As the outermost structure of the plant shoot, pubescence is crucial for plant resistance to herbivores. However, the underlying mechanism regulating pubescence density and insect resistance in soybean [Glycine max (L.) Merr.] remains largely unclear. Here, we identified the pubescence density-related gene Glycine soja KNOTTED1-like homeobox 1 (GsKNOX1), a member of the KNOX transcription factor family, in wild soybean (G. soja Sieb. & Zucc.) through a genome-wide association study. Overexpression of GsKNOX1 increased soybean pubescence density and resistance to common cutworm (Spodoptera litura Fabricius), reduced leaf size, and altered plant architecture. Furthermore, scanning electron microscopy revealed that GsKNOX1 overexpression decreased leaf epidermal cell area and increased leaf epidermal cell density. RNA sequencing revealed that GsKNOX1 affects the expression levels of several pubescence-related genes, including the dense pubescence (Pd1) gene and the pubescence positive regulator GLABRA2, and resistance-related genes such as lipoxygenase. Metabolomic analysis further demonstrated that GsKNOX1 mediates extensive metabolic reprogramming, leading to the marked accumulation of defense-related metabolites, including flavonoids, terpenoids, and alkaloids. Bimolecular fluorescence complementation and luciferase complementation assays validated the interaction between GsKNOX1 and Pd1. Dual-luciferase transient expression assays revealed that the GsKNOX1-Pd1 protein interaction exhibits stronger activation of glabrous (P1) compared with Pd1 alone. Application evaluation revealed that moderate GsKNOX1 expression does not obviously affect the seed yield per plant in soybean. This study highlights the significant roles of GsKNOX1 in regulating soybean pubescence density and insect resistance and provides a gene target for improving insect resistance in soybean breeding.

Understanding the mechanisms underlying plant stress tolerance is crucial for improving plant resilience, particularly under challenging environmental conditions. This study investigates the role of long-chain acyl-CoA synthetases in Salix matsudana (SmLACSs), focusing on their evolutionary relationships, functional characterization, and response to environmental stresses. Through a comprehensive analysis, 25 SmLACSs were identified, classified into seven distinct clades, with Clade VII representing a newly discovered subfamily in willow. Evolutionary analysis revealed that segmental duplication and whole-genome duplication were key mechanisms for the expansion of SmLACSs. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis further indicated that SmLACSs play a role in lipid metabolism, cuticle formation, and stress response pathways. Using RNA-seq and qRT-PCR, differential expression patterns of SmLACSs under salt or submergence stress were observed, highlighting their contribution to stress tolerance, particularly in maintaining cell membrane integrity and lipid homeostasis. These findings provide valuable insights into the roles of SmLACSs in willow’s resilience, and offer potential targets for improving stress tolerance in plants.

Roots are vital for crop growth, development, yield, and tolerance to various types of environmental stress. Numerous genetic loci associated with soybean root morphological traits have been identified, but few genes associated with these traits have been reported. This study identified seven quantitative trait loci (QTLs) containing stable SNPs significantly associated with the root dry weight in soybeans through a genome-wide association study. Among these QTLs, qRDW14-2 presented the greatest significance. In qRDW14-2, the gene GmRGD14, encoding the lysophosphatidic acid acyltransferase LPAT4, was identified as a candidate. GmRGD14, in block63, which contained the significant SNP S14_6521715, had the highest expression level in soybean roots, and its Arabidopsis homologous mutant lpat4 presented more lateral roots than did the control Col-0. GmRGD14 was localized primarily to the cell membrane and endoplasmic reticulum. The heterologous overexpression of GmRGD14 in Arabidopsis significantly increased the lateral root number, which was similar to the phenotype of atlpat4. Furthermore, overexpression of GmRGD14 resulted in a greater total root length, root tip number, root surface area, and root volume in the hairy roots of transgenic soybean plants than in those of control soybean plants, whereas knockdown of the gene via RNA interference in soybean hairy roots resulted in the opposite phenotype. GmRGD14, which is highly genetically variable in wild soybean, has been gradually utilized during soybean domestication. Overall, this study revealed that GmRGD14 is a new key gene involved in root growth, providing a promising genetic target for breeding elite soybean varieties with strong root systems.

