Search Results (301)

The fruiting stage of soybean (Glycine max L.) is critical for determining both its yield and quality, thereby influencing global production. While some studies have provided partial explanations for the occurrence of Fusarium species on soybean seeds and pods, the fungal diversity affecting soybean pods in Sichuan Province, a major soybean cultivation region in Southwestern China, remains inadequately understood. In this study, 182 infected pods were collected from a maize–soybean relay strip intercropping system. A total of 10 distinct pod-infecting fungal genera (132 isolates) were identified, and their pathogenic potential on soybean seeds and pods was evaluated. Using morphological characteristics and DNA barcode markers, we identified 43 Fusarium isolates belonging to 8 species, including F. verticillioides, F. incarnatum, F. equiseti, F. proliferatum, F. fujikuroi, F. oxysporum, F. chlamydosporum, and F. acutatum through the analysis of the translation elongation factor gene (EF1-α) and RNA polymerases II second largest subunit (RPB2) gene. Multi-locus phylogenetic analysis, incorporating the Internal Transcribed Spacer (rDNA ITS), β-tubulin (β-tubulin), Glyceraldehyde 3-phosphate dehydrogenase (GADPH), Chitin Synthase 1 (CHS-1), Actin (ACT), Beta-tubulin II (TUB2), and Calmodulin (CAL) genes distinguished 37 isolates as 6 Colletotrichum species, including C. truncatum, C. karstii, C. cliviicola, C. plurivorum, C. boninense, and C. fructicola. Among these, F. proliferatum and C. fructicola were the most dominant species, representing 20.93% and 21.62% of the isolation frequency, respectively. Pathogenicity assays revealed significant damage from both Fusarium and Colletotrichum isolates on soybean pods and seeds, with varying isolation frequencies. Of these, F. proliferatum, F. acutatum, and F. verticillioides caused the most severe symptoms. Similarly, within Colletotrichum genus, C. fructicola was the most pathogenic, followed by C. truncatum, C. karstii, C. cliviicola, C. plurivorum, and C. boninense. Notably, F. acutatum, C. cliviicola, C. boninense, and C. fructicola were identified for the first time as pathogens of soybean pods under the maize–soybean strip intercropping system in Southwestern China. These findings highlight emerging virulent pathogens responsible for soybean pod decay and provide a valuable foundation for understanding the pathogen population during the later growth stages of soybean. Full article

Soybean (Glycine max (L.) Merr.) is one of the most important global economic crops, extensively utilized in the production of food, animal feed, and industrial raw materials. As the demand for soybeans continues to rise, improving both the yield and quality of soybeans has become a central focus of agricultural research. To accelerate the genetic improvement of soybean, genome selection (GS) and genome-wide association studies (GWAS) have emerged as effective tools and have been widely applied in various crops. In this study, we conducted GWAS and GS model evaluations across five soybean phenotypes (Glycitin content, Oil, Pod, Total isoflavone content, and Total tocopherol content) to explore the effectiveness of different GWAS methods and GS models in soybean genetic improvement. We applied several GWAS methods, including fastGWA, BOLT-LMM, FarmCPU, GLM, and MLM, and compared the predictive performance of various GS models, such as BayesA, BayesB, BayesC, BL, BRR, SVR_poly, SVR_linear, Ridge, PLS_Regression, and Linear_Regression. Our results indicate that markers selected through GWAS, when used in GS, achieved a prediction accuracy of 0.94 at a 5 K density. Furthermore, Bayesian models proved to be more stable than machine learning models. Overall, this study offers new insights into soybean genome selection and provides a scientific foundation for future soybean breeding strategies. Full article

