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PubMed2026

Adaptation to Plant Defence in an Agricultural Insect Pest: Integrating Genome Scans and Gene Expression in the Soybean Aphid Reveals Multi-Genic Pathways.

In agroecosystems, intense selection pressures cause species to adapt and spread, often leading to the evolution and persistence of pests. Understanding how pests rapidly adapt can help develop sustainable strategies for their management and improve agroecosystem health. Pest adaptation involves stable variations in DNA sequence, as well as dynamic shifts in gene expression, often mediated by non-coding regulatory elements. We examined adaptation to plant defences in the soybean aphid, Aphis glycines, in which virulent aphids have overcome plant defences and avirulent aphids have not. Previous data with laboratory colonies suggested that virulent aphids have higher overall gene expression, including transposable elements, some of which influence gene regulation. However, we lack information on how genetic variation in natural populations impacts adaptation and potentially gene regulation. We integrated population genome scans of field-collected, soybean aphid populations with gene expression profiles of virulent and avirulent laboratory colonies to uncover connections between genetic differentiation and gene regulation for virulence. Genome scan methods found 2144 single nucleotide polymorphisms (SNPs) with significant genetic differentiation (i.e., outliers) in field-collected populations. These SNPs were near 1004 genes, representing 5.16% of the effective number of genes. Based on previous RNA-Seq data with laboratory colonies, we found 3160 genes and 147 long non-coding RNAs (lncRNAs) with differential expression among virulent and avirulent biotypes. By integrating both data sets, we identified 16 genes and 5 long non-coding RNAs with differential expression and that were associated with an outlier SNP (within 10 kbp). We validated SNPs with additional field collected aphids and found an aphid clone with stronger virulence than our laboratory virulent colony, surviving on 2 different aphid-resistant soybean varieties. This new virulent clone had fixed allele differences at 9 SNPs compared to our avirulent and other virulent colony. Field collected soybean aphids matching the phenotype of this new virulent clone had significant genetic differentiation with 3 outlier SNPs near genes related to zinc transport and lachesin compared to field collected avirulent aphids. Our entire data reinforced the importance of a potential multi-genetic response to overcome plant defence and generates new insights into complex genetic and regulatory mechanisms involved in insect-plant interactions.

Animals↗
PubMed2026

Soybean α-Amylase Gene Family: Structure and Expression in Response to Abiotic Stresses.

α-Amylases are involved in starch breakdown, thereby influencing plant development. Information on the α-amylase genes in soybean is limited. Here, we identified five soybean α-amylase genes from subfamilies AtAMY1 (GmaAMY5), AtAMY2 (GmaAMY4), AtAMY3 (GmaAMY1, GmaAMY3), and AMY6 (GmaAMY2). In silico analysis indicated that all five genes were actively expressed in leaves, flowers, and pods but weakly in roots. GmaAMY1-GmaAMY5 mRNAs were predicted to be targets of miRNAs associated with stress response, organ development, and nitrogen fixation. Putative GmaAMY1-GmaAMY5 proteins contained α-amylase-specific catalytic domain, signatures, and active sites. Short-term abiotic stresses (100 mM NaCl, 2.5-20% PEG, and 4 °C cold) applied to the cv. Doka affected both GmaAMY1-GmaAMY5 expression and the content of starch and soluble sugars in leaves. GmaAMY1 gene expression increased in response to NaCl and PEG, GmaAMY2 in response to PEG, and GmaAMY5 in response to NaCl. Salt stress suppressed the expression of the GmaAMY2-GmaAMY4 genes. The mRNA levels of all five genes increased after 2 h of cold exposure. Under salinity stress, there was inverse correlation of starch content with GmaAMY4 expression (r = -0.5135, p = 0.0293) and overall GmaAMY1-GmaAMY5 expression (r = -0.6318, p = 0.0049), suggesting a possible role of GmaAMY genes in protecting soybean from salinity by maintaining the starch/soluble sugars balance. Our results may aid in the breeding of stress-tolerant soybean varieties.

