Soybean Development Research Articles

Root morphology, nitrogen metabolism and amino acid metabolism in soybean under low phosphorus stress.

Phosphorus deficiency is a major influence on growth and development of soybean. Therefore, improving phosphorus utilization efficiency in soybean is a research priority for the soybean community. In this experiment, Liaodou 13 (high phosphorus utilization: HPE) and Tiefeng 3 (low phosphorus utilization: LPE) were used as test varieties. We investigated changes in root morphology, amino acid content, and content of key substances of the nitrogen metabolic pathway with normal phosphorus (0.5 mM) and low phosphorus (0.005 mM) treatments. The results showed that the root length, root surface area and number of lateral roots of HPE roots were higher than those of LPE roots under normal and low phosphorus conditions. The contents of different types of amino acids showed different trends in two varieties. The HPE showed small change in the content of total hydrolyzed amino acids under the low phosphorus condition when compared to the normal phosphorus treatment by a 6.67% decrease, on the contrary LPE showed a drastic decrease by 20.36%. However, HPE exhibited similar decreasing trends in the contents of hydrolyzed and free aspartic acid with the low phosphorus treatment. Moreover, the contents of free histidine and valine in LPE were significantly increased by 657.84% and 149.29% respectively, in contrast to significant decreases in HPE. In aspects of major nutrient elements, the contents of phosphorus, total nitrogen and ammonia nitrogen in both HPE and LPE varieties decreased to dramatic levels. However, the nitrate nitrogen content significantly increased 78.51% for HPE and 65.12% for LPE. Compare to the normal condition, the GOGAT activity in HPE decreased by 5.18% but increased by 33.10% in LPE. Compare to the normal condition, the GS activity in HPE increased by 7.26% but decreased by 21.72% in LPE under phosphorus deficiency. In summary, the phosphorus-efficient soybean variety HPE exhibited superior tolerance to low phosphorus deficiency through advantageous root morphology, phosphorus uptake and transfer capability, and balanced amino acid metabolism and nitrogen metabolism pathways.

Post-Flowering Photoperiod Sensitivity of Soybean in Pod-Setting Responses.

The development of soybean (Glycine max) is regulated by the photoperiod, with genes related to photoperiod sensitivity primarily focused on the flowering time. However, their roles in post-flowering reproductive development and the mechanisms by which the photoperiod affects them are not yet determined. In this study, we found that pod formation is sensitive to the photoperiod. Long-day conditions tended to extend the time from flowering to pod formation, and the first wave of flowers tended to fall off. Additionally, the photoperiod affected the pistil morphology; under short-day conditions, the stigma had a curved hook-like structure that facilitated better interaction with the filaments when pollen was released, ultimately influencing the timing of pod formation. Photoperiod-insensitive mutants, lacking E1 family and Evening Complex (EC) genes, showed no difference in the pod formation time under long-day or short-day conditions. Hormone content analysis and transcriptome data analysis indicated that various hormones, reactive oxygen species (ROS) burst pathway signals, and the application of sucrose solution in vitro might influence floral organ abscission.

Genetic Adaptations of Soybean to Cold Stress Reveal Key Insights Through Transcriptomic Analysis.

Low temperatures greatly restrict the development, growth, and productivity of soybeans, with their effects differing across various cultivars. The present work investigated the transcriptome and physiological reactions of two soybean cultivars, namely "KD52" exhibiting cold tolerance and "DS17" displaying cold sensitivity, to cold stress across a precisely defined period. The soybean plants were subjected to cold treatment at 6 °C for durations of 0, 2, 4, and 8 h. A comparative physiological marker study revealed distinct reactions to cold stress in the two cultivars. The findings showed that increased malondialdehyde levels provided evidence of DS17's heightened vulnerability to lipid peroxidation and membrane degradation. In contrast, the KD52 cultivar exhibited increased activities of antioxidant enzymes, including peroxidase and superoxide dismutase, in response to cold exposure, suggesting a strong antioxidant defense system against oxidative stress. The transcriptomic analysis revealed dynamic responses, mapping 54,532 genes. Within this group, a total of 234 differentially expressed genes (DEGs) were found to be consistently changed at several time intervals, showing unique expression patterns across the two cultivars. Analysis of the association between these important DEGs and the physiological indicators revealed candidate genes that may be involved in controlling oxidative damage and antioxidant defenses. Some key genes showed a progressive rise in expression over time in both cultivars, with a more significant acceleration in KD52, and are probably involved in promoting adaptation processes during extended periods of cold exposure. The identification of improved defense mechanisms in KD52, together with the identification of crucial genes, offers great prospects for enhancing the cold stress resilience of soybean.