Understanding trait relationships is fundamental in soybean breeding because the goal is to maximize simultaneous gains. Standard multi-trait genome-wide association studies (MT-GWAS) identify variants linked to multiple traits but fail to capture phenotypic structures or interrelations. Structural Equation Models (SEM) account for covariances and recursion, enabling the decomposition of single nucleotide polymorphism (SNP) effects into direct or indirect components and identifying pleiotropic regions. We applied SEM to analyze morphology (pod thickness, PT) and yield traits (number of pods, NP; number of grains, NG; hundred-grain weight, HGW). The dataset comprised 96 soybean individuals genotyped with 4070 SNP markers. The phenotypic network was constructed using the hill-climbing algorithm, a class of score-based methods commonly applied to learn the structure of Bayesian networks, and structural coefficients were estimated with SEM. According to coefficient signs, we identified negative interrelationships between NG and HGW, and positive ones between NP and NG, and HGW and PT. NG, HGW, and PT showed indirect SNP effects. We also found loci jointly controlling traits. In total, 46 candidate genes were identified: 7 associated exclusively with NP and 4 associated with NG. An additional 15 genes were common to NP and NG, 3 were common to NP and HGW, 6 were common to NG and HGW, and 11 were common to NP, NG, and HGW. In summary, SEM-GWAS revealed novel relationships among soybean traits, including PT, supporting breeding programs. Full article

β-D-xylosidases (BXLs) are pivotal enzymes in xylan degradation, playing essential roles in plant development and stress responses. In this study, we identified 29 GmBXL genes in soybean through homolog alignment. Phylogenetic analysis classified these genes into three groups, with Group III being legume-specific. The GmBXLs are unevenly distributed across 15 chromosomes, with their expansion driven by both tandem and segmental duplications. Conserved motif and domain analyses revealed functional conservation, particularly in family 3 of glycoside hydrolase domains. Promoter regions of GmBXLs are enriched with hormone-responsive and stress-related cis-elements, indicating their involvement in diverse biological processes. Tissue-specific expression analysis revealed differential GmBXLs expression across leaves, roots, flowers, and seeds, with GmBXL13 and GmBXL26 exhibiting notably high transcript levels in pods and seeds. Under salt stress, 26 GmBXLs exhibited significant expression changes, with 20 genes up-regulated in both leaves and roots, highlighting their roles in salt tolerance. These findings enhance our understanding of the evolutionary and functional characteristics of GmBXLs, providing valuable insights for molecular breeding of salt-tolerant soybean varieties. Full article

Sustainable agriculture supports environmental protection, climate change mitigation, and forage security to meet the growing demands of livestock production. Given the critical role of macro- and microelements in animal health, diversified and balanced feed production is essential and can be achieved through the sustainable integration of legumes and cereals. This research evaluated the impact of soybean–common millet intercropping and biofertilizer application on the elemental composition and yield performance of forage biomass. Three intercropping patterns were tested: S1M1—alternating rows, S2M2—alternating two-row strips, and S2M4—alternating two-row soybean with four-row millet strips, alongside monoculture controls. The biofertilizer Coveron (BF) was also assessed. The S2M2 combination provided the highest land equivalent ratios for both fresh and dry biomass (1.10 and 1.12, respectively), despite a reduction in millet yield. Considering the elements, the S2M2 combination notably enhanced the accumulation of Ca and B (by 13.2% and 13.0%, respectively, compared to S1) in the soybean vegetative part and Cr and Mn in the reproductive part (by 53.5% and 17.1%, respectively). In contrast, sole soybean showed the highest P levels in both vegetative (3.45 g kg⁻¹) and reproductive parts (4.56 g kg⁻¹). Regarding Al, its accumulation was reduced in intercropped millet. The S1M1 combination increased Mg and S concentrations in both parts of millet biomass (up to 17.3% and 18.4% in the vegetative part, compared to M1). While BF generally had a limited impact on forage biomass yield and elemental accumulation, it increased Mg, P, and S concentrations in soybean pods, as well as concentrations of B, Mn, and Mo in the panicle, simultaneously decreasing P, Cr, and Zn concentrations in the vegetative part of millet. Accordingly, soybean–common millet intercropping in the S2M2 configuration offers a sustainable solution for efficient land utilization and element-enriched forage production. Full article