Glycine max↗
PubMed2025

Dissecting seed composition QTL from wild soybean: fine-mapping, candidate gene identification, and evaluation of introgression effects on agronomic performance.

Seed composition QTL from wild soybean were confirmed and validated in two genetic backgrounds across multiple environments, candidate genes were identified, and agronomic performance of backcross introgression lines was evaluated. Through selection for soybean yield, breeders have inadvertently reduced seed protein content and increased oil due to phenotypic and genetic correlations between these three traits. Therefore, identifying alleles that increase protein without adversely affecting oil and yield is of interest for breeders and the entire soybean value chain. Previously, a G. max × G. soja population was used to map a protein-associated region to ~ 4.6 Mbp on chromosome (Chr) 14. The G. soja allele significantly increased protein 6.5-7.2 g kg-1, without significantly decreasing oil. Additionally, two oil quantitative trait loci (QTL) were reported on Chrs 8 and 14. In this study, we aimed to confirm the Chr 14 protein QTL, evaluate QTL effects on seed composition and agronomic performance, and further fine-map to identify candidate genes. We validated and fine-mapped the Chr 14 protein QTL to a 0.6 Mbp region in a different genetic background, where the G. soja allele significantly increased protein by 9.3 g kg-1. Further, we confirmed the Chr 14 oil QTL linked to the protein QTL and the Chr 8 oil QTL. Chr 14 protein QTL effects on agronomic traits were evaluated in a backcross population across eight environments. The QTL significantly increased protein content, without significantly impacting oil, maturity, or plant height. While the QTL impacted yield and lodging, its effect and significance varied within environments. The candidate genes identified for these three validated seed composition QTL, along with additional molecular markers developed, offer valuable resources for improving seed composition in soybean breeding programs.

Quantitative Trait Loci↗
PubMed2026

The Jumonji C domain-containing proteins GmJMJ19 and GmJMJ20 link florigen signaling with epigenetic regulation of photoperiodic flowering and post-flowering plant height in soybean.

Soybean (Glycine max) is a photoperiod-sensitive legume whose latitudinal adaptation depends on the precise control of flowering time and plant height. Histone demethylases of the JmjC domain-containing (JMJ) protein family have been implicated in these processes across plant species, but their specific roles in soybean remain largely unexplored. Here, we identify soybean GmJMJ19 and GmJMJ20, two closely related JMJD5/KDM8 orthologs, as master epigenetic regulators that coordinately control both photoperiodic flowering and post-flowering plant height. Both genes exhibit intrinsic, rhythmic expression peaking at ZT12, and their encoded proteins physically interact with the florigen proteins FT2a and FT5a. Loss-of-function mutants display delayed flowering under long days (LDs) and increased plant height under both LDs and short days (SDs), whereas overexpression phenocopies the mutant flowering phenotype, indicating revealing a critical dosage requirement for proper function. Mechanistically, GmJMJ19 and GmJMJ20 are recruited by the FT/FD transcriptional complex to directly activate AP1a and AP1c expression through chromatin modulation. Population genomic analyses reveal distinct selection signatures: GmJMJ19 underwent sustained directional selection during cultivation, whereas GmJMJ20 experienced an early domestication sweep with limited subsequent change. Haplotype analysis identifies coordinated latitudinal clines, with the JMJ19H1/JMJ20H1 combination predominating at high latitudes to promote early flowering and limit height, while JMJ19H2/JMJ20H2 and wild JMJ19H3/JMJ20H3 alleles prevail at low latitudes, conferring later flowering and increased height. Collectively, our findings establish GmJMJ19 and GmJMJ20 as central chromatin regulators linking florigen signaling to downstream target expression and provide valuable allelic resources for breeding regionally adapted soybean varieties across a wide range of latitudinal environments.

Histone modulation↗
PubMed2026

Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.

