Integrated omics data of two annual ryegrass (Lolium multiflorum L.) genotypes reveals core metabolic processes under drought stress

Abstract

Background: Annual ryegrass (Lolium multiflorum L.) is a commercially important, widely distributed forage crop that is used in the production of hay and silage worldwide. Drought has been a severe environmental constraint in its production. Nevertheless, only a handful of studies have examined the impact of short-term drought stress on annual ryegrass. The aim of this study was to explore how stress-induced core metabolic processes enhance drought tolerance, or adaptation to drought, in annual ryegrass.

Results: We profiled the transcriptomes, proteomes, and metabolomes of two annual ryegrass genotypes: the drought-resistant genotype "Abundant 10" and drought-susceptible genotype "Adrenalin 11." We identified differentially expressed metabolites and their corresponding proteins and transcripts that are involved in 23 core metabolic processes, in response to short-term drought stress. Protein-gene-metabolite correlation networks were built to reveal the relationships between the expression of transcripts, proteins, and metabolites in drought-resistant annual ryegrass. Furthermore, integrated metabolic pathways were used to observe changes in enzymes corresponding with levels of amino acids, lipids, carbohydrate conjugates, nucleosides, alkaloids and their derivatives, and pyridines and their derivatives. The resulting omics data underscored the significance of 23 core metabolic processes on the enhancement of drought tolerance or adaptation to drought in annual ryegrass.

Conclusions: The regulatory networks were inferred using MCoA and correlation analysis to reveal the relationships among the expression of transcripts, proteins, and metabolites that highlight the corresponding elements of these core metabolic pathways. Our results provide valuable insight into the molecular mechanisms of drought resistance, and represent a promising strategy toward the improvement of drought tolerance in annual ryegrass.

Keywords: Annual ryegrass (Lolium multiflorum); Drought; Metabolism; Metabolome; Omics; Proteome; Transcriptome.

Fig. 1

Representative images of two L. multiflorum genotypes under long term drought stress for 5 weeks (a and b). Morphological and physiological characters of annual ryegrass were measured after drought stress for 7 to 35 days (c–k). Different letters above bars indicate significant differences (P < 0.05) between different time points

Fig. 2

Comparison of upregulated and downregulated proteins in resistant and susceptible genotypes (a); Differentially expressed proteins (DEPs) were identified by a Gene Ontology (GO) analysis (b); DEPs involved in metabolic pathways related to metabolites identified by LC-MS were dramatically affected by drought in annual ryegrass (0, 1, 2, and 24 h) (c)

Fig. 3

Differentially expressed genes involved in core metabolic pathways in two L.multiflorum genotypes at four time points (0, 1, 2, and 24 h) during drought treatment (a–d)

Fig. 4

Integrative analysis of multiple omics data using MCoA and GSEA. The first two components defined by MCoA (a). The proportion of variation explained by each component (b). The GSEA of the first loading vector for the lipid metabolism (c) and amino acid metabolism gene sets (d). Each dot represents a plant genotype; the same genotype from different datasets are linked by segments. The length of segments connecting annual ryegrass is correlated with the similarity among datasets

Fig. 5

Trends in changes in transcripts and their corresponding proteins and metabolites, displaying the core metabolic processes involved in the response to drought in annual ryegrass

Fig. 6

Establishment of correlation networks for the identification of regulatory mechanisms in drought-resistant L. multiflorum