Plant roots play crucial roles in their response to drought conditions. However, the molecular responses in soybean roots to drought stress remain unclear. We investigated the alterations in the protein expression in the roots of a drought-resistant soybean cultivar ‘Jiyu 47’ during the seedling phase based on tandem mass tag (TMT) proteomics analysis. The results revealed significant variations in the expression of the proteins involved in several metabolic pathways in soybean roots, including sucrose metabolism, abscisic acid (ABA) metabolism, and the ATP-binding cassette (ABC) transporter pathway. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed a coordinated expression pattern of the proteins involved in the various cellular pathways responding to drought stress in soybean. The increased production of sucrose and betaine enhanced the inhibition of the damage caused by reactive oxygen species (ROS) and the tolerance of drought stress. The results of the physiological variations showed that sucrose metabolism, ABA metabolic mechanism, and the ABC transporter pathways played an important role in the antioxidant defense system in response to drought stress in soybean roots. The results of quantitative real-time PCR revealed the up-regulated expression of three genes (i.e., GmPYR1, GmHO-1, and GmSOD) involved in ABA biosynthesis and the signaling pathway. This study provides novel insights into the comprehension of the molecular pathways regulating the soybean root response to drought stress.

Phospholipid N-methyltransferase (PLMT) plays an important role in the synthesis of phosphatidylcholine (PtdCho). The aim of this study was to characterize the molecular properties of GmPLMT and the expression of soybean GmPLMT and its effects on the production of lipid metabolites. Results showed that GmPLMT composed of mainly α-helix was a hydrophobic and transmembrane protein. In soybean leaves, GmPLMT was highly expressed during seedling and flowering stages. In transgenic Arabidopsis thaliana, the highest and lowest expression levels of GmPLMT were detected at flowering and maturity stages, respectively. The total phospholipid contents in soybean grains were decreased from 7.2% (35 days after flowering) to 4.8% (55 days after flowering) and then increased to 7.0% (75 days after flowering). The contents of PtdCho showed a similar pattern to that of total phospholipids. In transgenic A. thaliana seeds, the contents of total phospholipids and PtdCho were significantly increased. Significantly positive correlations were revealed between expression of GmPLMT and contents of both PtdCho and crude fats, and between the contents of PtdCho and both linoleic acid and linolenic acid, suggesting that increased expression of GmPLMT improved the production of lipid metabolites. This study provided solid experimental evidence for further improvement of soybean quality based on GmPLMT in the molecular breeding of soybeans.

The soybean GmPEAMT1/GmPLMT double-knockout mutant (Dko) was constructed to investigate how the disruption of phospholipid-related genes affects reproductive traits, seed nutrient composition, and associated molecular responses under experimental conditions. Dko plants showed coordinated changes in photosynthetic parameters and reproductive structures: the number of pollen grains and ovules was reduced, whereas pollen and ovule size-related traits were increased, while mature seed number and 100-seed weight were maintained. Developing Dko seeds showed higher protein content and increased levels of 12 out of 18 measured amino acids, particularly alanine and cysteine. Transcriptomic and qRT-PCR analyses further indicated coordinated changes in amino acid, pantothenate, coenzyme A, glycerolipid, and glycerophospholipid-related pathways. Lipidomics provided complementary evidence of changes in phospholipid-associated and other lipid molecular features, whereas total seed lipid content showed no significant difference from the control. Together, these results suggest that GmPEAMT1/GmPLMT disruption was associated with variations in reproductive traits at the developmental stages examined and seed nutrient allocation, with lipid-feature changes representing one component of a broader multi-omic response. The proposed lipid and amino acid metabolic remodeling in GmPEAMT1/GmPLMT double-knockout soybean seeds should be regarded as a working hypothesis because direct metabolic flux, protein abundance, and enzyme activity are not measured.