Genomic structural variants (SVs) are major sources of genetic variation and have profound impacts on phenotypic traits. However, their functional effects remain largely unexplored in soybean. Here, we resequence 940 soybean accessions. Together with 44 publicly available datasets, we identify 602,281 SVs. Using a graph-based genome, we detect an additional 58,760 presence/absence variations (PAVs) that broadly affect gene expression. Population genomic analyses reveal that SVs serve as a core driving force for soybean domestication and improvement. Integrating SVs with QTLs for oil and protein content, and performing GWAS on 27 traits, we identify key functional SVs. These include transposable element insertions altering seed coat color, multiple insertions within a cytochrome P450 gene modifying flower and hypocotyl color, and a GmMATE1 deletion enhancing seed size. Together, our study establishes a comprehensive SV map of soybean, offering a valuable resource for dissecting the genetic basis of complex traits to accelerate molecular breeding.

Glycine max↗
PubMed2026

Genome-wide identification, characterization, evolutionary analysis, and expression profiling of the FCS-like zinc finger (FLZ) gene family in soybean (Glycine max L.) under abiotic stresses.

Drought and salinity limit soybean yield. Despite their role in the SnRK1 energy-sensing complex, a systematic study of FCS-Like Zinc Finger (FLZ) proteins in soybean has not been reported. We performed a genome-wide identification of the GmFLZ gene family, identifying 40 members distributed across 18 of the 20 soybean chromosomes. Phylogenetic analysis of 87 FLZ proteins from Glycine max, Arabidopsis thaliana, and Oryza sativa revealed four major evolutionary clades, suggesting that diversification predates the separation of monocots and dicots. Structural analysis identified ten conserved motifs, with Motifs 1 and 2 present in all family members. Gene duplication analysis identified 304 paralogous pairs, most arising from segmental duplication. Ka/Ks analysis indicated localized positive selection in six gene pairs and purifying selection in 97.9% of pairs. Tissue-specific expression profiling across nine tissues showed that GmFLZ5, GmFLZ15, GmFLZ25, and GmFLZ34 had the highest expression levels detected across the GmFLZ family, with GmFLZ5 the most highly expressed member in leaves, nodules, and stem and showing moderate expression in pod, root, and root hairs, whereas GmFLZ18, GmFLZ23, and GmFLZ37 showed root-preferential expression. RT-qPCR validation under drought (20% PEG-6000) and salt (200 mM NaCl) treatments in the Giza 5 cultivar showed that 36 and 34 of the 40 GmFLZ genes, respectively, exhibited at least a two-fold change in expression, with GmFLZ21 and GmFLZ35 among the most strongly induced under salt stress. These findings provide an evolutionary and functional framework for the GmFLZ family and identify candidate genes for future functional studies in soybean stress tolerance.

Glycine max↗
PubMed2026

Photoperiod and UV-B orchestrate ICR1 to control seed isoflavonoid accumulation in soybean.

Being sessile, plants optimize their physiological and metabolic processes in response to ambient environmental cues, such as light. However, the molecular mechanisms underlying environmental regulation of seed isoflavonoid biosynthesis in soybean remain largely elusive. Here, our genome-wide association study (GWAS) identifies Isoflavone Content Regulator 1 (ICR1), encoding a Regulator of Chromosome Condensation (RCC1) family protein, as a positive regulator of seed isoflavonoid accumulation in soybean. The CONSTANS (CO) homolog GmCOL2b directly suppresses ICR1 transcription by binding to a CORE cis-element. Notably, nature variations flanking the CORE sequence influence GmCOL2b binding affinity, thereby modulating ICR1 transcription and seed isoflavone content. We further demonstrate that photoperiod significantly affects seed isoflavone content, with short-day (SD) conditions promoting isoflavonoid accumulation by relieving GmCOL2b-mediated repression of ICR1, while UV-B radiation facilitates ICR1 protein accumulation. Subsequently, ICR1 interacts with GmMYB12B2 to enhance seed isoflavonoid biosynthesis. Our findings elucidate how soybean integrates environmental light signals, including photoperiod and UV-B signaling that vary across seasons or latitudes, to coordinate seed isoflavonoid biosynthesis, providing a valuable genetic resource for improving soybean nutritional quality.