Soybean (Glycine max) is a predominantly self-pollinating crop; however, its flowers exhibit traits associated with insect pollination. While several studies report yield benefits from floral visitation, others suggest little or no effect, and few have assessed pollen limitation through direct hand-pollination experiments. Here, we assess pollinator contribution and pollen limitation through two manipulative common garden experiments using different soybean cultivars. First, we assessed the contribution of pollinators by comparing reproductive variables between caged (pollinator excluded) and open-pollinated plants over two growing seasons. Second, we supplemented flowers with cross-pollen to test for pollen limitation, evaluating pollen-tube growth, pod set, seed number per pod, and seed weight. Pollinator exclusion did not significantly reduce total pod or seed production per plant, but open pollination increased seed set (seeds per flower) by ~16%. In contrast, hand supplementation substantially improved reproductive success at the flower level, tripling pod set probability and increasing seed number per pod by 40%. Additionally, both open-pollinated and hand-pollinated flowers exhibited higher pollen-tube growth relative to autonomous selfing. These findings highlight that even in largely self-compatible crops like soybean, additional pollen input can enhance reproductive success and help bridge the gap between the ecological and agronomic dimensions of pollination. Full article

Understanding the genetic architecture of complex traits is crucial for crop improvement and molecular breeding. We developed a mutagenized soybean population using carbon ion beam irradiation and conducted genome-wide association studies (GWAS) to identify variants controlling key agronomic traits. Whole-genome resequencing of 199 M4 lines revealed 1.48 million SNPs, predominantly C→T transitions, with population structure analysis identifying three distinct genetic groups. GWAS across five traits revealed striking differences in genetic architecture: the podding habit showed extreme polygenic control with 87,029 significant associations of small effect, while pubescence color exhibited oligogenic inheritance with only 122 variants. Hundred-seed weight displayed moderate complexity (4637 associations) with the largest effect sizes (−3.74 to 5.03) and major QTLs on chromosomes 4, 7, and 15–20. Growth habit involved 12,136 SNPs, including a strong chromosome 3 association (−log₁₀(p-value) > 50). Flower color showed 2662 associations clustered on chromosome 15. Functional analysis of 18,542 candidate genes revealed trait-specific pathway enrichments: flavonoid biosynthesis for flower color, phloem transport for seed weight, auxin signaling for growth habit, and amino acid transport for podding habit. This study demonstrates how mutagenesis-induced variation, combined with association mapping, reveals evolutionary constraints that shape genetic architectures, providing insights for genetics-assisted breeding strategies. Full article

Global food security is challenged by population growth and the environmental toll of conventional fertilizers. Enhancing biological nitrogen fixation (BNF) in legumes like soybean (Glycine max) is a sustainable fertilization alternative. This study investigates a graphitic carbon nitride/iron oxide (Fe₂O₃/g–C₃N₄ or FC) nanocomposite as a dual–functional fertilizer to improve iron (Fe) nutrition and BNF in soybeans. A pot experiment was conducted using different FC concentrations (10, 100, and 200 mg kg⁻¹), alongside controls. Results showed that the 100 mg kg⁻¹ FC treatment (FC2) was most effective, significantly increasing soybean biomass, nodule number, and nodule fresh weight. The FC2 treatment also enhanced photosynthetic rates and chlorophyll content (SPAD values) while reducing stomatal conductance and transpiration, indicating improved water–use efficiency. Furthermore, FC application bolstered the plant’s antioxidant system by increasing the activity of superoxide dismutase (SOD) and peroxidase (POD). Elemental analysis confirmed that FC treatments significantly increased the uptake and translocation of Fe and nitrogen (N) in plant tissues. These findings demonstrate that the FC nanocomposite acts as a highly effective nanofertilizer, simultaneously addressing iron deficiency and boosting nitrogen fixation to promote soybean growth. This work highlights its potential as a sustainable solution to enhance crop productivity and nutrient use efficiency in modern agriculture. Full article