Arsenite (AsIII), regarded as a hazard to human health and food safety, restrains root growth. This event has received little attention, and the mechanism underlying how AsIII affects auxin dynamics to repress root growth remains unknown. Here, our results have suggested that AsIII-inhibited root growth possibly involved an elevated auxin level in roots, as supported in multiple experiments such as (1) transgenic DII-VENUS and DR5rev::GFP; (2) IAA determination by enzyme-linked immunosorbent assay; (3) phenotype analysis of taa1 (defective in auxin biosynthesis) mutant; and (4) the external application of 1-naphthylphthalamic acid (NPA) to manipulate auxin transport. This consequence could be explained through up-regulated transcriptional levels of auxin biosynthesis-related genes in whole plants. Phenotypes of auxin transport-related carriers have displayed that loss of PIN7 and AUX1, but not PIN1/2/3 transporters, ameliorated the extent of AsIII-induced root growth inhibition. Moreover, AsIII specifically enhanced the abundance of PM-localized PIN7 and AUX1 involved in transcriptional but not post-transcriptional regulation. A real-time in vitro observation of PM-localized PIN2 using the transgenic pPIN2::PIN2-Dendra2 line has revealed that AsIII did not influence the endocytosis of PM-localized PIN2 carriers in root apices. Overall, our results propose that AsIII stress-elevated auxin level in the root apex possibly involves up-regulation transcriptional levels of auxin biosynthesis- and auxin transport-related genes but does not target PIN2 dynamics, finally, leading to auxin accumulation in root apices and root growth inhibition.

Herbivory is destructive for crop production in many regions worldwide. The induced plant response to herbivores promotes resistance; therefore, characterizing the mechanisms underlying natural host resistance is highly important. However, the genetic components of resistance to herbivores in the staple food crop soybean remain elusive. Here, a key defense gene, GmMYC3, was identified via joint linkage and association mapping in soybean. GmMYC3 encodes an MYC2 transcription factor that is rapidly activated after jasmonic acid treatment or herbivore attack and confers resistance to a major pest, the common cutworm (CCW), in soybean. GmMYC3 positively regulates multiple biotic stress-related genes, among which GmMYC3 triggers high expression of Kunitz-type trypsin inhibitors alongside its homolog GmMYC1 and downstream GmWRKY56. GmMYC3 overexpression results in massive accumulation of trypsin inhibitors in soybean leaves, interferes with the protein digestion and absorption function in larvae that are fed these leaves, and retards larval and pupal development of the CCW. The results of the field tests of the transgenic plants corroborate the defense role of GmMYC3. Evolutionary and population genetic analyses suggest that the elite haplotype of GmMYC3 contributes to resistance against the CCW without significant reduction in seed yield and quality. Notably, this haplotype appears at a low frequency in domesticated germplasms. This study sheds light on the molecular mechanism underlying plant resistance to the CCW and provides potentially valuable resources for breeding soybean plants with elevated resistance against this pest.

The jasmonic acid (JA) pathway is central for plant defence against herbivores, and genes related to this pathway have received increased attention. Here, we evaluated the functions of the allene oxide cyclase (AOC)-encoding gene GmAOC3 and the caleosin-encoding gene GmCLO1, which may affect JA synthesis in soybean, and explored the anti-insect mechanisms of these two genes. The overexpression of GmAOC3 increased soybean resistance to the common cutworm (CCW). The strongest resistance to CCW was observed in the GmAOC3-overexpressing line GmAOC3-OE-1. Whole-genome resequencing and expression analysis revealed that in this line, GmCLO1 silencing was caused by insertion of the GmAOC3 gene into the GmCLO1 sequence. GmCLO1 expression responded to CCW induction. Compared with the controls, the knockdown or knockout of GmCLO1 increased soybean resistance to CCW. Conversely, the overexpression of GmCLO1 decreased CCW resistance. Transcriptomic and metabolomic analyses revealed that the gmclo1-knockout line shared 653 differentially expressed genes (DEGs) and 87 differentially abundant metabolites with the GmAOC3-OE line. Among these common DEGs, anti-insect genes related to JA, such as the 9-lipoxygenase gene Glyma.13G347800, the vegetative storage protein gene Glyma.08G200100, and the trypsin inhibitor gene Glyma.06G219900, showed upregulated expressions in both lines. Additionally, JA and JA-isoleucine contents were notably elevated in the GmAOC3-OE-1 line but decreased in the GmCLO1-overexpressing line. Measurements of yield-related traits revealed that GmAOC3 overexpression and/or GmCLO1 knockout did not affect soybean yield. In conclusion, we identified two new target genes for insect-resistant soybean breeding and contributed to an in-depth understanding of the JA-mediated insect resistance mechanisms in soybeans.

