Vegetative soybean (maodou or edamame) serves as a nutrient-rich food source with significant potential for mitigating global nutritional deficiencies. This study undertook a thorough examination of the nutritional profiles and transcriptomic landscapes of six soybean cultivars, including three common cultivars (Heinong551, Heinong562, and Heinong63) and three fresh maodou cultivars (Heinong527, HeinongXS4, and HeinongXS5). Nutrient analysis of the seeds disclosed notable differences in the levels of protein, fat, soluble sugars, vitamin E, calcium, potassium, magnesium, manganese, iron, and zinc across the cultivars. Through comparative transcriptome profiling and RNA sequencing, distinct variations in differentially expressed genes (DEGs) were identified between fresh and traditional maodou cultivars. Functional enrichment analyses underscored the involvement of DEGs in critical biological processes, such as nutrient biosynthesis, seed development, and stress responses. Additionally, association studies demonstrated robust correlations between specific DEG expression patterns and seed nutrient compositions across the different cultivars. Sankey diagrams illustrated that DEGs are strongly linked with seed quality traits, revealing potential molecular determinants that govern variations in nutritional content. The identified DEGs and their relationships with nutritional profiles offer valuable insights for breeding programs focused on developing cultivars with improved nutritional quality, tailored to specific dietary needs or industrial applications.

The pseudo response regulator (PRR) gene is an important component of the core oscillator involved in plant circadian rhythms and plays an important role in regulating plant growth and development and stress responses. In this study, we investigated the function of GmPRR7b by overexpression and gene editing approaches. It was found that GmPRR7b plays a role in delaying flowering. While GmPRR7b overexpressing plants showed significantly delayed flowering compared to untransformed WT, GmPRR7b edited plants flowered earlier than the control WT. On the basis of previous research results and bioinformatics analysis, we re-identified 14 soybean PRR genes and analysed their rhythmic expression. Based on the rhythmic expression pattern, we found that GmPRR5/9a and GmPRR5/9b interacted with GmPRR7b by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments. Combined with the expression regulatory networks of the GmPRR7b, we inferred a possible regulatory mechanism by which GmPRR7b affects flowering through quit rhythm expression. These research elements provide valuable references for understanding growth, development, and circadian regulation in soybean.

Background: Polyphenol oxidases (PPOs) form a multigene family that is widely distributed in plants, animals, and insects. To date, PPOs have been identified in plants such as Populus L. and Solanum tuberosum L., but studies on PPOs in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.) remain limited. Methods: To clarify the nature, structure, evolution, expression pattern, and interaction network of PPOs in these plants, we performed bioinformatics analysis and evaluated the expression patterns of PPOs in soybean and wild soybean throughout the growth period and under salt stress. Results: We identified 17 and 15 genes belonging to the PPO family. These genes were distributed across chromosomes 7 and 6 and could be divided into three groups. Most of these genes only contained one coding sequence (CDS), and their gene structure, conserved motifs, and 3D structures were very similar. Although there were a few intraspecies gene duplications, 75 gene replication pairs between soybean and wild soybean were detected. A Ka/Ks analysis showed that the PPOs in these plants were mainly subjected to purity selection. Moreover, the expression of the PPO genes varied greatly during different stages of the growth period and under salt stress, showing high temporal and spatial specificity. The protein interaction networks of these genes appeared to be quite distinct. Through the interaction analysis of the candidate gene GmPPO2 selected under salt stress, Glyma.07G059000, Glyma.10G279000, and Glyma.03G167900 were identified as the candidate genes regulating salt stress tolerance in soybean. Conclusions: These findings provide a foundation for further research on the evolution of soybean and wild soybean, as well as the functions of the PPO gene family.