Journal Article↗
PubMed2024

PSEUDO-RESPONSE REGULATOR 3b and transcription factor ABF3 modulate abscisic acid-dependent drought stress response in soybean.

The circadian system plays a pivotal role in facilitating the ability of crop plants to respond and adapt to fluctuations in their immediate environment effectively. Despite the increasing comprehension of PSEUDO-RESPONSE REGULATORs and their involvement in the regulation of diverse biological processes, including circadian rhythms, photoperiodic control of flowering, and responses to abiotic stress, the transcriptional networks associated with these factors in soybean (Glycine max (L.) Merr.) remain incompletely characterized. In this study, we provide empirical evidence highlighting the significance of GmPRR3b as a crucial mediator in regulating the circadian clock, drought stress response, and abscisic acid (ABA) signaling pathway in soybeans. A comprehensive analysis of DNA affinity purification sequencing and transcriptome data identified 795 putative target genes directly regulated by GmPRR3b. Among them, a total of 570 exhibited a significant correlation with the response to drought, and eight genes were involved in both the biosynthesis and signaling pathways of ABA. Notably, GmPRR3b played a pivotal role in the negative regulation of the drought response in soybeans by suppressing the expression of abscisic acid-responsive element-binding factor 3 (GmABF3). Additionally, the overexpression of GmABF3 exhibited an increased ability to tolerate drought conditions, and it also restored the hypersensitive phenotype of the GmPRR3b overexpressor. Consistently, studies on the manipulation of GmPRR3b gene expression and genome editing in plants revealed contrasting reactions to drought stress. The findings of our study collectively provide compelling evidence that emphasizes the significant contribution of the GmPRR3b-GmABF3 module in enhancing drought tolerance in soybean plants. Moreover, the transcriptional network of GmPRR3b provides valuable insights into the intricate interactions between this gene and the fundamental biological processes associated with plant adaptation to diverse environmental conditions.

Glycine max↗
PubMed2026

The transcription factors GmBBX17 and GmSTFs antagonistically regulate shade avoidance in soybean by oppositely modulating GmSRG1 transcription.

High-density planting represents a promising strategy to enhance crop productivity. However, this agronomic practice inevitably triggers shade avoidance responses, manifested as stem and petiole elongation, suppressed branching, and altered petiole angles. Elucidating the molecular underpinnings of shade avoidance remains imperative for rationalizing planting density strategies in crop production. Here, we report that soybean SHADE-REDUCED GENE 1 (GmSRG1) inhibits the stem and petiole growth both in white light and low ratio of Red:Far-red light conditions in soybean. GmSRG1 likely represents a catalytically inactive homolog of xyloglucan endotransglucosylase/hydrolase that lacks the conserved active site. Despite its enzymatic deficiency, it is associated with enhanced xyloglucan-degrading activity and prevents xyloglucan accumulation in soybean. GmBBX17 binds to the GmSRG1 promoter to repress its transcription, whereas GmSTFs (GmSTF1 and GmSTF2) transcriptionally activate GmSRG1. GmBBX17 physically interacts with GmSTFs to antagonistically regulate GmSRG1 expression. Unlike GmSRG1, its close homolog GmXTH23 is associated with increased xyloglucan accumulation and reduced xyloglucan-degrading activity, while GmSRG1 physically interacts with GmXTH23 and counteracts this GmXTH23-associated effect. Our work reveals an integrated regulatory network comprising the GmBBX17-GmSTFs transcriptional module and the GmSRG1-GmXTH23 regulatory module, which collectively govern shade avoidance architecture in soybean.

Glycine max↗
PubMed2026

Flavonoid biosynthesis mediated by GmF3Hs contributes to drought tolerance in soybean.

