduction in lignin levels in Tartary buckwheat stems and seeds both colonized and uncolonized by S. indica, in contrast to an increase in flavonoid levels in leaves and seeds of Tartary buckwheat colonized and uncolonized by the same fungi.

Discussion: Findings indicate that the process of synthesizing lignin and flavonoids could offer valuable insights into how S. indica enhances Tartary buckwheat's yield and quality.

Keywords: RNA-seq; Serendipita indica; Tartary buckwheat; flavonoid biosynthesis; lignin biosynthesis; phenylpropanoid biosynthesis.

Figure 1

Analyzing plant phenotypes of Tartary buckwheat after inoculation with S. indica. (A) Control (CK) and S. indica colonized (P) Tartary buckwheat plants; (B) Fresh and dry weights of Aboveground parts and Root of CK and P Tartary buckwheat plants. Values are expressed as mean ± SD (standard deviation) of three replicates. *p < 0.05; **p < 0.01.

Figure 2

Differentially expressed gene statistics (A) and the volcano plot of P vs CK (B). P: S. indica colonized Tartary buckwheat plants and CK: S. indica uncolonized Tartary buckwheat plants.

Figure 3

Sample correlation heatmap (A) and Comparison group of P vs CK heatmap (B). (A) The red color shows the number of up regulated genes, and the green color shows the number of down regulated genes. P: S. indica colonized Tartary buckwheat plants and CK: S. indica uncolonized Tartary buckwheat plants.

Figure 4

Histogram of the GO enrichment. Analyses with the top 10 entries with the smallest p-value selected for each Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). The left histogram is the -log₁₀ (p-value) and the right histogram is the DEGs number of the corresponding.

Figure 5

The GO and KEGG enrichment analyses of DEGs. (A) Bubble diagram for GO enrichment analysis of differential genes. (B) Bubble diagram for KEGG enrichment analysis of differential genes.

Figure 6

Lignin content and expression levels of genes of S. indica colonized (P) and non-colonized (CK) Tartary buckwheat. (A) Lignin content in stems and seeds of P and CK Tartary buckwheat. (B) Expression levels of genes related to the lignin biosynthesis pathway in P and CK Tartary buckwheat of seeds. (C) Expression levels of genes related to the lignin biosynthesis pathway in P and CK Tartary buckwheat of stems. (D) Histochemical analysis of stem cross-section lignin with Safranin-fixed green dyeing. Scale bar in (D) = 50 μm. Values are presented as mean ± SD (standard deviation) of three replicates. *p < 0.05; **p < 0.01; ***p < 0.001; ns p > 0.05.

Figure 7

Flavonoids content and expression levels of genes of S. indica colonized (P) and non-colonized (CK) Tartary buckwheat. (A) Total flavonoids in leaves and seeds of P and CK Tartary buckwheat. (B) Expression levels of genes related to the flavonoid biosynthesis pathway in P and CK Tartary buckwheat seeds. Values are presented as mean ± SD (standard deviation) of three replicates. *p < 0.05; **p < 0.01; ***p < 0.001.

Figure 8

Lignin biosynthetic pathway involved in Tartary buckwheat the response to S.indica. Red and green indicate upregulation and downregulation, respectively. Intensity of the colors is proportional to the log₂FC.

Figure 9

Summary diagram for the promotive effects of S. indica on tartarybuckwheat growth. Yellow and green arrows indicate the flavonoid biosynthesis pathway and lignin biosynthesis pathway, respectively. Red and green boxes indicate up and down regulation of gene expression.