Multi-Omics Analysis Provides Insights into Green Soybean in Response to Cold Stress

Abstract

Green soybean (Glycine max (L.) Merrill) is a highly nutritious food that is a good source of protein and fiber. However, it is sensitive to low temperatures during the growing season, and enhancing cold tolerance has become a research hotspot for breeding improvement. Background/Objectives: The underlying molecular mechanisms of cold tolerance in green soybean are not well understood. Methods: Here, a comprehensive analysis of transcriptome and metabolome was performed on a cold-tolerant cultivar treated at 10 °C for 24 h. Results: Compared to control groups, we identified 17,011 differentially expressed genes (DEGs) and 129 differentially expressed metabolites (DEMs). The DEGs and DEMs were further subjected to KEGG functional analysis. Finally, 11 metabolites (such as sucrose, lactose, melibiose, and dehydroascorbate) and 17 genes (such as GOLS, GLA, UGDH, and ALDH) were selected as candidates associated with cold tolerance. Notably, the identified metabolites and genes were enriched in two common pathways: 'galactose metabolism' and 'ascorbate and aldarate metabolism'. Conclusions: The findings suggest that green soybean modulates the galactose metabolism and ascorbate and aldarate metabolism pathways to cope with cold stress. This study contributes to a deeper understanding of the complex molecular mechanisms enabling green soybeans to better avoid low-temperature damage.

Keywords: colds stress; green soybean (Glycine max (L.) Merrill); metabolome; molecular mechanism; transcriptome.

Figure 1

Transcriptome analysis of green soybeans (QXD15). (A) MA plot of the DEGs in response to cold stress. (B) Functional Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway classification of DEGs (top 20 listed).

Figure 2

Metabolomics analysis of green soybeans (QXD15). (A) Classification of metabolites. (B) PCA of metabolites. (C) Volcano plot of the DEMs in response to cold stress. (D) KEGG pathway classification of DEMs (top 20 listed). (E) Heatmap of 31 DAMs under cold stress. Scaled values of the relative contents of metabolites were used for z-scale normalization.

Figure 3

The genes and metabolites identified in the galactose metabolism pathway in response to cold stress. Blue represents the metabolites or genes that changed under cold stress. GOLS: inositol 3-alpha-galactosyltransferase [EC:2.4.1.123]; RFS: raffinose synthase [EC:2.4.1.82]; GLA: alpha-galactosidase [EC:3.2.1.22]; INV: beta-fructofuranosidase [EC:3.2.1.26]; UGP2: UTP-glucose-1-phosphate uridylyltransferase [EC:2.7.7.9].

Figure 4

The genes and metabolites identified in the ascorbate and aldarate metabolism pathways in response to cold stress. Blue represents the metabolites or genes that changed under cold stress. UGDH: UDPglucose 6-dehydrogenase [EC:1.1.1.22]; USP: UDP-sugar pyrophosphorylase [EC:2.7.7.64]; GLCAK: glucuronokinase [EC:2.7.1.43]; GULO: L-gulonolactone oxidase [EC:1.1.3.8]; DHAR: glutathione dehydrogenase/transferase [EC:1.8.5.1 2.5.1.18]; ALDH: aldehyde dehydrogenase (NAD+) [EC:1.2.1.3]; GME: GDP-D-mannose 3′, 5′-epimerase [EC:5.1.3.18 5.1.3.-]; VTC2_5: GDP-L-galactose phosphorylase [EC:2.7.7.69]; VTC4: inositol-phosphate phosphatase/L-galactose 1-phosphate phosphatase [EC:3.1.3.25 3.1.3.93]; GalDH: L-galactose dehydrogenase [EC:1.1.1.316]; APX: L-ascorbate peroxidase [EC:1.11.1.11]; AO: L-ascorbate oxidase [EC:1.10.3.3].