Quantitative and qualitative damage caused by Halyomorpha halys (Hemiptera: Pentatomidae) on soybean crop at different growth stages

The brown marmorated stink bug Halyomorpha halys, an invasive species native to East Asia, is now present and abundant on soybean throughout Europe where it has become a major pest damaging the crop. Because a better understanding of the impact of H. halys is crucial to implement effective and sustainable pest management, the present study aimed to assess the stages at which soybean is most susceptible to H. halys attacks, and the qualitative and quantitative alterations caused by its feeding on soybean seeds. Therefore, soybean plants were exposed to stink bug adults for 2 weeks at different development stages and were examined at harvest for damage. Stay-green syndrome occurred most severely as a result of H. halys attacks at soybean development stages R4-R5. In the same period, the bug feeding activity significantly reduced the number of seeds per pod, thus indicating a higher damage rate at the R4-R5 stage when soybean surveillance should be intensified in order to properly target pest management strategies. The lower number of seeds per pod corresponded to an increase in the seed weight due to plant compensation mechanisms, leading to grain yields that did not differ in relation to the time of attack or the rate of damaged seeds. However, while not causing overall a loss of weight production, H. halys attacks were shown to cause qualitative damage to soybean seeds, especially by altering protein content and mobilizing several primary metabolites from storage macromolecules, which will have to be considered depending on the intended use of the production.

Genome-wide association study revealed some new candidate genes associated with flowering and maturity time of soybean in Central and West Siberian regions of Russia.

The duration of flowering and maturity is an important agricultural trait determining the suitability of a variety for cultivation in the target region. In the present study, we used genome-wide association analysis (GWAS) to search for loci associated with soybean flowering and maturity in the Central and West Siberian regions of Russia. A field experiment was conducted in 2021/2022 at two locations (Orel and Novosibirsk). A germplasm collection of 180 accessions was genotyped using SoySNP50K Illumina Infinium Bead-Chip. From the initial collection, we selected 129 unrelated accessions and conducted GWAS on this dataset using two multi-locus models: FarmCPU and BLINK. As a result, we identified 13 loci previously reported to be associated with duration of soybean development, and 17 new loci. 33 candidate genes were detected in these loci using analysis of co-expression, gene ontology, and literature data, with the best candidates being Glyma.03G177500, Glyma.13G177400, and Glyma.06G213100. These candidate genes code the Arabidopis orthologs TOE1 (TARGET OF EAT 1), SPL3 (SQUAMOSA PROMOTER BINDING PROTEIN LIKE 3), the DELLA protein, respectively. In these three genes, we found haplotypes which may be associated with the length of soybean flowering and maturity, providing soybean adaptation to a northern latitudes.

Seed treatment with biostimulant doses in soybean development and gas exchange

Seed treatment with biostimulant doses in soybean development and gas exchange

Development and nutritional properties of whole wheat, little millet and soybean based pasta

Development and nutritional properties of whole wheat, little millet and soybean based pasta