Flavonoids are central to abiotic stress responses, yet the specific signaling roles and evolutionary dynamics of flavonoid biosynthetic intermediates in crop drought adaptation remain elusive. Here, we demonstrate that dihydrokaempferol (DHK) and dihydroquercetin (DHQ), specific intermediate products of the soybean flavanone 3-hydroxylases GmF3H1/2, function as potent signaling molecules that mitigate drought stress. Exogenous DHK/DHQ promoted abscisic acid-dependent stomatal closure and enhanced drought tolerance across diverse dicot species, including soybean and tobacco, highlighting a broadly conserved stress-mitigating signaling mechanism. CRISPR/Cas9-generated gmf3hs double mutants exhibited severe drought hypersensitivity due to compromised redox homeostasis and defective stomatal regulation, which could be specifically rescued by DHK/DHQ application. Furthermore, the loss of GmF3H triggered a distinct reproductive trade-off under stress, leading to increased pod initiation but severe filling defects. Multiomics network analysis revealed extensive rewiring of broader stress-responsive pathways and identified upstream transcription factors, among which GmPHL11 directly binds to and activates the GmF3H1 promoter; overexpression of GmPHL11 promoted DHK accumulation and enhanced drought stress tolerance in soybean hairy roots. Finally, population genomic analyses demonstrated that the GmF3H1H1 haplotype, which confers superior enzymatic activity and robust root growth under drought stress, might have undergone positive selection during soybean domestication. Collectively, our findings redefine the role of GmF3H-derived specific intermediates as potent signaling molecules, providing comprehensive mechanistic and evolutionary insights into flavonoid-mediated drought resilience, developmental trade-offs, and molecular breeding in crops.

Drought Resistance↗
PubMed2026

Integrative Multi-Omics Analysis of Stem Growth Habit Divergence in Wild Soybean (Glycine soja).

Stem architecture is a major determinant of lodging resistance, biomass accumulation, and harvest efficiency in soybean. However, the molecular features associated with contrasting stem growth habits in wild soybean remain incompletely characterised. Here, we performed an integrated transcriptomic, metabolomic, and epigenomic analysis of stem growth-habit divergence in wild soybean, comparing the wild-type accession ZYD7068 with contrasting vining and erect mutant lines derived from carbon-ion beam mutagenesis. Pairwise transcriptomic comparisons identified between 20 311 and 28 705 differentially expressed genes per contrast, with a core set of 2672 genes consistently altered across the comparisons. Functional enrichment, gene set variation analysis, and gene set enrichment analysis converged on xylem and phloem pattern formation as a prominent molecular pathway associated with growth-habit divergence. Random forest analysis identified BBR-BPC and ARF transcription factor families as major molecular discriminators, while metabolomic profiling revealed distinct metabolic profiles involving amino-acid-derived and lipid-associated metabolites. Whole-genome bisulfite sequencing revealed context-specific DNA methylation differences, including substantial variation in CHG methylation among erect mutant lines. Integrated network and in silico perturbation analyses prioritised four candidate genes associated with vascular development for future functional validation. Together, these results provide a multi-layer molecular resource for investigating stem growth-habit divergence in G. soja and establish testable candidate pathways and genes for subsequent functional studies and soybean improvement.

glycine soja↗
PubMed2025

Cell-type-specific response to silicon treatment in soybean leaves revealed by single-nucleus RNA sequencing and targeted gene editing.

Mineral nutrient uptake and deposition profoundly influence plant development, stress resilience, and productivity. Silicon (Si), though classified as a non-essential element, significantly influences a plant's physiology, particularly in fortifying defense responses and mitigating stress. While the genetic and molecular mechanisms of Si uptake and transport are well studied in monocots, particularly rice, their role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. In this study, we utilized single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. We identified distinct cellular populations, including a unique Si-induced or Si-associated cell cluster within vascular cells, suggesting a specialized mechanism of Si distribution. Si treatment notably induced the expression of defense-related genes, with a pronounced enrichment in vascular cells, underscoring their pivotal role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in phytoalexin biosynthesis, salicylic acid, and immune receptor signaling, suggesting transcriptional priming of genes involved in defense responses. Further investigation of Si transporters revealed precise expression of an Si efflux gene in epidermal cells in response to Si treatment. We also validated the role of efflux Si transporters using a Xenopus oocyte assay and CRISPR/Cas9 genome editing of composite soybean plant roots. This study provides critical insights into the biotic stress regulatory networks influenced by Si treatment in soybean leaves at the single-cell level, thus laying the foundation for enhancing stress tolerance through optimized mineral nutrient uptake.

