Search Results (123)

The domesticated species currently available in the market have been developed through the breeding of wild relatives. Breeding strategies using wild relatives with high genetic diversity are attracting attention as an important approach for addressing climate change and ensuring sustainable food supply. However, studies examining gene expression variation in multiple wild and domesticated species are limited. Therefore, we aimed to investigate the changes in gene expression associated with domestication. We performed a meta-analysis of public gene expression data of domesticated species of rice, tomato, and soybean and their presumed ancestral species using 21 pairs for rice, 36 pairs for tomato, and 56 pairs for soybean. In wild relatives, the expression of genes involved in osmotic, drought, and wound stress tolerance was upregulated, with 18 genes included in the top 5% of DW scores. In domesticated species, upregulated expression was observed in genes related to auxin and those involved in the efflux of heavy metals and harmful substances, with 36 genes included in the top 5% of DW scores. These findings provide insights into how domestication influences changes in crop traits. Thus, our findings may contribute to rapid breeding and the development of new varieties capable of growing in harsh natural environments. Hence, a new cultivation method called “de novo domestication” has been proposed, which combines the genetic diversity of currently unused wild relatives and wild relatives with genome editing technologies that enable rapid breeding. Full article

Soybean (Glycine max L.) is grown worldwide to obtain edible oil, livestock feed, and biodiesel. However, drought and salt stress are becoming serious challenges to global soybean cultivation as they retard the growth of soybean plants and cause significant yield losses. Voltage-dependent anion-selective channel (VDAC) proteins are well-known for their role in drought and salt tolerance in crop plants. In this study, we identified 111 putative VDAC genes randomly distributed in genomes of 14 plant species, including cultivated soybean (Glycine max) and wild soybean (Glycine soja). The comparative phylogenetic studies classified these genes into six different clades and found the highest structural similarities among VDAC genes of G. max and G. soja. From the conserved domain database, porin-3 (PF01459) was found to be the conserved domain in all VDAC proteins. Furthermore, gene annotation studies revealed the role of GmaVDAC proteins in voltage-gated anion channel activity. These proteins were also found to interact with other proteins, especially mitochondrial receptors. A total of 103 miRNAs were predicted to target fifteen GmaVDAC genes. In G. max, these genes were found to be segmentally duplicated and randomly distributed on twelve chromosomes. Transcriptomic analysis revealed that the GmaVDAC18.2 gene showed overexpression in root nodules, whereas the GmaVDAC9.1, GmaVDAC18.1, and GmaVDAC18.2 genes showed overexpression under drought and salt stress conditions. Full article

Soybean (Glycine max (L.) Merr.) is a critical crop in China, serving as a primary source of food, oil, and animal feed. Drought stress significantly impacts soybean growth and yield. MicroRNAs (miRNAs) play crucial roles in plant drought responses. The miR164 family is highly conserved across plant species and has been shown to participate in drought responses in a range of plants, yet the function of miR164 in soybean remains unclear. In this study, we identified GmNAC35 as a direct target of miR164 through published degradome sequencing data and 5′ RLM-RACE assays. Under drought stress, miR164 members (e.g., MIR164a, MIR164f, and MIR164k) rapidly down-regulated, reaching their lowest expression at 2 h and returning to basal levels within 6 h. Conversely, GmNAC35 showed an inverse pattern, indicating negative regulation by miR164. Overexpression of GmNAC35 enhanced drought tolerance in transgenic soybean plants, as evidenced by higher survival rates and reduced water loss. Transcriptomic analysis revealed that GmNAC35 modulates stress-responsive pathways, including ABA signaling and phenylpropanoid biosynthesis. Our findings indicate that miR164 negatively regulates GmNAC35, a positive regulator of drought tolerance. This enhances our understanding of the molecular mechanisms of drought tolerance in soybean and may inform strategies for breeding drought-resistant varieties. Full article

The Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes (xm and Yu1). We identified SRS members and analyzed their intra-species distribution patterns, including copy number variation (CNV) and interchromosomal translocations. A novel standardized nomenclature (Accession_SiSRSN[.n]_xDy or xTy) was proposed to unify gene family nomenclature, enabling the direct visualization of member number variation across germplasms and the identification of core/variable members while highlighting chromosomal translocations. Focusing on the two high-quality genomes, both harboring six core SRS members, we performed whole-genome collinearity analysis with Arabidopsis, rice, maize, soybean, and green foxtail. Ka/Ks analysis of collinear gene pairs revealed purifying selection acting on SiSRS genes. Promoter analysis identified abundant stress-responsive cis-elements. Among core members, the xm_SiSRS5 gene exhibited the highest expression during vegetative growth but showed significant downregulation under drought and salt stress, suggesting its role as a key negative regulator in abiotic stress responses. This study demonstrates the utility of pan-genomics in resolving gene family dynamics and establishes SiSRS5 as a critical target for stress tolerance engineering in foxtail millet. Full article