Rationality of soybean farmers: the findings from rainfed field agroecosystems

Purpose. This research aims to examine the factors that influence the rationality and income of soybean farmers, especially in rain fed field agroecosystems. Methodology / approach. The research was designed quantitatively with a type of survey on 263 soybean farmers from a total population of 768 farmers spread across Jatiwaras and Pancatengah subdistricts, Tasikmalaya Regency, which is one of the centres for soybean development in West Java, Indonesia. The determination of the farmer sample was carried out proportionally randomly using the Slovin formula with an error rate of 5 %. The data analysed is primary data obtained directly from farmers using a questionnaire with a Likert scale consisting of 5 answer choices. The analytical tool used is Structural Equation Model (SEM) with AMOS to determine the influence between variables. Results. The research results show that: (1) Farmer characteristics have a significant positive relationship with farmer motivation. These characteristics are a strong driving force to increase their motivation in soybean farming to be even better in an effort to increase their income; (2) Farmer characteristics have a significant positive effect on farmer rationality. The older the age, the higher the education, and the greater the burden of responsibility borne by the farmers’ family, the more rational they consider soybean cultivation to be, which means that they will be more cautious in growing soybeans to minimise the risk of losses they may incur; (3) Farmer motivation has a significant positive effect on farmer rationality. The stronger farmers’ motivation in soybeans farming, the more rational it makes them in thinking about farming as well as possible; (4) Farmer rationality has a significant positive effect on income. The more rational the thinking of farmers in soybean farming, in the sense that they can effectively use social networks, efficiently grow soybeans and adopt technology, the more they can increase production, which ultimately increases income. Originality / scientific novelty. This study focuses more on the rationality of smallholder farmers in Indonesia, who have many structural disadvantages, such as limited land ownership, average age of farmers, low education level and many family responsibilities, which are constraints to soybean farming; how smallholder farmers are related to motivation in soybean farming and whether this farmers’ rationality can increase their income, while several previous studies only discussed farmers’ rationality without considering socioeconomic factors, especially smallholder farmers. Practical value / implications. This research provides evidence that there is a relationship between farmer characteristics and motivation which has a significant effect on farmer rationality so that in the end it can increase income. The results of this research have implications for government policies in efforts to increase farmers’ income by increasing their capacity through intensive and sustainable agricultural extension activities. The existence of more intensive and sustainable agricultural extension activities can increase the knowledge and insight of small farmers in soybean farming, which in turn can motivate farmers to think and act more rationally so that they can better optimise all the resources they have.

Co-composting of tail vegetable with flue-cured tobacco leaves: analysis of nitrogen transformation and estimation as a seed germination agent for halophyte.

Resource utilization of tail vegetables has raised increasing concerns in the modern agriculture. However, the effect and related mechanisms of flue-cured tobacco leaves on the product quality, phytotoxicity and bacterially-mediated nitrogen (N) transformation process of tail vegetable composting were poorly understood. Amendments of high-dosed (5% and 10% w/w) tobacco leaves into the compost accelerated the heating process, prolonged the time of thermophilic stage, increased the peak temperature, thereby improving maturity and shortening composting duration. The tobacco leaf amendments at the 10% (w/w) increased the N conservation (TN and NH4-N content) of compost, due to the supply of N-containing nutrient and promotion of organic matter degradation by tobacco leaves. Besides, tobacco leaf amendments promoted the seed germination and root development of wild soybean, exhibiting the feasibility of composting product for promoting the growth of salt-tolerant plants, but no dose-dependent effect was found for tobacco leaf amendments. Addition of high dosed (5% and 10% w/w) tobacco leaves shifted the bacterial community towards lignocellulosic and N-fixing bacteria, contributing to increasing the compost maturity and N retention. PICRUSt 2 functional prediction revealed that N-related bacterial metabolism (i.e., hydroxylamine oxidation and denitrifying process) was enhanced in the tobacco leaf treatments, which contributed to N retention and elevated nutrient quality of composting. To the best knowledge, this was the first study to explore the effect of tobacco waste additives on the nutrient transformation and halophyte growth promotion of organic waste composting. These findings will deepen the understanding of microbially-mediated N transformation and composting processes involving flue-cured tobacco leaves.

