Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis

Abstract

Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.

Keywords: Stipa grandis; heavy grazing; metabolic; proteomic; transcriptomic.

Figure 1

Differentially expressed genes (DEGs) between non-grazed (NG) and heavy-grazing (HG) plants of Stipa grandis. (A) Heatmap analysis of DEGs. (B) KEGG pathway enrichment analysis of DEGs.

Figure 2

Proteome profile and differentially expressed proteins (DEPs) between NG and HG plants of S. grandis. (A) Venn diagram of proteins annotated from the GO, KEGG, and COG databases. (B) Coefficient of variation cumulative curve for NG and HG samples. (C) Quantitative analysis of the proteome of NG and HG samples. Green, red, and black represent down-regulated, up-regulated, and non-significantly changed proteins, respectively. (D) GO term enrichment analysis of DEPs between NG and HG samples. BP, biological process; CC, cellular component; and MF, molecular function. (E) KEGG pathway enrichment analysis of DEPs between NG and HG samples.

Figure 3

Qualitative and quantitative analysis of metabolites in leaves of S. grandis. (A) Classification of all identified metabolites. (B) Principal component analysis scatterplot of leaf samples from NG and HG plants. (C) Cluster analysis heatmap of all identified metabolites. The color scale indicates the abundance of each metabolite.

Figure 4

Differentially accumulated metabolites (DAMs) between NG and HG plants of S. grandis. (A) Cluster analysis heatmap of DAMs. (B) KEGG pathway enrichment analysis of DAMs.

Figure 5

Enriched KEGG pathways common to DAMs, DEPs, and DEGs between NG and HG plants of S. grandis. (A) Histogram of KEGG pathways common to DAMs and DEGs. (B) Heatmap of KEGG pathways common to DEPs and DEGs.

Figure 6

Phenylpropanoid biosynthesis, and flavone and flavonol biosynthesis pathways in S. grandis in response to heavy grazing. (A) Joint analysis of the DAMs, DEPs, and DEGs. Red and blue letters represent up- and down-regulation, respectively. Upper-case letters indicate proteins and italicized upper-case letters indicate genes. Orange line indicate biosynthetic step is not clear. The heatmap represents the corresponding expression levels of (B) DAMs, (C) DEPs, and (D) DEGs in the NG and HG groups. The color scale indicates the relative expression level.

Figure 7

Tryptophan metabolism pathway in S. grandis in response to heavy grazing. (A) Joint analysis of the DAMs, DEPs, and DEGs. Red and blue letters represent up- and down-regulation, respectively. Upper-case letters indicate proteins and italicized upper-case letters indicate genes. Orange lines represent biosynthetic steps that are not clear. The heatmap represents the corresponding expression levels of (B) DAMs, (C) DEPs, and (D) DEGs in the NG and HG groups. The color scale indicates the relative expression level.