The soybean is an important source of protein and is gaining popularity in Ghana due to a rising demand for its use in the poultry industry. However, the grain yield of soybeans is relatively low in the Upper West Region due to infertile soil and climate change. This study evaluated root nodulation and symbiotic effectiveness in 31 rhizobial isolates obtained from the nodules of soybeans planted at Da in the Upper West Region, Ghana, as well as measured photosynthetic activity of the soybean plants grown under glasshouse conditions. This study further assessed the tolerance of the rhizobial isolates to different levels of temperature, drought, salinity, and pH in the laboratory and also measured the ability of the isolates to produce indole-3-acetic acid. An infrared gas analyser and the ¹⁵N and ¹³C natural abundance techniques were used to assess the photosynthetic activity, N₂ fixation, and water-use efficiency, respectively. The results showed that the test isolates that induced greater photosynthetic rates from higher stomatal conductance also stimulated increased water loss via leaf transpiration in soybean plants. Isolates TUTGMGH9 and TUTGMGH19 elicited much higher shoot δ¹³C in the soybean host plant and induced higher shoot biomass, C accumulation, percent relative symbiotic effectiveness, and N₂ fixation relative to Bradyrhizobium strain WB74 and 5 mM of nitrate, which were used as positive controls. Although isolate TUTGMGH9 did not grow at 40 °C, it showed growth at 5% of PEG-6000, NaCl, and a low pH while also producing moderate IAA. However, for better utilisation of these rhizobial isolates as bioinoculants, their growth performance needs to be assessed under field conditions to ascertain their competitiveness and symbiotic efficacy. Full article

The regulation of downstream responsive genes by transcription factors (TFs) is a critical step in the stress response system of plants. While bZIP transcription factors are known to play important roles in stress reactions, their functional characterization in soybeans remains limited. Here, we identified a soybean bZIP gene, GmbZIP60, which encodes a protein containing a typical bZIP domain with a basic region and a leucine zipper region. Subcellular localization studies confirmed that GmbZIP60 is localized in the nucleus. Expression analysis demonstrated that GmbZIP60 is induced by salt stress, drought stress, and various plant hormone treatments, including abscisic acid (ABA), ethylene (ETH), and methyl jasmonate acid (MeJA). Overexpressing GmbZIP60 (OE-GmbZIP60) in transgenic soybean and rice enhanced tolerance to both salt and drought stresses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that the expression levels of abiotic stress-responsive genes were significantly higher in transgenic plants than in wild-type (WT) plants under stress conditions. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) analysis further confirmed that GmbZIP60 directly binds to the promoters of abiotic stress-related genes induced by ABA, ETH, JA, and salicylic acid (SA). Overall, these findings revealed GmbZIP60 as a positive regulator of salt and drought stress tolerance. Full article

ACS (1-aminocyclopropane-1-carboxylic acid synthase) is a member of the aminotransferase superfamily and a pyridoxal phosphate-dependent enzyme. ACS is also a rate-limiting enzyme for the biosynthesis of ethylene and has been linked with plant development, growth, and stress responses. However, information on ACS genes in the soybean genome is limited. In this study, we identified ACS genes in soybean through phylogenetic trees and conserved motifs and analyzed their cis-acting elements, subcellular localization, and expression patterns. Twenty-two members of the ACS family were identified in soybean, and they were divided into four subfamilies based on phylogenetic relationships. Moreover, the results of Arabidopsis mesophyll protoplasts showed that GmACS1, GmACS8, and GmACS15 were all localized in the nucleus and cell membrane. Cis-regulatory elements and qRT-PCR analyses indicated markedly increased levels of GmACS transcripts under hormone treatments and abiotic stress conditions (drought, alkalinity, and salt). In addition, under different abiotic stresses, the potential functional variations across the GmACS isoforms were mirrored in their differential expression. The analysis of transcriptional response to salinity indicated that salt stress might primarily be mediated by the GmACS15 gene. GmACS15 was also found to reduce salt-induced oxidative damage by modulating the ROS-scavenging system, cellular redox homeostasis, and maintaining intracellular Na⁺/K⁺ balance. The results of this investigation revealed the involvement of the ACS gene family in soybean stress-response pathways, including the identification of a potential target for enhancing salt tolerance in soybean. Full article