Genes of photoperiod sensitivity and early maturity E1-E4: dynamics of soybean growth in different daylength conditions

Background. Morphometric indicators are crucial for evaluating the development and productivity of soybeans. They are influenced by genetic and environmental factors. The use of nearly isogenic soybean lines is a convenient model for determining the impact of early maturity genes and daylength on growth indicators. The aim of this study was to determine the influence of different daylengths and early maturity genes on soybean morphometric indicators under conditions of the temperate zone (at the latitude of Kharkiv – 50° N). Materials and Methods. The study involved nearly isogenic soybean lines of the “Clark” cultivar with varying sensitivity to daylength. The research covers the results of field experiments over three seasons using different soybean lines. After reaching the V3 stage, some plants were subjected to short-day conditions for 14 days. Morphological indicators of ten plants per experimental variant were determined: plant height, dry weight, leaf number, and leaf surface area of soybean plants. Morphometric measurements were taken on the day of the beginning of different daylength treatments and on days 7, 14 and 21. The study results are presented as the mean values of the investigated parameters (plant height, dry weight, number of leaves and leaf surface area of soybean plants). Results. It was shown that under long-day conditions, dominant alleles of the E1 and E3 genes increased the dry weight of plants, while the dominant allele E2 increased plant height. The dominant allele E4 had no significant effect on plant height and weight indicators of soybean plants. Plants with dominant alleles of genes E1-E4 under long-day conditions had smaller leaf area compared to lines with recessive alleles of these genes. Conclusions. The obtained results on the relationships between genetic and environmental factors in influencing soybean plant height, weight, and leaf area can be useful in improving soybean yield and selecting cultivars that will be productive in high latitude conditions.

Gene editing and overexpression of soybean miR396a reveals its role in salinity tolerance and development

MicroRNAs (miRNAs) are versatile regulators of gene expression at both the transcription and post-transcription levels. The microRNA miR396 plays vital roles in growth, development, and resistance to abiotic stresses in many plant species. However, the roles and functions of miR396 in soybeans are not well understood. Here, we report that Gm-miR396a influences soybean development and salinity tolerance. We found that soybean miR396a was responsive to salt stress. Gm-miR396a gene-edited lines (miR396a-GEs), created using CRISPR/Cas9, exhibited more branches, higher grain yields, and greater salinity tolerance than control plants. The transcripts in lines with altered abundance of miR396a-GE were significantly enriched for biological processes related to hormone regulation. Overexpression of the Gm-miR396a precursor (pre-miR396a-OE) resulted in developmental deficiencies including dwarfness, abnormal inflorescences and flowers, smaller and fewer seeds, and small leaves with larger and more numerous stomata. Transcriptome analysis indicated photosynthesis-related genes were downregulated in pre-miR396a-OE plants. These results contribute valuable insights into the function of Gm-miR396a in soybeans and hold promise for enhancing soybean yield and salinity tolerance through germplasm innovation.

Non-CG DNA hypomethylation promotes photosynthesis and nitrogen fixation in soybean

Non-CG DNA methylation, a plant-specific epigenetic mark mainly regulated by chromomethylase (CMT), is known to play important roles in Arabidopsis thaliana. However, whether and to what extent non-CG DNA methylation modulates agronomic traits in crops remain to be explored. Here, we describe the consequences of non-CG DNA hypomethylation on development, seed composition, and yield in soybean (Glycine max). We created a Gmcmt mutant line lacking function of all four CMT genes. This line exhibited substantial hypomethylation of non-CG (CHG and CHH) sites. Non-CG hypomethylation enhanced chromatin accessibility and promoted or repressed the expression of hundreds of functionally relevant genes, including upregulation of GOLDEN-LIKE 10 (GmGLK10), which led to enhanced photosynthesis and, unexpectedly, improved nitrogen fixation efficiency. The Gmcmt line produced larger seeds with increased protein content. This study provides insights into the mechanisms of non-CG methylation-based epigenetic regulation of soybean development and suggests viable epigenetic strategies for improving soybean yield and nutritional value.