Seven co-localized QTLs that control low-sulfur tolerance in soybean seedlings were identified. Two putative candidate genes and 3 promising parental cross combinations were further predicted. Low-sulfur nutrient stress severely affects yield and quality in soybean production. However, genetic studies related to soybean tolerance to low-sulfur conditions are insufficient. Here, soybean tolerance to low-sulfur conditions was evaluated according to ten traits at the seedling stage. A total of 72 quantitative trait loci (QTLs) and 103 quantitative trait nucleotides (QTNs) related to low-sulfur tolerance in soybean seedlings were detected via linkage analysis and genome-wide association analysis (GWAS) in a recombinant inbred line (RIL) population and a natural population, respectively. Among these loci, 7 co-localized QTLs were identified via two methods across chromosomes 1, 6, 8, 9, 14, and 17. Glyma.17G167100, which includes two significant SNPs (AX-93862060 and AX-93862061), and Glyma.14G169300 were suggested as putative candidate genes on the basis of transcriptome data, haplotype analysis and real-time quantitative PCR. In addition, 3 promising parental cross combinations with the aim of improving low-sulfur tolerance have been designed across favorable alleles, which were determined on the basis of the co-localized QTLs and relative values of trait phenotypes in three environments. These results provide important evidence for understanding the genetic basis of low-sulfur tolerance in soybean and may be helpful in the breeding of new soybean varieties with high tolerance to low-sulfur soil.

GmIQD63 interacts with GmCDPK38 to mediate soybean defense against the common cutworm, and its elite haplotype enhances resistance without a significant yield penalty, providing a potential breeding resource. Soybean (Glycine max) production is severely threatened by the common cutworm (Spodoptera litura Fabricius), necessitating the identification of resistance genes for molecular breeding. Calcium-dependent protein kinases (CDPKs) are critical regulators of plant defense responses; however, the substrate network of GmCDPK38, a negative regulator of soybean resistance to this pest, remains elusive. In this study, we combined phosphoproteomic analysis of the gmcdpk38 mutants with bimolecular fluorescence complementation assays to identify 12 potential GmCDPK38-interacting partners. Among these, GmIQD63, an IQ67 domain protein homologous to Arabidopsis AtIQD1 (a known insect resistance regulator), emerged as a key candidate. The physical interaction between GmCDPK38 and GmIQD63 was further validated through yeast two-hybrid and luciferase complementation imaging assays. Sequence analysis revealed that GmIQD63 encodes a 477-amino acid polypeptide containing multiple stress- and hormone-responsive cis-acting regulatory elements in its promoter region, along with a conserved IQ67 domain characteristic of plant IQD IIIb subfamily members. Subcellular localization experiments confirmed its plasma membrane targeting. Functional characterization via RNA interference-mediated silencing of GmIQD63 in soybean hairy roots significantly enhanced susceptibility to the common cutworm. Population genetic analysis of 341 soybean accessions uncovered natural variation in GmIQD63, with haplotype H5 in wild soybeans conferring enhanced resistance to the common cutworm without compromising agronomic traits. Notably, H5 is rare in cultivated soybeans, suggesting its untapped potential for breeding insect-resistant varieties. This study identifies GmIQD63 as a novel GmCDPK38-interacting partner essential for soybean defense and provides a molecular foundation for developing insect-resistant cultivars.