Seed oil and protein contents are critical agronomic traits that determine soybean quality. However, the key loci and corresponding genes controlling these quality traits remain to be elucidated. Here, we performed bulked segregant analysis by sequencing (BSA-seq) using an F4 population derived from a cross between the cultivars Heinong 35 (HN35) and Dengke 3 (DK3). A major soybean oil and protein quantitative trait locus (QTL) designated as q-OP18 was identified on chromosome 18, and the sugar transporter gene GmSWEET46 was further cloned. Haplotype analysis revealed that a single-nucleotide polymorphism (SNP) in the sixth exon of GmSWEET46 results in an amino acid change between HN35 and DK3 and is associated with seed oil and protein content, suggesting its important role in determining seed quality in soybean. GmSWEET46 is expressed during the early stages of seed and pod development and localizes to the plasma membrane, indicating its potential function as a sugar transporter. Further studies demonstrated that GmSWEET46 can regulate seed protein content, oil content, and seed size in Arabidopsis and soybean. Collectively, this study provides a novel locus and gene for regulating soybean seed traits and offers valuable resources for the breeding of high-quality and high-yielding soybean cultivars. Full article

Glycerol-3-phosphate acyltransferases (GPATs) catalyze the initial and rate-limiting step of glycerolipid biosynthesis, yet their contribution to salt tolerance in the soybean (Glycine max (L.) Merr.) plants remains largely uncharacterized. In this study, a total of 27 GmGPAT genes were identified, and their evolutionary relationships, chromosomal distribution, conserved motifs, and cis-regulatory elements were comprehensively analyzed. Through transcriptomic and qPCR analyses, many GmGPATs were found to be predominantly expressed in roots, with GmGPAT1, a plastid-targeted isoform, displaying the most rapid and pronounced transcriptional activation under salt stress. GFP-fusion experiments in transient expression assays confirmed plastid localization of GmGPAT1. Heterologous expression in Escherichia coli together with enzyme kinetics analyses validated its enzymatic function as a GPAT family member. The soybean hairy-root lines overexpressing GmGPAT1 exhibited enhanced root elongation, increased biomass, and improved photosynthetic efficiency under 120 mM NaCl stress, while CRISPR/Cas9 knockout mutants showed pronounced growth inhibition. Physiological assays demonstrated that GmGPAT1 overexpression mitigated oxidative damage by limiting reactive oxygen species (ROS) accumulation and lipid peroxidation, increasing antioxidant enzyme activities (CAT, SOD, POD), and elevating the ratios of AsA/DHA and GSH/GSSG. These changes contributed to redox homeostasis and improved Na⁺ extrusion capacity. A genome-wide association study (GWAS) involving 288 soybean accessions identified a single nucleotide polymorphism in the GmGPAT1 promoter that was significantly correlated with salt tolerance, and the beneficial Hap1 allele emerged as a promising molecular marker for breeding. Together, these analyses emphasize the status of GmGPAT1 as a major regulator of salt stress adaptation through the coordinated modulation of lipid metabolism and redox balance, extend the functional annotation of the soybean GPAT family, and highlight new genetic resources that can be leveraged to enhance tolerance to salt stress in soybean cultivars. Full article

In South Korea, reclaimed coastal tidelands (RTLs) are generally used for rice cultivation rather than upland cultivation; however, there is growing social pressure to change the use of RTLs to upland crop production to increase the self-sufficiency rate regarding grain. However, RTLs are not suitable for cultivating upland crops due to their high salinity, poor drainage, and shallow groundwater levels. Therefore, it is necessary to develop a cost-effective drainage method, such as surface drainage. This study investigated the effects of slope construction on surface drainage and on the growth and yield of soybean (Glycine max (L.) Merr.) in poorly drained fields at the Saemangeum RTL, which is the largest RTL district in South Korea. Slopes were constructed at angles of 0°, 3°, and 5°; soybean was sown in June 2023 (wet season) and May 2024 (dry season); and growth of soybean was monitored at the flowering, pod-filling, and harvest stages. Soil pH, electrical conductivity (EC), and mineral nitrogen (NH₄⁺ and NO₃⁻) were measured monthly, while daily changes in soil water content were measured using soil sensors. As expected, slope construction enhanced surface runoff from the upper to lower slope areas under heavy rainfall, but soil erosion was also increased. Soybean growth and yield were higher in the upper sites for the wet-season conditions mainly due to lowered moisture stress. For the dry-season, there was no significant differences in soybean growth and yield across the slopes due to drought and high temperatures during flowering and pod-filling stages. Soybean growth and yield parameters were negatively correlated with both soil water content and pH. Slope construction improves surface drainage but does not consistently translate into higher soybean yields, highlighting its limited agronomic and economic value when used alone. Instead, integrated management practices combining drainage improvement, supplemental irrigation, and soil erosion reduction need to be implemented to support sustainable upland cropping in coastal RTLs. Full article

