Cadmium (Cd) is a toxic, non-essential heavy metal, with significant stress to plants such as soybean (Glycine max). High Cd concentration in the soil inhibits various stages of soybean growth, including seed germination, vegetative growth, and the reproduction stage. Phosphate, a vital macronutrient, has been shown to alleviate Cd-induced stress; however, the molecular mechanisms remain poorly understood. This study aimed to explore the interactive effects of Cd and phosphate on soybeans at the physiological, transcriptomic, and metabolic levels using a multi-omics approach. Experiments were conducted where soybean plants were treated with different concentrations of Cd and phosphate. The results indicated that Cd stress significantly reduced plant height, photosynthetic rate, and transpiration rate, while phosphorus application mitigated these effects, reducing Cd absorption in both roots and shoots. Furthermore, antioxidant enzyme activities (superoxide dismutase, catalase, and peroxidase) were significantly enhanced by phosphate under Cd stress, which scavenged reactive oxygen species (ROS) generated by cadmium, thereby protecting cells from oxidative stress damage. Transcriptome and metabolome analyses revealed substantial changes in gene expression and metabolite profiles in response to Cd and phosphate treatments. Notably, phosphorus treatment induced the up-regulation of genes involved in stress response, root development, and metal transport, while altering metabolic pathways related to phenolic acids, flavonoids, and lipids. This research provided new insights into the molecular mechanism by which phosphorus enhanced the activity of antioxidant enzymes, thereby improving the plant’s antioxidant defense capacity and reducing the toxic effects of cadmium in soybeans, offering potential strategies for enhancing crop resilience against heavy metal contamination.

High-density planting is crucial for maximizing the genetic potential of soybean cultivars to achieve higher yields. However, increasing the planting density can lead to the risk of plant lodging. Therefore, the identification of gene loci associated with lodging resistance is considered critical for the development of high-yielding, lodging-resistant soybean cultivars. In this study, 338 natural soybean accessions from the similar latitude were used to identify candidate genes associated with lodging resistance. Based on 9,400,987 SNPs, the soybean population was classified into three subpopulations. Genome-wide association analysis revealed that under planting densities of 300,000 and 150,000 plants/ha, a total of 20 significant SNPs were repeatedly detected under both planting densities, distributed across 14 chromosomes of soybeans. A hotspot region was identified on chromosome 19, from which seven candidate genes were detected. Based on haplotype and gene expression analyses, Glyma.19g212800 (SUS3) and Glyma.19g212700 (GH9B13) were found to be associated with significant phenotypic variations and were identified as candidate genes. RNA-seq analysis showed that DEGs were primarily enriched in the starch and sucrose metabolism pathways. The differential expression of Glyma.19g212800 among soybean haplotypes was further validated by qRT-PCR. By participating in sucrose decomposition and polysaccharide metabolism processes, it regulated cellulose content, thereby affecting the soybean plant lodging. This study facilitated the dissection of genetic networks underlying lodging traits in soybean, which benefits the genetic improvement of high-yield soybean with dense planting.

Disorders in soybean seed-filling can lead to wrinkled seeds, affecting yield and quality. Previous studies have demonstrated that some soybean cultivars from Jiamusi, Heilongjiang Province (cold-temperate continental monsoon, ~3.5 °C mean annual temperature, ~530 mm precipitation) exhibit seed-filling disorders when cultivated in Shenyang, Liaoning Province (mid-temperate semi-humid continental monsoon, ~8.3 °C, ~610 mm). However, the causes and regulatory mechanisms remain unclear. In this study, Henong 76 (a soybean cultivar with seeds less prone to wrinkling) and Heihe 43 (a soybean cultivar with seeds prone to wrinkling) were used as experimental materials. They were sown simultaneously in Jiamusi and Shenyang, respectively, to explore the causes of seed-filling disorders in Heihe 43. The results indicated that there were significant differences in the contents of soluble sugars and starch, as well as in the activities of sucrose synthase and invertase, between the seeds of Henong 76 and Heihe 43 grown in Shenyang. However, no significant differences were found between them in Jiamusi. Transcriptomic and metabolomic analyses suggested that genes related to controlling starch hydrolysis (isoamylase, α-amylase, and glycogen phosphorylase) and sucrose synthesis and decomposition (sucrose synthase, invertase, glucose-6-phosphate isomerase, and phosphoglucomutase) in Heihe 43 were upregulated in Shenyang. In contrast, genes regulating plant hormone signal transduction (auxin, gibberellin, abscisic acid, and cytokinin) were generally downregulated. These changes led to differences in metabolites, resulting in the occurrence of seed-filling disorders. Furthermore, we analyzed the climatic conditions of the two cultivars during the soybean seed-filling period. The results indicated that high temperature might be the primary meteorological factor contributing to the occurrence of seed-filling disorders. All results indicated that the insufficient accumulation of sugars in seeds due to exposure to high temperatures during the seed-filling period is the primary cause of the prone-to-wrinkling phenomenon of the Heihe 43 cultivar under the ecological conditions of Shenyang.

Defective seed filling, which manifests as seed wrinkling, severely impairs the yield and commercial quality of soybean crops. Soybean varieties independently developed in Heilongjiang Province exhibit distinct phenotypic variations in seed wrinkling across diverse ecological planting regions, whereas the molecular and physiological mechanisms driving such differences remain largely uncharacterized. In this study, two soybean genotypes with divergent heat resistance, namely, the heat-sensitive cultivar HH43 and the heat-tolerant cultivar HN76, were planted in three distinct ecological sites for comparative analysis. Statistical results indicated that ecological conditions serve as the predominant factor regulating seed-wrinkling variation, with high temperatures occurring during the seed-filling stage identified as the key abiotic stress trigger. Excessively high ambient temperatures triggered abnormal sucrose accumulation in the pod husks of heat-vulnerable HH43, disrupting the coupling relationship between sucrose metabolism and energy supply and thereby restricting starch biosynthesis in developing seeds. Transcriptome profiling combined with weighted gene co-expression network analysis (WGCNA) further demonstrated that heat stress significantly suppressed the expression of energy transport-related genes and induced the dysregulated expression of starch synthesis-associated genes in susceptible soybean plants, and these transcriptional alterations were further verified via qRT-PCR assays. Collectively, short-term extreme high temperatures interrupt the carbon transport and allocation process from pod husks to seeds in heat-sensitive soybean cultivars. By contrast, heat-tolerant genotypes can sustain a stable physiological metabolism and molecular regulatory networks to effectively cope with high-temperature stress during the seed-filling period.