Microbial inoculants as a means of improving soil and crop yields

The article presented the results of studies of the influence of microbial inoculants Rhizobium japonicum and Azospirillum brasilense on the growth and development of soybean (Glycine max) at the initial stages of its development. The study was conducted on three experimental plots: a control plot without treatment, a plot with Rhizobium japonicum inoculum and a plot with Azospirillum brasilense inoculum. The main indicators were evaluated: plant height, number of leaves, root system development and total biomass at different stages of plant growth, as well as laboratory analysis of nitrogen content in plant tissues. The results of the study showed that the inoculants had a significant impact on all measured parameters compared to the control plot. In particular, the plants in the plot with Rhizobium japonicum showed 50% higher growth and development of the root system, which was confirmed by the formation of root nodules responsible for nitrogen fixation. Azospirillum brasilense also improved plant growth and root system development, but its effect was less pronounced compared to Rhizobium japonicum. Nitrogen content analysis showed that plants in the Rhizobium japonicum plot had 45% higher tissue nitrogen content compared to the control plot, indicating effective nitrogen fixation. In plants treated with Azospirillum brasilense, the nitrogen content was also 25% higher, but without nodule formation, the effect was less pronounced. The aim of the study was to evaluate the effectiveness of microbial inoculants in improving plant growth and development in the early stages of vegetation, to investigate their effect on root system productivity, nitrogen uptake and total plant biomass, and to determine the optimal conditions for maximising the impact of inoculants in agricultural conditions. The results emphasised the importance of using microbial inoculants to increase soybean productivity and resistance in the early stages of its development. The application of Rhizobium japonicum provided a greater increase in biomass, root system and nitrogen assimilation, which makes this inoculant more effective than Azospirillum brasilense

Evaluating the market positions of soybean oil-producing countries in the world market

Abstract Soybeans have an essential position as the main legume crop in the world food system. This research focuses on four high-producer countries of soybean, i.e., India, the Netherlands, Brazil, and the USA. The subject of soybeans as a vegetable oil includes soybean seeds, soybean oil, soybean oil cake, and refined soybeans. This research aims to identify opportunities for the industrial development of soybeans and their derivatives from socio-economic aspects in the world. The analytical method used in this soybean research is the BCG matrix. The data collection used is secondary data from several countries that export soybeans from 2020 to 2021, as well as a literature review of several kinds of literature. Soybean exporters in 2021 are in first place, namely Brazil (USD 39 billion), the United States (USD 27.8 billion) is in second place, Paraguay (USD 2.99 billion) is in third place, The Netherlands (USD 462 million) is in 7th place, and India (USD 22.9 million) is in 33rd place. The analysis results from soybean research show that Argentina took the cash cow position in the BCG matrix and has excellent potential for development in the soybean industry and its derivative products to meet market trends worldwide.

Effect of physiologically active substances on the growth, development and yield of soybeans

The results of research on the influence of physiologically active substances on the growth, development and yield of soybean in the conditions of the Middle Volga region are presented. The study of preparations was carried out on the released soybean variety Yuzhanka. The preparations Mival Agro, Vitanol NP (N 10%, P 30%), Vitanol NP (N 30%, P 10%) and NanoSilica were applied at the dosages recommended by the manufacturers. The experiment scheme included four variants of treatments with preparations and control (water). The preparations were applied for pre-sowing seed treatment and spraying of vegetative plants. The growth regulator Mival Agro (seed and plant treatment) provided a 23.1% increase in yield. Treatment with Vitanol NP (N 10%, P 30%) gave an 18.3% yield increase compared to the control. The highest yield was obtained in the variant with Vitanol NP treatment (N 30%, P 10%), which exceeded the control variant by 68.8%. The yield increase when treated with NanoSilicon exceeded the control variant by 29.4%. Application of all physiologically active substances had a positive effect on the growth, development and productivity of soybean plants. Application of Vitanol NP (N 10%, P 30%) had a positive effect on the yield structure parameters such as plant height (527 cm) and lower bean attachment height (15.8 cm). Vitanol NP (N 30%, P 10%) and NanoSilica preparations contributed to the increase in the number of beans (18.1–18.2 pcs). Also, the studied preparations had a positive effect on 1000 seed weight, plant height and height of the lower bean attachment, compared to the control.

