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Rhythms produced by the endogenous circadian clock play a critical role in allowing plants to respond and adapt to the environment. While there is a well-established regulatory link between the circadian clock and responses to abiotic stress in model plants, little is known of the circadian system in crop species like soybean. This study examines how drought impacts diurnal oscillation of both drought responsive and circadian clock genes in soybean. Drought stress induced marked changes in gene expression of several circadian clock-like components, such as LCL1 -, GmELF4 - and PRR -like genes, which had reduced expression in stressed plants. The same conditions produced a phase advance of expression for the GmTOC1 -like, GmLUX -like and GmPRR7 -like genes. Similarly, the rhythmic expression pattern of the soybean drought-responsive genes DREB- , bZIP- , GOLS -, RAB18 - and Remorin -like changed significantly after plant exposure to drought. In silico analysis of promoter regions of these genes revealed the presence of cis-elements associated both with stress and circadian clock regulation. Furthermore, some soybean genes with upstream ABRE elements were responsive to abscisic acid treatment. Our results indicate that some connection between the drought response and the circadian clock may exist in soybean since (i) drought stress affects gene expression of circadian clock components and (ii) several stress responsive genes display diurnal oscillation in soybeans.

Rhizosphere soil is one of the most diverse microbial environments worldwide and is recognized as an ecosystem undergoing continuous transformation. Microorganisms inhabiting the rhizosphere soil play diverse roles in maintaining and stabilizing the environment. Consequently, plant-associated habitats serve as a dynamic environment influenced by various microbial composition factors. Genetically modified plants have introduced numerous traits into agriculture to address productivity-limiting factors, such as drought. This study aimed to assess the microbial diversity in the rhizosphere soils of drought-tolerant transgenic (AtAREB1) and conventional (cultivar BR 16) soybean plants. Bacterial communities were investigated using a cultivation-independent approach, utilizing pooled samples from the respective soils, followed by pyrosequencing of the 16S rRNA gene. In addition, physicochemical parameters of the soils were evaluated. The results indicated that the microbial diversity in the rhizosphere soil of both transgenic and conventional plants remained unchanged, with similar taxonomic distributions observed in both bacterial communities. Analysis of physicochemical parameters in both soils suggested a potential direct relationship between these properties and the microbial community profile, with implications for soil nutrient content and physical composition. These results are positive for biosafety when using the transgenic cultivar compared with the conventional crop.

Soybean plays a crucial role in global food security and the economy, but its yield is often limited by water deficit (WD) and water excess (WE). Understanding the molecular mechanisms that regulate responses to these stresses is essential to improve crop resilience. In this study, we analyzed nine ABA-induced genes involved in WD and WE signaling using transcriptome libraries, RT-qPCR, gas exchange analysis, and root morphology. A total of 4412 and 2597 genes were differentially expressed under WE and WD, respectively. The response to exogenous ABA varied between conditions, reflecting stress-specific adaptations. Among 10 genes exclusively expressed under WE, only ERF1 and Peroxydase showed increased transcript levels after ABA treatment, being similarly regulated under both WD and WE. These results reveal distinct molecular and physiological responses to ABA depending on water status, highlighting potential targets for genetic improvement. The identified genes provide insights into ABA-mediated regulation of soybean stress tolerance and represent promising candidates for breeding strategies aimed at enhancing resilience to water-related stresses. Ultimately, this study contributes to a deeper understanding of soybean adaptation mechanisms, supporting sustainable crop management and productivity under challenging environmental conditions.