Drought stress threatens agriculture and food security, significantly impacting soybean yield and physiology. Despite the documented role of nanosilica (n-SiO₂) in enhancing crop resilience, its full growth-cycle effects on soybeans under drought stress remain elusive. This study aimed to evaluate the efficacy of n-SiO₂ at a concentration of 100 mg kg⁻¹ in a soil medium for enhancing drought tolerance in soybeans through a full life-cycle assessment in a greenhouse setup. To elucidate the mechanisms of n-SiO₂ action, key physiological, biochemical, and yield parameters were systematically measured. The results demonstrated that n-SiO₂ significantly increased silicon content in shoots and roots, restored osmotic balance by reducing the Na⁺/K⁺ ratio by 40%, and alleviated proline accumulation by 35% compared to the control, thereby mitigating osmotic stress. Enzyme activities related to nitrogen metabolism, including nitrate reductase (NR) and glutamine synthetase (GS), improved by 25–30% under n-SiO₂ treatment compared to the control. Additionally, antioxidant activity, including superoxide dismutase (SOD) levels, increased by 15%, while oxidative stress markers such as hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) decreased by 20–25% compared to the control. Furthermore, yield components were significantly enhanced, with pod number and grain weight increasing by 15% and 20%, respectively, under n-SiO₂ treatment compared to untreated plants in drought conditions. These findings suggest that n-SiO₂ effectively enhances drought resilience in soybeans by reinforcing physiological and metabolic processes critical for growth and yield. This study underscores the potential of n-SiO₂ as a sustainable amendment to support soybean productivity in drought-prone environments, contributing to more resilient agricultural systems amidst increasing climate variability. Future research should focus on conducting large-scale field trials to evaluate the effectiveness and cost-efficiency of n-SiO₂ applications under diverse environmental conditions to assess its practical viability in sustainable agriculture. Full article

Zanthoxylum planispinum var. Dingtanensis (hereafter Z. planispinum) has excellent characteristics, including Ca and drought tolerance. It can flourish in stony soils, and it is used as a pioneer plant in karst rocky desertification control. However, soil degradation, coupled with the removal of nutrients absorbed from the soil by Z. planispinum’s fruit harvesting, exacerbates nutrient deficiency. The effects of fertilization on soil nutrient utilization and microbial limiting factors remain unclear. Here, we established a long-term (3 year) field experiment of no fertilization (CK), organic fertilizer + chemical fertilizer + sprinkler irrigation (T1), chemical fertilizer + sprinkler irrigation (T2), chemical fertilizer treatment (T3), and leguminous (soybean) + chemical fertilizer + sprinkler irrigation (T4). Our findings indicate that fertilization significantly improved the nutrient uptake efficiency of Z. planispinum, and it also enhanced urease activity compared with CK. T1 increased soil respiration and improved water transport, and the soil nutrient content retained in T1 was relatively high. It delayed the mineralization rate of organic matter, promoted nutrient balance, and enhanced enzyme activity related to the carbon and nitrogen cycle. T4 caused soil acidification, reducing the activity of peroxidase (POD) and polyphenol oxidase (PPO). The soil microbial community in the Z. planispinum plantation was limited by carbon and phosphorus, and T1 mitigated this limitation. This study indicated that soil nutrient content regulated enzymatic activity by influencing microbial resource limitation, with organic carbon being the dominant factor. Overall, we recommend T1 as the optimal fertilization strategy for Z. planispinum plantations. Full article

The GS3 protein is a G protein widely conserved in plants, playing a pivotal role in growth, development, and stress responses. With the protein sequence of the AT1/GS3 gene in sorghum as a query, this study identified five GS3 gene family members in the soybean genome database and designated GmGS3-1 to GmGS3-5. Promoter cis-element analysis suggested that soybean GS3 is implicated in responses to abiotic stress. Additionally, collinearity analysis indicated that soybean GS3 genes are subject to purifying selection. Transcriptomic data of the five soybean GS3 genes revealed that the nuclear-localized gene GmGS3-1 is highly expressed in root tissues and significantly upregulated under salt and drought stress, as confirmed by qRT-PCR assays. Functional validation for salt and drought tolerance demonstrated that transgenic Arabidopsis plants exhibited higher fresh weight compared to wild-type (WT) controls. Furthermore, GmGS3-1 was found to interact with multiple G proteins, suggesting its synergistic role in the abiotic stress tolerance of soybean. These findings establish a theoretical framework for understanding the functional role of the GS3 gene family in soybean stress tolerance and development. Full article