Phosphorus deficiency significantly limits soybean production across 74% of China’s arable land. This study investigated the molecular mechanisms enabling soybean to access insoluble phosphorus through transcriptome sequencing of the Heinong 48 variety across four developmental stages (Trefoil, Flower, Podding, and Post-podding). RNA-Seq analysis identified 2755 differentially expressed genes (DEGs), with 2506 up-regulated and 249 down-regulated genes. Notably, early developmental stages showed the most substantial transcriptional reprogramming, with 3825 DEGs in the Trefoil stage and 10,660 DEGs in the Flower stage, compared to only 523 and 393 DEGs in the Podding and Post-podding stages, respectively. Functional enrichment analysis revealed 44 significantly enriched GO terms in the Trefoil stage and 137 in the Flower stage, with 13 GO terms shared between both stages. KEGG pathway analysis identified 8 significantly enriched pathways in the Trefoil stage and 21 in the Flower stage, including key pathways related to isoflavonoid biosynthesis, alpha-linolenic acid metabolism, and photosynthesis. Among 87 differentially expressed transcription factors from 31 families, bHLH (8.08%), bZIP (7.18%), and WRKY (5.94%) were most prevalent. These findings provide genetic targets for developing soybean varieties with improved phosphorus acquisition capacity, potentially reducing fertilizer requirements and supporting more sustainable agricultural practices. Full article

Accurate postharvest quality evaluation of soybeans is essential for preserving product value and meeting industry standards. Traditional inspection methods are often inconsistent, labor-intensive, and unsuitable for high-throughput operations. This study presents a non-destructive soybean classification approach using a simplified reflectance-mode hyperspectral imaging system equipped with a single light source, eliminating the complexity and maintenance demands of dual-light configurations used in prior studies. A spectral–spatial data fusion strategy was developed to classify harvested soybeans into four categories: normal, split, diseased, and foreign materials such as stems and pods. The dataset consisted of 1140 soybean samples distributed across these four categories, with spectral reflectance features and spatial texture attributes extracted from each sample. These features were combined to form a unified feature representation for use in classification. Among multiple machine learning classifiers evaluated, Linear Discriminant Analysis (LDA) achieved the highest performance, with approximately 99% accuracy, 99.05% precision, 99.03% recall and 99.03% F1-score. When evaluated independently, spectral features alone resulted in 98.93% accuracy, while spatial features achieved 78.81%, highlighting the benefit of the fusion strategy. Overall, this study demonstrates that a single-illumination HSI system, combined with spectral–spatial fusion and machine learning, offers a practical and potentially scalable approach for non-destructive soybean quality evaluation, with applicability in automated industrial processing environments. Full article