Coilia nasus is an economically important fish species that exhibits two distinct life history strategies: an anadromous form, which migrates from seawater to freshwater to spawn, and a freshwater-resident form that completes its entire life cycle in freshwater habitats. The taxonomic status of the freshwater-resident form (C. nasus taihuensis) has long remained unresolved, as it is unclear whether it represents a distinct subspecies or a divergent ecotype. To explore the evolutionary relationships between anadromous and freshwater-resident forms, we performed whole-genome resequencing of 12 geographical populations from the Yangtze River, Huaihe River, and Yellow River systems and obtained 8,701,537 high-quality single nucleotide polymorphisms (SNPs). Based on multiple analyses (NJ tree, PCA, and ADMIXTURE analysis), our study confirmed that C. nasus taihuensis is not a valid subspecies but rather a freshwater ecotype of C. nasus. Compared to anadromous C. nasus, freshwater-resident C. nasus taihuensis exhibited slightly higher genetic diversity, an elevated Tajima's D value, and lower levels of linkage disequilibrium, suggesting potential differences in demographic history and selective pressures. The estimated divergence time of approximately 4.6 thousand years ago between the two ecotypes coincides with the geological formation of Tai Lake. Whole-genome scans identified 290 selective sweep genes that underlie local adaptation in anadromous C. nasus. Several candidate genes were mainly involved in energy metabolism (SCD, HOAD, and DEGS2) and osmoregulation (CLCN4, IGF2, and LRP1), suggesting their potential contribution to highly efficient long-distance migration and adaptation to seawater. In contrast, freshwater-resident C. nasus taihuensis exhibited strong signatures of selection in genes related to osmotic and ionic balance (ATP1A1, AQP9, NBC, NHE3, and CA4), which may have driven the genetic divergence of this ecotype. Our comprehensive study provides valuable insights into the genetic basis of C. nasus, with critical implications for further conservation efforts of this ecologically valuable fish.

Soybean cyst nematode (SCN, Heterodera glycines) is one of the major pathogens of soybean worldwide. We utilized the CHIP-Seq (chromatin immunoprecipitation sequencing) and RNA-Seq (RNA sequencing) data from the transgenic GmMYB29 strain (Glycine Max roots). We then performed enrichment analysis using KEGG and GO to identify potential candidate genes within the promoter-binding region. A targeted regulatory relationship between the GmMYB29 and GmPP2C-37like genes was further identified using the dual-luciferase Assay (Luciferase, LUC) and yeast one-hybrid Assay (Y1H). Hairy roots with target gene overexpression and gene-edited hairy roots were generated, and their resistance to soybean cyst nematode (SCN) was evaluated. Meanwhile, the presence of reciprocal genes with GmPP2C-37like was determined by the yeast two-hybrid library screening method. The targeting relationship between GmMYB29 and GmPP2C-37like genes was further validated through the Y1H assay and LUC assay. Based on phenotypic assessments of SCN, transgenic soybean roots overexpressing GmPP2C-37like exhibited significantly enhanced resistance to SCN 3 compared to wild-type. Further analysis revealed that GmPP2C-37like collaborates with other regulatory factors to modulate soybean resistance against SCN. Yeast two-hybrid library (Y2H) screening identified 18 interacting proteins. These findings not only illuminate the functional role of GmPP2C-37like but also provide a foundation for dissecting its molecular network. Moreover, the results offer promising candidate genes for enhancing SCN resistance and optimizing soybean resilience through targeted genetic strategies.

Soybean (Glycine max (L.) Merr.) flowering time and plant height are critical agronomic traits that significantly influence yield and environmental adaptability. To clarify the regulatory mechanisms of flowering-related genes and their associations with plant height, a genome-wide identification of such genes in soybean were performed. This analysis used Arabidopsis thaliana flowering genes as references, employing BLASTP searches and pathway classification. All of the identified flowering-related genes were classified into eight regulatory pathways, with the photoperiod pathway (Ph) being the most prominent. Evolutionary and expression analyses revealed that core regulators (e.g., GmFTs, GmSOC1s) are conserved across pathways and are preferentially expressed in shoot apical meristems (SAMs). Additionally, both flowering-related genes and key hormones (e.g., IAA, GA, ABA) exhibited rhythmic responses to light signals. CRISPR-Cas9-mediated validation confirmed that genes GmSAUR46b regulates both flowering time and plant height, as mutants of this gene showed early flowering and reduced height. Notably, a large proportion of previously mapped flowering genes overlapped with our identified ones, while some remained undetected, likely due to whole-genome duplication and adaptive evolution, which generate new regulatory networks. Most of the identified flowering-related genes, however, have not been mapped, which highlights substantial uncharacterized potential in soybean flowering and plant height regulation. This provides a valuable molecular framework to guide soybean molecular breeding for enhanced yield and environmental adaptability.