BackgroundThe drought condition is responsible for considerable losses in soybean production, which in turn may result in billionaire losses. After drought perception, plants activate a cascade of protecting genes against water deficit (WD), many of which are responsive to abscisic acid, the most important phytohormone to plants’ adaptation. This work aimed to recover abscisic acid (ABA)-responsive differentially expressed genes (DEG) from an RNA-Seq, carried out from leaves and roots of drought-sensitive (BR16) and tolerant (Embrapa 48) soybean cultivars under mild (MiWD), moderate (MoWD), and severe (SWD) water-deficit treatments. Enriched ABA-responsive pathways important to drought tolerance in soybean were also identified.ResultsIn drought-sensitive and tolerant soybean cultivars, approximately 75% of genes were identified as ABA-responsive by containing more than two ABRE (ABA-responsive elements) in the promoter region. Most of these genes were positively regulated. Roots were the tissue with more ABA-responsive genes and pathways triggered in response to WD in both cultivars, although, on the tolerant cultivar, these pathways were higher expressed. The most important enriched ABA pathways observed in the roots of both cultivars were involved in sugar and sulfur amino acid biosynthesis, osmoregulation, and crosstalk among ABA and ethylene, jasmonate, auxin, and cytokinin. Other pathways enriched were involved in phytoalexin production, ROS homeostasis, and membrane stability by glycerolipid and glycerophospholipid production. ABA-responsive genes were also ordered based on their expression profile in tissue and cultivar, and nine confidence groups could be observed. More than 80% of these clustered genes showed the same regulation profile under MiWd, MoWD, and SWD treatments. Activation of ABA biosynthesis under water deficit was validated by RT-qPCR by increasing the expression level of NCED3, an important enzyme in this pathway, and GOLS, a known ABA-responsive gene.ConclusionsA robust catalog of ABA-responsive genes was made available in this work. Considering ABA’s role in drought-response mechanisms, the genes in the groups pointed out in this study would be reliable candidates to be used in strategies to develop soybean lines more tolerant to drought. This paper, presented for the first time, ABA-responsive genes and ABA-enriched pathways in contrasting soybean cultivars for drought tolerance.

Drought is one of the most stressful environmental factor causing yield and economic losses in many soybean-producing regions. In the last decades, transcription factors (TFs) are being used to develop genetically modified plants more tolerant to abiotic stresses. Dehydration responsive element binding (DREB) and ABA-responsive element-binding (AREB) TFs were introduced in soybean showing improved drought tolerance, under controlled conditions. However, these results may not be representative of the way in which plants behave over the entire season in the real field situation. Thus, the objectives of this study were to analyze agronomical traits and physiological parameters of (1Ab58), (1Bb2193), and (1Ea2939) GM lines under irrigated (IRR) and non-irrigated (NIRR) conditions in a field experiment, over two crop seasons and quantify transgene and drought-responsive genes expression. Results from season 2013/2014 revealed that line 1Ea2939 showed higher intrinsic water use and leaf area index. Lines 1Ab58 and 1Bb2193 showed a similar behavior to wild-type plants in relation to chlorophyll content. Oil and protein contents were not affected in transgenic lines in NIRR conditions. Lodging, due to plentiful rain, impaired yield from the 1Ea2939 line in IRR conditions. qPCR results confirmed the expression of the inserted TFs and drought-responsive endogenous genes. No differences were identified in the field experiment performed in crop season 2014/2015, probably due to the optimum rainfall volume during the cycle. These field screenings showed promising results for drought tolerance. However, additional studies are needed in further crop seasons and other sites to better characterize how these plants may outperform the WT under field water deficit.

Background Since drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we applied Illumina technology to sequence 36 cDNA libraries synthesized from control and drought-stressed soybean plants to verify the dynamic changes in gene expression during a 24-h time course. Cycling variables were measured from the expression data to determine the putative circadian rhythm regulation of gene expression. Results We identified 4866 genes differentially expressed in soybean plants in response to water deficit. Of these genes, 3715 were differentially expressed during the light period, from which approximately 9.55 % were observed in both light and darkness. We found 887 genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes, 35.52 % exhibited expression oscillations in a 24 h period. This number increased to 39.23 % when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Such differences in plants under stress were primarily observed in ZT0 (early morning) to ZT8 (late day) and also from ZT4 to ZT12. Stress-related pathways were triggered in response to water deficit primarily during midday, when more genes were up-regulated compared to early morning. Additionally, genes known to be involved in secondary metabolism and hormone signaling were also expressed in the dark period. Conclusions Gene expression networks can be dynamically shaped to acclimate plant metabolism under environmental stressful conditions. We have identified putative cycling genes that are expressed in soybean leaves under normal developmental conditions and genes whose expression oscillates under conditions of water deficit. These results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.