Fodder soybean (Glycine max L.) with high protein and yield is a popular forage grass in northeast China. Seasonal drought inhibits its growth and development during seedling stage. The objective of this study was to observe morpho-physiological changes in fodder soybean seedlings under melatonin (MT) treatments and identify appropriate concentration to alleviate the drought damage. Two varieties commonly used in northeast China were treated with 0, 50, 100, and 150 μM melatonin at soil water content of 30%. The results indicated that applying melatonin enhanced height, biomass and altered root morphology of fodder soybean seedlings under water-deficient conditions. The treatments with melatonin at different concentrations significantly reduced the contents of H₂O₂, O₂⁻ and MDA, while boosting the capacity of the antioxidant defense system and the content of osmotic adjustment substances. Meanwhile, increases in light energy capture and transmission efficiency were observed. Furthermore, treatment with melatonin regulated the expression levels of genes associated with photosynthesis and the antioxidant defense system. Notably, 100 μM melatonin treatment produced the most favorable effect in all treatments under drought conditions. These research results provide new information for enhancing the drought tolerance of fodder soybean using chemical measures. Full article

Vitamin E, comprising tocopherols and tocotrienols, is a crucial fat-soluble antioxidant that helps maintain intracellular redox homeostasis in plants when they are under stress. Soybeans are a significant source of natural vitamin E. GGDR catalyzes the formation of phytyl diphosphate (PDP), a key vitamin E precursor, and it is involved in chlorophyll degradation. The GmGGDR gene, identified via RNA-seq in soybean germplasms with high and low vitamin E contents, encodes GGDR, a key enzyme involved in both vitamin E synthesis and chlorophyll degradation. This study shows that the GmGGDR-encoded protein is hydrophilic and stable, predominantly expressed in leaves, and markedly responsive to gibberellins. The GmGGDR gene enhances the tolerance of transgenic Arabidopsis and soybean plants to salt and drought stresses; transgenic soybeans overexpressing GmGGDR exhibited an approximately 8-fold increase in POD activity, with no significant changes in SOD and CAT activities. Moreover, the GmGGDR gene enhances the levels of α-, γ-, δ-, and total tocopherol content in transgenic soybean and Arabidopsis plants and also increases the chlorophyll a levels in the leaves of these transgenic plants. The increases in α-tocopherol, γ-tocopherol, and δ-tocopherol and total tocopherol in transgenic Arabidopsis seeds ranged from 177.8% to 600.0%, 42.9% to 90.0%, 17.6% to 292.9%, and 71.4% to 127.3% over the control, respectively. Similarly, transgenic soybeans exhibited a minimum increase of 42.9%, 27.8%, 7.1%, and 25.0% in these tocopherol fractions. Overexpression of GmGGDR also significantly elevated chlorophyll a levels in the leaves of these transgenic plants by 33.3–112.5%. This study preliminarily elucidated the function of the GmGGDR gene. It provides a theoretical foundation for further research. It presents a novel strategy for the genetic enhancement of soybean vitamin E content. Full article

Background: Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of soybeans have been identified to have different drought tolerance levels. Objectives: Here, two soybean lines, Pana (drought sensitive) and PI 567731 (drought tolerant) were selected to identify chemical compounds and pathways which could be targets for metabolomic analysis induced by abiotic stress. Methods: Extracts from the two lines are analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The high mass resolution and accuracy of the method allows for identification of ions from hundreds of different compounds in each cultivar. The exact m/z of these species were filtered through SoyCyc and the Human Metabolome Database to identify possible molecular formulas of the ions. Next, the exact m/z values were converted into Kendrick masses and their Kendrick mass defects (KMD) computed, which were then sorted from high to low KMD. This latter process assists in identifying many additional molecular formulas, and is noted to be particularly useful in identifying formulas whose mass difference corresponds to two hydrogen atoms. Results: In this study, more than 460 ionic formulas were identified in Pana, and more than 340 ionic formulas were identified in PI 567731, with many of these formulas reported from soybean for the first time. Conclusions: Using the SoyCyc matches, the metabolic pathways from each cultivar were compared, providing lists of molecular targets available to profile effects of abiotic stress on these soybean cultivars. Key metabolites include chlorophylls, pheophytins, mono- and diacylglycerols, cycloeucalenone, squalene, and plastoquinones and involve pathways which include the anabolism and catabolism of chlorophyll, glycolipid desaturation, and biosynthesis of phytosterols, plant sterols, and carotenoids. Full article