Climate change has intensified extreme weather events and accelerated soil salinization, posing serious threats to crop yield and quality. Salinity stress, now affecting about 20% of irrigated lands, is expected to worsen due to rising temperatures and sea levels. At the same time, the global population is projected to exceed 9 billion by 2050, demanding a 70% increase in food production (UN, 2019; FAO). Agriculture, responsible for 34% of global greenhouse gas emissions, urgently needs sustainable solutions. Microbial inoculants, known as “plant probiotics,” offer a promising eco-friendly alternative by enhancing crop resilience and reducing environmental impact. In this study, we evaluated the plant growth-promoting (PGP) traits and melatonin-producing capacity of Bacillus aerius EH2-5. To assess its efficacy under salt stress, soybean seedlings at the VC stage were inoculated with EH2-5 and subsequently subjected to salinity stress using 150 mM and 100 mM NaCl treatments. Plant growth parameters, the expression levels of salinity-related genes, and the activities of antioxidant enzymes were measured to determine the microbe’s role in promoting plant growth and mitigating salt-induced oxidative stress. Here, our study shows that the melatonin-synthesizing Bacillus aerius EH2-5 (7.48 ng/mL at 24 h after inoculation in Trp spiked LB media) significantly improved host plant (Glycine max L.) growth, biomass, and photosynthesis and reduced oxidative stress during salinity stress conditions than the non-inculcated control. Whole genome sequencing of Bacillus aerius EH2-5 identified key plant growth-promoting and salinity stress-related genes, including znuA, znuB, znuC, and zur (zinc uptake); ptsN, aspA, and nrgB (nitrogen metabolism); and phoH and pstS (phosphate transport). Genes involved in tryptophan biosynthesis and transport, such as trpA, trpB, trpP, and tspO, along with siderophore-related genes yusV, yfhA, and yfiY, were also detected. The presence of multiple stress-responsive genes, including dnaK, dps, treA, cspB, srkA, and copZ, suggests EH2-5′s genomic potential to enhance plant tolerance to salinity and other abiotic stresses. Inoculation with Bacillus aerius EH2-5 significantly enhanced soybean growth and reduced salt-induced damage, as evidenced by increased shoot biomass (29%, 41%), leaf numbers (12% and 13%), and chlorophyll content (40%, 21%) under 100 mM and 150 mM NaCl compared to non-inoculated plants. These results indicate EH2-5′s strong potential as a plant growth-promoting and salinity stress-alleviating rhizobacterium. The EH2-5 symbiosis significantly enhanced a key ABA biosynthesis enzyme-related gene NCED3, dehydration responsive transcription factors DREB2A and NAC29 salinity stresses (100 mM and 150 mM). Moreover, the reduced expression of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) by 16%, 29%, and 24%, respectively, and decreased levels of malondialdehyde (MDA) and hydroxy peroxidase (H₂O₂) by 12% and 23% were observed under 100 mM NaCl compared to non-inoculated plants. This study demonstrated that Bacillus aerius EH2-5, a melatonin-producing strain, not only functions effectively as a biofertilizer but also alleviates plant stress in a manner comparable to the application of exogenous melatonin. These findings highlight the potential of utilizing melatonin-producing microbes as a viable alternative to chemical treatments. Therefore, further research should focus on enhancing the melatonin biosynthetic capacity of EH2-5, improving its colonization efficiency in plants, and developing synergistic microbial consortia (SynComs) with melatonin-producing capabilities. Such efforts will contribute to the development and field application of EH2-5 as a promising plant biostimulant for sustainable agriculture. Full article

Cadmium (Cd) is a highly toxic heavy metal that can greatly affect crops and pose a threat to food security. Plant growth-promoting rhizobacteria (PGPR) are capable of alleviating the harm of Cd to crops. In this research, a Cd-tolerant PGPR strain was isolated and screened from the root nodules of semi-wild soybeans. The strain was identified as Pseudomonas sp. strain KM25 by 16S rRNA. Strain KM25 has strong Cd tolerance and can produce indole-3-acetic acid (IAA) and siderophores, dissolve organic and inorganic phosphorus, and has 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Under Cd stress, all growth indicators of soybean seedlings were significantly inhibited. After inoculation with strain KM25, the heavy metal stress of soybeans was effectively alleviated. Compared with the non-inoculated group, its shoot height, shoot and root dry weight, fresh weight, and chlorophyll content were significantly increased. Strain KM25 increased the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities of soybean seedlings, reduced the malondialdehyde (MDA) content, increased the Cd content in the roots of soybeans, and decreased the Cd content in the shoot parts. In addition, inoculation treatment can affect the community structure of endophytic bacteria in the roots of soybeans under Cd stress, increasing the relative abundance of Proteobacteria, Bacteroidetes, Sphingomonas, Rhizobium, and Pseudomonas. This study demonstrates that strain KM25 is capable of significantly reducing the adverse effects of Cd on soybean plants while enhancing their growth. Full article