Morphological characterization and transcriptome analysis of rolled and narrow leaf mutant in soybean

BackgroundIn plants, the leaf functions as a solar panel, where photosynthesis converts carbon dioxide and water into carbohydrates and oxygen. In soybean, leaf type traits, including leaf shape, leaf area, leaf width, and leaf width so on, are considered to be associated with yield. In this study, we performed morphological characterization, transcriptome analysis, and endogenous hormone analysis of a rolled and narrow leaf mutant line (rl) in soybean.ResultsCompared with wild type HX3, mutant line rl showed rolled and narrower leaflet, and smaller leaf, meanwhile rl also performed narrower pod and narrower seed. Anatomical analysis of leaflet demonstrated that cell area of upper epidermis was bigger than the cell area of lower epidermis in rl, which may lead rolled and narrow leaf. Transcriptome analysis revealed that several cytokinin oxidase/dehydrogenase (CKX) genes (Glyma.06G028900, Glyma.09G225400, Glyma.13G104700, Glyma.14G099000, and Glyma.17G054500) were up-regulation dramatically, which may cause lower cytokinin level in rl. Endogenous hormone analysis verified that cytokinin content of rl was lower. Hormone treatment results indicated that 6-BA rescued rolled leaf enough, rescued partly narrow leaf. And after 6-BA treatment, the cell area was similar between upper epidermis and lower epidermis in rl. Although IAA content and ABA content were reduced in rl, but exogenous IAA and ABA didn’t affect leaf type of HX3 and rl.ConclusionsOur results suggest abnormal cytokinin metabolism caused rolled and narrow leaf in rl, and provide valuable clues for further understanding the mechanisms underlying leaf development in soybean.

Effects of phosphate fertilization and sulfadiazine on plant growth, root morphology, nitrogen and phosphorus uptake of soybean and maize

Low soil phosphorus (P) availability is a limiting factor for crop production. Application of livestock manure as organic fertilizer can increase soil P availability, but may cause soil contamination with antibiotics such as sulfadiazine (SD), thus adversely affecting plant growth and nutrient uptake. The effects of P (0 and 50 mg kg−1) and SD (0, 1, 10, and 100 mg kg−1) levels on plant growth, root development, and nitrogen (N) and P uptake of maize and soybean were examined in a pot experiment using a loess soil as the test soil. High levels of SD considerably inhibited plant growth of both crops. Both P fertilization and SD negatively affected root development of both crops, especially at higher SD levels. For both crops, the average root diameter and the proportion of thick roots increased with increasing soil SD level. When soil SD level was ≤10 mg kg−1, the effects of P fertilization and SD on plant N and P concentrations, and N:P, N- and P-utilization efficiency were not significant in most cases. The effects of SD on plant N and P nutrition could not be of a great concern when soil SD level was ≤10 mg kg−1. Overall, soil SD pollution could reduce plant biomass and inhibit root development of soybean and maize, with a stronger effect on root development than on plant biomass at a high soil SD level (≥10 mg kg−1). In agricultural production, attention should be paid to soil SD pollution via manure application.

Effect of sugarcane bagasse biochar on soybean germination and initial growth

Biochar is known as an excellent soil conditioner and a powerful carbon sequestration tool. However, to expand its use, it is necessary to understand potential adverse effects. To better address this issue, biochar was prepared from sugarcane bagasse. The effect of biochar on the germination of soybean seeds was evaluated, and a greenhouse experiment was conducted to assess the response of soybean seedlings to biochar application at different rates (CK, 0% w/w; BC1, 1% w/w; BC3, 3% w/w; and BC5, 5% w/w). Thirty days after sowing, growth parameters, soil physicochemical attributes, and microbiota were evaluated. The biochar exhibited a low O/C ratio (0.18) and an irregular porous surface, which promoted improvements in the soil's physical, chemical, and biological attributes. It also demonstrated no phytotoxic effects in germination tests for application rates up to 50 t/ha. The results of the soybean cultivation showed that the BC3 and BC5 treatments significantly increased the fresh mass of the aerial part by 64% and 86%, respectively, compared to CK. These treatments also significantly increased the fresh mass of the root system by 23% and 423%, respectively. These results highlight the potential of biochar in promoting early soybean development.

Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis.

Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD)analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.

A spatially resolved multiomic single-cell atlas of soybean development.

Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.