Pattern recognition receptors (PRRs) are pivotal for plant immunity, yet their discovery in crops is hindered by lineage-specific divergence. We demonstrate that microbe-associated molecular patterns (MAMPs) often activate immunity through phylogenetically unrelated, convergently evolved PRRs across plant lineages. Using the Phytophthora-derived MAMP RLK6 as a prototype, we identified two leucine-rich repeat receptor-like proteins (LRR-RLPs), NbRKR1 and NbRKR2, that redundantly perceive RLK6 in the model plant Nicotiana benthamiana. Strikingly, soybean retained RLK6 responsiveness despite lacking NbRKR1/2 orthologs. By integrating AlphaFold3 structural prediction with functional screening in N. benthamiana receptor mutants, we uncovered GmRLP30 as the convergent RLK6 receptor in soybean. Phylogenetic analysis revealed RKR1/2 conservation in Solanaceae but their absence in Capsicum annuum, which encodes a truncated RKR1 variant incapable of activating RLK6 immunity. Critically, heterologous expression of NbRKR1 or GmRLP30 in pepper restored RLK6 perception, confirming functional equivalence. These results establish a direct receptor-mediated communication between pathogen and host surfaces, an ortholog-independent pipeline for rapid PRR mining across crops, and a foundation for engineering synthetic immune interfaces with durable disease resistance.

The precise mutation prediction of the Epidermal Growth Factor Receptor (EGFR) holds paramount importance in clinical practice. Nevertheless, the persisting challenge lies in accurately conducting genomic profiling of lung cancer using a single biopsy sample, given the inherent tumor heterogeneity. To address this issue, an innovative approach using similarity-based multimodal data fuzzy fusion was presented to predict EGFR mutation. Initially, radiomics features were extracted from computerized tomography scans to quantitatively characterize tumors within the region of interest. Subsequently, three independent fundamental learners were trained based on preprocessed multimodal medical data. Once these fundamental learners generate membership degrees, fuzzy sets for EGFR genotyping were established. The Tanimoto coefficient was then employed to evaluate the similarity between the membership degrees of observed cases and ideal solutions. Ultimately, de-fuzzification through similarity ranking yielded a robust prediction for the EGFR mutation. The proposed multimodal medical data fuzzy fusion demonstrates promising predictive performance, achieving an area under curve value of 0.8878 in an independent test cohort. The proposed work has the potential to serve as a robust and intelligent decision-making system for clinicians.

In the original publication [...].

Background: Sulfur (S) is a vital element for the normal growth and development of plants, performing crucial biological functions in various life processes. Methods: This study investigated thirteen S utilization efficiency (SUE)-related traits at the seedling stage of wheat using a recombinant inbred line (RIL) population. The quantitative trait loci (QTLs) were mapped by genetic mapping. Thirteen S utilization efficiency-related traits were investigated under two hydroponic culture trials with low S (0.1S, T1), moderate S (0.5S, T2), and high S (1.5S, T3) levels, using the wheat RILs. Results: A total of 170 QTLs for the thirteen traits in different treatment environments were identified. Among them, 89, 103, and 101 QTLs were found in T1, T2, and T3, respectively. A total of 63 QTLs were found in the multiple treatment environments, the other 107 QTLs only being detected in a single treatment environment. Among them, thirteen relatively high-frequency QTLs (RHF-QTLs) and eleven QTL clusters were found. Five (QSh-1D, QRn-1D, QSdw-1D, QTdw-1D, and QTsc-1D) and six (QRdw-6A, QSdw-6A, QTdw-6A, QRsc-6A, QSsc-6A, and QTsc-6A) RHF-QTLs were identified in QTL clusters C3 and C10, respectively. Conclusion: These thirteen RHF-QTLs and eleven QTL clusters are expected to apply to the molecular marker-assisted selection (MAS) of wheat.

