Xiaoming Li

Glycosyltransferases (GTs) are key enzymes that catalyze the transfer of sugar moieties to diverse acceptor molecules and play important roles in a wide range of biological processes, including plant growth, development, and environmental adaptation. However, glycosyltransferase family 4 (GT4), the second-largest GT family, remains poorly characterized in soybean. In this study, we identified 60 GT4 family members in the soybean genome based on sequence information from the CAZy database and systematically characterized their phylogenetic relationships, genomic organization, and expression patterns by integrating genomic and multidimensional transcriptomic data. Furthermore, using a previously established soybean ethyl methanesulfonate (EMS) mutant population, we identified GmSPS8 as a candidate gene potentially involved in the regulation of seed weight. Notably, natural variation and haplotype analyses revealed that GmSPS8 is located within a genomic region subject to domestication selection, suggesting its potential involvement in the evolutionary selection of soybean seed size. In sum, we systematically characterized the soybean GT4 gene family and identified GmSPS8 as a potential domestication-associated candidate gene for seed weight regulation, providing new insights into the functional characterization of soybean GT4 family members and the identification and utilization of genes associated with soybean yield-related traits.

The legume crop soybean forms a symbiosis with rhizobia to fix atmospheric nitrogen (N) in specialized organs called root nodules. However, the mechanisms regulating early infection of the root epidermis and nodule‐primordium formation in the cortex for proper nodule formation remain unclear in soybean. Here, we report a single‐cell transcriptome analysis of mock‐ and rhizobia‐inoculated soybean roots at 4 days after inoculation, an important control point for autoregulation of nodulation and nodule‐primordium formation. We profiled 21,500 cells and detected 12 major cell clusters, and identified 193 infected‐cell‐specific, 205 epidermis‐specific and 180 cortex‐specific DEGs. Gene‐ontology enrichment and gene‐regulatory network analyses uncovered key pathways such as reactive oxygen species‐mediated hormone signaling involved in coordinating defense signaling and symbiotic pathways. We also identified and functionally validated an ethylene‐activated circuit comprising GmWRKY6.3/6.4 transcription factors and select downstream GmNod19 targets, in which genes act as positive regulators by promoting infection‐thread formation during early nodulation, thereby shaping nodule formation. This study showcases how single‐cell transcriptomics and gene‐regulatory networks provide hypotheses for identification and characterization of previously unappreciated regulatory circuits, broadens our understanding of precise genetic control underlying symbiosis establishment, and underscores how functional diversification of nodulation genes has occurred across legumes.

Background: Heat shock protein 100 (HSP100) is a key molecular chaperone that maintains intracellular proteostasis and enhances plant tolerance. However, the HSP100 gene family in soybean (Glycine max) has not been systematically characterized. Methods: In this study, we performed genome-wide identification and comprehensive analysis of the GmHSP100 gene family and analyzed their phylogeny, genomic distribution, synteny, protein structures, subcellular localization, promoter cis-elements, and expression patterns under heat and salt stresses via bioinformatics approaches and quantitative real-time PCR (qRT-PCR) validation. Results: Thirteen GmHSP100 members were identified, which were classified into CLPB, CLPC and CLPD subfamilies. Segmental and whole-genome duplications primarily drove the expansion of this gene family. All encoded proteins possessed conserved AAA+ ATPase domains, with distinct motifs across subfamilies. Most proteins localized to the cytoplasm, while CLPC and CLPD targeted chloroplasts and GmCLPB4 localized to mitochondria. Promoter analysis identified numerous elements associated with light, hormone and stress responses. Expression profiling showed strong tissue specificity and time-dependent stress-treatment induction. Heat stress triggered rapid and strong upregulation of the GmHSP100s, whereas salt stress salt stress induced their relatively delayed and sustained expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the GmHSP100 gene family in soybean, providing a foundational framework for understanding the functions of GmHSP100 in stress adaptation.