Glycine max↗
PubMed2025

Yield and yield component trait analysis with DArT genotyping for GWAS in soybean grown in drought conditions of Kazakhstan.

Development of drought tolerant cultivars of soybean is the single best way to address the challenge of global climate change and very limited water resources for crop irrigation in Central Asia including Kazakhstan. A set of 188 soybean cultivars with diverse origins was assessed for genome-wide association study (GWAS) for yield and eight yield-related traits in both irrigated (well-watered, WW) and non-irrigated (drought) conditions during 2 years in field trials in South-Eastern Kazakhstan. The 295K Diversity array technology (DArT) analysis was applied, and 16K filtered DArT markers were used for genotyping of 183 soybean accessions. In the results, 41 quantitative trait nucleotides (QTN) were identified as significantly associated with nine studied traits. To verify these results, bulk segregant analysis (BSA) was carried out in six breeding lines originating from two crosses between high-yielding under drought cvs, Sponsor and Zen, with drought sensitive cv Lastochka. The evaluation of combined results revealed 10 most significant QTN and eight most promising putative candidate genes, which were selected and tested for their gene expression using RT-qPCR under drought compared with WW controls. Among them, glucose-6-phosphate isomerase (G6PI), pentatricopeptide repeats (PPR) protein, and ABC transporter, associated with seed yield, seed weight per plant, and plant height, were highly upregulated in drought tolerant genotypes. In contrast, two other genes, Rab-GDP dissociation inhibitor (Rab-GDI) and Transducin with WD40 repeats, associated with seed yield, showed repression in the same genotypes. These verified genes involved in the control of yield and yield-related traits can be used for marker-assisted selection to develop novel genotypes and new soybean cultivars tolerant to strong drought in Kazakhstan and in other countries with similar conditions.

Diversity array technology (DArT)↗
PubMed2026

Two Bacillus PGPB Strains in Wheat and Soybean: Wheat Growth Promotion Without Detectable Rhizosphere Microbiome Restructuring.

Plant growth-promoting bacteria (PGPB) are increasingly deployed as biofertilizers, yet the link between an inoculant's genomic potential and its realized effect on the plant is rarely assessed within an integrative framework that jointly captures the rhizosphere microbiome, plant phenotype, and strain genome. Two Bacillus strains-B. halotolerans 1453 and B. pumilus 630-were applied to wheat and soybean in a factorial pot experiment (2 strains &#xd7; 2 application methods &#xd7; 3 frequencies + control, 3-4 replicates). Rhizosphere samples (n = 67 after filtering) were profiled by 16S rRNA sequencing with PICRUSt2 functional prediction and compositional validation (Aitchison PERMANOVA, ALDEx2, ANCOM-BC2). The PGPB gene repertoire was characterized by genome mining (481 marker genes, 14 categories). Wheat phenotype (six traits) and soybean height were analyzed with models appropriate for count data (Negative Binomial and binomial GLMs) for treatment-vs.-control comparisons, and with factorial ANOVA for decomposition into main effects and interactions. Crop identity was the dominant factor shaping both microbiome structure and function (PERMANOVA R2 = 14.7% taxonomically and R2 = 7.8% functionally, both p < 0.001), with biologically meaningful taxonomic differences between wheat and soybean; strain, application count and method had no significant effect on community composition (R2 < 4% each), and co-occurrence networks showed no reliable differences between crops once read depth and sample size were controlled for. Despite this neutrality at the microbiome level, inoculation significantly increased wheat spike count (NB-GLM, all 12 treatments vs. control, padj 0.0002-0.031), ear weight, and stem count, with application count the strongest source of variability and a pronounced strain &#xd7; application count. Strain 1453 outperformed 630 in spike count (+23.1%, p = 0.012) and ear weight (+20.4%, p = 0.023); we hypothesize that this may be related to its more complete DNRA pathway (narGHI + nirB-nirD) and biocontrol genes (bacE, srfAA). Strain 630 produced a less pronounced effect than strain 1453 but was subject to smaller fluctuations across replicates (CV &#x2248; 16-21% vs. &#x2248;24-26% for 1453), which may reflect better resilience to environmental fluctuations, possibly due to its confirmed rsbV/rsbW stress-tolerance regulon. Rhizosphere microbiome composition differed clearly by crop (wheat vs. soybean) but showed no detectable response to strain, application method, or application count. Despite this lack of a microbiome signal, inoculation significantly increased wheat spike count and ear weight, with the magnitude and stability of this effect differing by strain. We hypothesize that this strain-dependent difference relates to underlying genomic differences-particularly in nitrogen metabolism (DNRA pathway) and stress-tolerance genes-though this link has not been tested directly and remains a hypothesis for future work.