The soybean transcriptome displays strong variation along the day in optimal growth conditions and also in response to adverse circumstances, like drought stress. However, no study conducted to date has presented suitable reference genes, with stable expression along the day, for relative gene expression quantification in combined studies on drought stress and diurnal oscillations. Recently, water deficit responses have been associated with circadian clock oscillations at the transcription level, revealing the existence of hitherto unknown processes and increasing the demand for studies on plant responses to drought stress and its oscillation during the day. We performed data mining from a transcriptome-wide background using microarrays and RNA-seq databases to select an unpublished set of candidate reference genes, specifically chosen for the normalization of gene expression in studies on soybean under both drought stress and diurnal oscillations. Experimental validation and stability analysis in soybean plants submitted to drought stress and sampled during a 24 h timecourse showed that four of these newer reference genes (FYVE, NUDIX, Golgin-84 and CYST) indeed exhibited greater expression stability than the conventionally used housekeeping genes (ELF1-β and β-actin) under these conditions. We also demonstrated the effect of using reference candidate genes with different stability values to normalize the relative expression data from a drought-inducible soybean gene (DREB5) evaluated in different periods of the day.

Soybean is a rich source of vegetal protein for both animal and human consumption. Despite the high levels of protein in soybean seeds, industrial processing to obtain soybean bran significantly decreases the final protein content of the byproducts. To overcome this problem, cultivars with higher protein contents must be developed. However, selecting the target proteins is difficult because of the lack of information on the proteome profile of soybean bran. Therefore, this study obtained the comparative proteomic profiles of both natural coatless seeds and defatted bran from an elite tropical-soybean cultivar. Thus, their extracts were characterized using LC–MS/MS and a total of 550 proteins were identified. Among these, 526 proteins were detected in coatless seeds and 319 proteins in defatted bran. Moreover, a total of 139 proteins were identified as presenting different levels of content in coatless seeds and defatted bran. Among them, only 46 were retained after the seed processing. These proteins were clustered in several important metabolic pathways, such as amino-acid biosynthesis, sugar biosynthesis, and antioxidant activity, meaning that they could act as targets for bioactive products or genome editing to improve protein quality and quantity in soybean grains. These findings can enhance our understanding regarding protein robustness for both soybean crops and the commercial bran improvement because target proteins must remain intact after processing and must be bioactive when overexpressed. Overall, the soybean bran proteomic profile was explored for the first time, providing a valuable catalogue of target proteins that can tolerate the industrial process.

Flowering is an important trait in major crops like soybean due to its direct relation to grain production. The circadian clock mediates the perception of seasonal changes in day length and temperature to modulate flowering time. The circadian clock gene ( ) was identified in and is believed to play a key role in the integration of photoperiod, circadian regulation, and flowering. The molecular circuitry that comprises the circadian clock and flowering control in soybeans is just beginning to be understood. To date, insufficient information regarding the soybean negative flowering regulators exist, and the biological function of the soybean ( ) remains unknown. Here, we investigate the family members in soybean and functionally characterize a homologous gene. The constitutive overexpression of delayed flowering in Arabidopsis, showing the functional conservation among plants as part of the flowering control machinery. We also show that alters the expression of Arabidopsis key flowering time genes ( and ), and this down-regulation is the likely cause of flowering delay phenotypes. Furthermore, we identified the network genes to infer the participation of in soybeans. The data generated in this study provide original insights for comprehending the role of the soybean circadian clock ELF4 gene as a negative flowering controller.

The present study aimed to identify the relationship between lignin content in soybean pods, pod dehiscence rate, gene expression from phenylpropanoid pathway, cell wall lignification, and deterioration of seed due to weather. To evaluate the weathering deterioration, an experiment simulating 150 mm of rainfall was performed in greenhouse conditions. Gene expression was assessed by RT-qPCR. Results showed that soybean cultivars BRS Jiripoca and BRS 388 RR considered tolerant to weathering deterioration, presented higher levels of lignin content in pods. The data showed that dehiscence rate was neither a trait involved in weathering deterioration tolerance nor in lignin content in soybean pods. Lignin content and weathering deterioration were highly negatively correlated, probably due to changes in cell wall permeability to water accordingly to lignin level. Higher expression levels of genes involved in lignin biosynthesis and cell wall lignification were identified in both tolerant cultivars, however, with opposite expression profiles and in different developmental phases, suggesting a possible temporal strategy to cope with environmental adverse conditions.