Background Proper flowering time is important for the growth and development of plants, and both too early and too late flowering impose strong negative influences on plant adaptation and seed yield. Thus, it is vitally important to study the mechanism underlying flowering time control in plants. In a previous study by the authors, genome-wide association analysis was used to screen the candidate gene SISTER OF FCA ( SSF ) that regulates FLOWERING LOCUS C ( FLC ), a central gene encoding a flowering suppressor in Arabidopsis thaliana . Results SSF physically interacts with Protein arginine methyltransferase 5 (PRMT5, SKB1). Subcellular co—localization analysis showed that SSF and SKB1 interact in the nucleus. Genetically, SSF and SKB1 exist in the same regulatory pathway that controls FLC expression. Furthermore, RNA-sequencing analysis showed that both SSF and SKB1 regulate certain common pathways. Conclusions This study shows that PRMT5 interacts with SSF, thus controlling FLC expression and facilitating flowering time control.

Perfluoroalkyl acid (PFAA) pollution of freshwaters has attracted a great deal of attention and poses a challenge to the restoration of river ecosystems. However, detailed studies on the impact of PFAAs and their alternatives on microbial plankton communities are lacking, and few studies have examined the adaptability of those communities to PFAAs. In this study, water samples were obtained from water bodies in the vicinity of the largest perfluorinated industrial park in Asia for comparative analysis. The spatial distribution of 19 PFAAs and 4 alternatives as well as their effect on microbial community structure were investigated through field sampling. The maximum total concentration of perfluoroalkyl carboxylic acids (PFCAs) at an industrial wastewater treatment plant was 2423.48 ng/L. The primary components included perfluorooctanoic acid (PFOA, 43.15%, 1045.82 ng/L), perfluorohexanoic acid (PFHxA, 27.10%, 656.70 ng/L) and perfluorobutanoic acid (PFBA, 20.13%, 487.85 ng/L). The maximum total concentration of PFAA alternatives was 48.59 ng/L, with hexafluoropropylene oxide dimer acid (HFPO-DA) accounting for 97.43%. The microbial community was mainly composed of Proteobacteria, Actinobacteriota, Bacteroidota, and Cyanobacteria. While Verrucomicrobiota tolerated PFAAs, significant effects on microbial community structure were determined for PFCAs and PFSAs, albeit with clear differences. Short-chain PFAAs had a similar impact on the microbial community as the restricted long-chain PFAAs. Thus, our study demonstrated the potentially negative impact of PFAAs on the microbial plankton community in the natural environment and the combined effect of poor water quality. The result provides new directions for investigations of PFAA pollution in freshwater environments.

River regulation has a key role in water resource management, but the introduced pollutants cannot be underestimated. This study reported spatiotemporal variations of perfluoroalkyl acids (PFAAs) significantly affected by river regulations in a standard example of urban river network with bidirectional flow in China. Perfluoroalkyl sulfonic acids (PFSAs), mostly of domestic origin, dominated during discharge, and perfluoroalkyl carboxylic acids (PFCAs), industrial pollutants, during diversion. The estimated PFAA flux into the Yangtze River during discharge was 1.22 × 102 kg with 62.5 % from Taihu Lake and 37.5 % from the river network. And that from the Yangtze River during diversion was 90.2 kg with 72.2 % into Taihu Lake and 27.8 % into the river network. Our findings show that PFAAs can exert pressure on regional water security that most of the urban river network was at medium risk. This study improves understandings of the role of river regulations in urban water networks and provides solid reference for risk assessment.

Five loci related to soybean protein and amino acid contents were colocated by performing linkage mapping and GWAS. The haplotype analysis showed that Glyma.08G109100 may be useful to improve the soybean seed composition. Soybean (Glycine max (L.) Merr.) seeds are good protein sources. Although genetic variation is abundant, natural variation in seed amino acids and their derived traits is lacking across soybean accessions. Here, we determined the contents of protein and 17 amino acids, obtained 36 derived traits based on the protein and total amino acid contents, and derived 34 traits based on seven amino acid family groups. Furthermore, we performed a linkage analysis of the contents of 17 amino acids and 73 amino acid-derived traits based on the recombinant inbred line (RIL)-derived Kefeng No. 1 × Nannong 1138–2. Six hundred thirty-nine quantitative trait loci (QTLs) were identified, explaining 6.07–39.00