Triticum↗
PubMed2026

Genome-Wide Identification of the Soybean GH5 Gene Family and Functional Analysis of GmGH5-22 in Salt Tolerance.

Plant GH5 family genes function in both cell wall biosynthesis and stress responses. However, comprehensive studies on GH5 genes in the soybean remain limited. Here, we identified 28 GmGH5 genes from the soybean genome. Phylogenetic analysis assigned these genes to three subfamilies (I-III), with no representatives in subfamily IV. The GmGH5 family harbors 15 conserved motifs, which are largely similar within subfamilies but differ across subfamilies. Additionally, exon-intron structures (2-7 introns) exhibit clade-specific patterns, with members within the same clade sharing similar intron numbers and lengths, whereas distinct clades show some variation. The promoter regions of GmGH5 genes contained various cis-acting regulatory elements associated with stress responses and developmental processes. Transcriptome-based expression profiling revealed distinct tissue-specific expression patterns of GmGH5 genes. RT-qPCR further confirmed their differential expression under salt, alkaline, cold, and drought stresses, especially a significant increase in GmGH5-22 expression under salt stress (approximately 22-fold at 6 h, **** p < 0.0001). Furthermore, GmGH5-22 was highly expressed in roots, and transient expression in tobacco leaves showed its peripheral localization, which aligns with its predicted extracellular localization, suggesting that GmGH5-22 is highly likely localized to the cell wall. Overexpression of GmGH5-22 in soybean hairy roots significantly improved tolerance to salt stress. These findings establish a foundation for functional characterization of GmGH5 genes and provide viable targets for molecular breeding to enhance salt tolerance in soybeans.

GH5 family↗
PubMed2026

Targeted expression of Glycine max isoflavone synthase enhances daidzein and genistein content in soybean.

Isoflavonoids are key secondary metabolites in leguminous plants that play essential roles in plant physiology and provide significant health benefits to humans. In the isoflavone biosynthetic pathway, isoflavone synthase (IFS) catalyzes the conversion of naringenin and liquiritigenin into the bioactive isoflavones genistein and daidzein. This study aimed to enhance genistein and daidzein accumulation in soybean seeds through genetic engineering. Agrobacterium tumefaciens strain EHA105 harboring the binary vector pCAMBIA1301 containing GmIFS under the control of a seed-specific promoter (Gm&#x3b2;-conglycinin) was used to transform modified half-seed explants of soybean cv. JS335. Hygromycin-B-resistant plants were regenerated, hardened, and confirmed by histochemical GUS assay. Molecular analysis by PCR validated the presence of the GmIFS transgene, yielding a 700&#xa0;bp amplicon. Biochemical analysis revealed that seeds of T&#x2080; transgenic plants showed a 1.53-fold increase in total phenolic content and a 3.67-fold increase in flavonoid content compared to non-transformed controls. Antioxidant assays demonstrated significantly higher DPPH radical-scavenging activity and ferric-reducing antioxidant power (FRAP) in GmIFS-overexpressing plants. HPLC analysis further indicated that transgenic seeds accumulated, on average, 4.07-fold higher daidzein and 1.75-fold higher genistein levels relative to control plants. qRT-PCR analysis showed significantly elevated GmIFS expression in immature cotyledons, mature cotyledons, and seeds of transgenic plants. Overall, these results demonstrate that GmIFS overexpression effectively enhances isoflavone production in soybean seeds, highlighting the potential of metabolic engineering of biosynthetic pathway genes to improve nutritional quality.