Drought stress is one of the major adversity stresses affecting soybean (Glycine max [L.] Merr.) yield. Late embryogenesis abundant protein (LEA protein) is a large family of proteins widely distributed in various types of organisms, and this class of proteins plays an important role in protecting proteins, membrane lipids, and lipids inside the cell. The soybean GmPM35 gene is a member of the LEA_6 subfamily. The expression of the GmPM35 gene was significantly increased after drought stress in soybeans. A subcellular localization assay confirmed that the gene acts on the cell membrane. Against wild-type Arabidopsis thaliana, we found that Arabidopsis lines overexpressing the GmPM35 gene were significantly more drought-tolerant at germination and seedling stages under drought stress. To further investigate the drought tolerance function of this gene in soybeans, nine overexpression lines of the T₃ generation soybean GmPM35 gene and two editing lines of the T₃ generation soybean GmPM35 gene were obtained by Agrobacterium-mediated method using a wild-type soybean strain (JN28) as a receptor. Germination rate, root length, chlorophyll (CHL) content, Proline (Pro) content, malondialdehyde (MDA) content, superoxide anion (O₂^•−) content, hydrogen peroxide (H₂O₂) content, (NBT, DAB) staining, and activities of antioxidant enzymes (CAT, SOD, POD), and photosynthetic physiological indexes of the three different types of strains were measured and analyzed before and after drought stress. Combined with the results of rehydration experiments and physiological and biochemical indices, we found that overexpression of the GmPM35 gene protected the activities of antioxidant enzymes under drought stress. The activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) were increased by an average of 34.28%, 26.12%, and 30.01%, respectively, in soybean plants overexpressing the GmPM35 gene compared with wild-type soybeans. Under drought stress conditions, soybean plants overexpressing the GmPM35 gene showed an average increase of 76.81% in photosynthesis rate (Pn), 39.8% in transpiration rate (Tr), 126% in stomatal conductance (Gs), 47.71% in intercellular CO₂ concentration (Ci), and 26.44% in instantaneous water use efficiency (WUEi). The improvement of these indexes helped to reduce the accumulation of reactive oxygen species (ROS) in the plants. In addition, we found that under drought stress, the MDA content was reduced by an average of 18.8%, and the Pro content was increased by an average of 60.14% in soybean plants overexpressing the GmPM35 gene, and the changes in these indexes indicated that the plants had stronger antioxidant and osmoregulatory capacities in response to drought stress. In summary, this experiment demonstrated that the GmPM35 gene plays an important role in soybean tolerance to drought stress, and by overexpressing the GmPM35 gene, soybean plants can better tolerate drought stress and maintain normal physiological functions. Full article

Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. Endophytic and rhizospheric microbial diversity analyses were conducted with soybean plants cultivated during the 2023 growing season amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, surviving and non-surviving soybean plants were collected from two plots of a Louisiana soybean field severely damaged by extreme heat and drought conditions in 2023. Although no significant difference was observed between surviving and non-surviving plants in microbial diversity of the rhizosphere, obvious differences were found in the structure of the endophytic microbial community in root tissues between the two plant conditions. In particular, the bacterial genera belonging to Proteobacteria, Pseudomonas and Pantoea, were predominant in the surviving root tissues, while the bacterial genus Streptomyces was conspicuously dominant in the non-surviving (dead) root tissues. Co-occurrence patterns and network centrality analyses enabled us to discern the intricate characteristics of operational taxonomic units (OTUs) within endophytic and rhizospheric networks. Additionally, we isolated and identified bacterial strains that enhanced soybean tolerance to drought stresses, which were sourced from soybean plants under a drought field condition. The 16S rDNA sequence analysis revealed that the beneficial bacterial strains belong to the genera Acinetobacter, Pseudomonas, Enterobacter, and Stenotrophomonas. Specific bacterial strains, particularly those identified as Acinetobacter pittii and Pseudomonas sp., significantly enhanced plant growth metrics and reduced drought stress indices in soybean plants through seed treatment. Overall, this study advances our understanding of the soybean-associated microbiome structure under drought stress, paving the way for future research to develop innovative strategies and biological tools for enhancing soybean resilience to drought. Full article