Glycine max↗
PubMed2026

A single-nucleus transcriptome atlas of soybean anthers.

Anther development is crucial for plant sexual reproduction. However, a high-resolution, cell-type-specific transcriptomic atlas of this process is lacking for the legume crop soybean (Glycine max). Here, we construct a comprehensive transcriptional atlas of developing soybean anthers using single-nucleus RNA sequencing (snRNA-seq). We identify and characterize nine distinct cell types spanning both somatic and reproductive lineages. Our analysis reveals robust transcriptional continuity across anther developmental stages and dynamic reprogramming during key transitions. Notably, the shift from diploid meiocytes to haploid unicellular microspores is marked by the induction of previously inactive genes, despite an overall reduction in transcript abundance. Subsequently, within bicellular microspores, generative and vegetative cell lineages exhibit sharply divergent transcriptional programs: generative cells specialize in mRNA export and turnover, whereas vegetative cells up-regulate translational machinery. Evolutionary analysis further indicates that generative-cell-specific genes are subject to more relaxed purifying selection compared to those specific to vegetative cells. Functional validation using mutants generated by CRISPR/Cas9-mediated genome editing and EMS mutagenesis reveals the essential roles of OSD1A and PKSA in pollen development and fertility. This high-resolution atlas provides fundamental insights into the transcriptional regulation of soybean anther development and serves as a valuable resource for manipulating male fertility to advance hybrid breeding programs. The data are available at https://databases.genedenovo.com/pollen.

Glycine max↗
PubMed2026

Multiplex FAD2/FATB Editing Generates Ultra-High-Oleic, Low-Saturate Soybean With Increased Seed Fatty Acid Content.

Oleic acid (18:1), saturated fatty acid (SFA), and polyunsaturated fatty acid (PUFA) levels are important traits for storage stability and edibility. In this study, we aimed to develop high-oleic soybean (Glycine max) by simultaneously targeting fatty acid desaturase 2 (FAD2) and fatty acyl-ACP thioesterase B (FATB) gene families using CRISPR/Cas9. Considering the paleopolyploid genome of soybean, multiple sgRNAs were designed to target GmFAD2-1, GmFAD2-2, and GmFATB genes expressed during seed development. Compared with targeting GmFAD2-1 alone (~83%), additional editing of GmFAD2-2B, GmFAD2-2C, and GmFATB1a increased the 18:1 fatty acid content to over 90%. Editing of GmFATB significantly reduced the SFA content by more than 40% compared with wild-type (WT). Reduced absolute SFA content was also observed in GmFAD2-only edited lines with decreased GmFATB expression. Notably, all evaluated high-oleic genotypes in the Williams82-background showed higher mean total fatty acid (TFA) content than the WT, both per unit seed mass and per seed. Correlation analysis of 805 individual seed profiles from Williams82-background lines further characterized the relationship between 18:1 fatty acid composition and TFA content per unit seed mass. Gene expression analysis revealed no consistent increase in triacylglycerol (TAG) synthesis genes, whereas the expression of sugar-dependent 1 (SDP1) was reduced. In contrast, genes involved in phosphatidic acid (PA) metabolism, including diacylglycerol kinase (DGK) and phospholipase D (PLD), were partially upregulated. These transcriptional changes support a hypothesis that altered lipid turnover may contribute to the higher TFA phenotype. Collectively, this study defines effective multiplex target combinations for ultra-high oleic, low-saturated soybean.

FAD2↗