Soybean cyst nematode (SCN, Heterodera glycines) is one of the most yield-limiting nematodes in soybean production. Application of synthetic nematicides is a critical component in the integrated management of SCN in China. However, resistance has developed in SCN to conventional nematicides, leading to the failure of these nematicides in some fields. It is pivotal for the soybean industry to develop new nematicides that can achieve sustainable nematode control. Seed treatment is a promising control approach. Fluopyram is widely used to control various plant-parasitic nematodes (PPNs); however, it is currently not registered as a seed treatment in China for use in controlling SCN. In this study, the efficacy of fluopyram as a seed treatment to manage SCN was evaluated through in vitro tests, greenhouse experiments, and field trials. In vitro tests showed that fluopyram caused a high mortality of H. glycines second-stage juveniles (J2s), with 50% lethal concentration (LC50) value of 0.96 mg/L that was superior to abamectin. In greenhouse experiments, compared with the untreated control, seed treatment with fluopyram at 0.15 mg active ingredient (a.i.)/seed provided significant SCN control, while maintaining excellent soybean root length and shoot fresh weight, better than the commercially available seed treatment with a 35.6% formulation of abamectin + carbendazim + thiram at 10 mL/kg seed. Moreover, in split-root experiments, fluopyram treatment at 0.15 mg a.i./seed reduced number of J2s inside the roots by 65.3% and induced resistance to SCN. Fluopyram also enhanced activities of phenylalanine ammonia-lyase (PAL) and peroxidase (POD), which was associated with the increased expressions of the defense-related genes GmNPR1-1, GmSAMT1 and GmACS9b. In two consecutive years of field trials, fluopyram seed treatment at 0.15 mg a.i./seed exhibited significant control of SCN. Compared to the control, it reduced numbers of cysts on the roots, cysts in the soil, and nematode juveniles inside the roots by 57.5%, 52.2%, 63.6% in 2023, and 63.7%, 57.2%, 67.9% in 2024, respectively. These results indicated that fluopyram not only exhibited strong nematicidal activity against H. glycines but also induced systemic resistance in soybean. In summary, fluopyram seed treatment has the potential to manage SCN in the field and warrants further studies.

Mesocotyl elongation is the key determinant of deep-sowing tolerance in maize. Sowing at an appropriate depth allows the seedling to exploit water and nutrients stored in deeper soil layers, thereby enhancing its ability to withstand drought and other abiotic stresses. Mesocotyl elongation is regulated by the phytohormones brassinosteroid (BR), auxin (IAA), gibberellin (GA), and reactive oxygen species (ROS). However, whether and how BR coordinates IAA, GA, and ROS to control mesocotyl elongation in maize remains unclear. Here, we demonstrated that BRs orchestrate ROS, IAA, and GA signaling to remodel cell-wall metabolism in mesocotyl cells, promote cell elongation, and, consequently, strengthen deep-sowing tolerance. BR promoted mesocotyl elongation through multiple routes: (1) decreasing the contents of cell-wall components (hemicellulose, cellulose, and pectin); (2) activating cell-wall-loosening enzymes (cellulase, pectinase, and acidic xylanase); and (3) disturbing ROS homeostasis by elevating superoxide dismutase (SOD) activity. Combined treatments of BR with either IAA or GA further enhanced mesocotyl elongation in a concentration-dependent manner. In deep-sowing trials (15 cm), application of BR alone or in combination with IAA or GA markedly increased mesocotyl length and emergence rate, thereby improving deep-sowing tolerance. Our work indicated that BR integrated ROS, IAA, and GA signals to restructure the cell wall and derived mesocotyl cell elongation, providing both theoretical insights and practical strategies for breeding maize varieties with enhanced deep-sowing tolerance.

Summary: Salt stress is a major challenge that has a negative impact on soybean growth and productivity. Therefore, it is important to understand the regulatory mechanism of salt response to ensure soybean yield under such conditions. In this study, we identified and characterized a miR160a–GmARF16–GmMYC2 module and its regulation during the salt–stress response in soybean. miR160a promotes salt tolerance by cleaving GmARF16 transcripts, members of the Auxin Response Factor (ARF) family, which negatively regulates salt tolerance. In turn, GmARF16 activates GmMYC2, encoding a bHLH transcription factor that reduces salinity tolerance by down‐regulating proline biosynthesis. Genomic analysis among wild and cultivated soybean accessions identified four distinct GmARF16 haplotypes. Among them, the GmARF16^H3 haplotype is preferentially enriched in localities with relatively saline soils, suggesting GmARF16^H3 was artificially selected to improve salt tolerance. Our findings therefore provide insights into the molecular mechanisms underlying salt response in soybean and provide valuable genetic targets for the molecular breeding of salt tolerance.

Background: Soil salinity is a primary factor limiting soybean (Glycine max) productivity. Breeding soybean for tolerance to high salt conditions is therefore critical for increasing yield. To explore the molecular mechanism of soybean responses to salt stress, we performed a comparative transcriptome time-series analysis of root samples collected from two soybean cultivars with contrasting salt sensitivity. Results: The salt-tolerant cultivar ‘Qi Huang No.34’ (QH34) showed more differential expression of genes than the salt-sensitive cultivar ‘Dong Nong No.50’ (DN50). We identified 17,477 genes responsive to salt stress, of which 6644 exhibited distinct expression differences between the two soybean cultivars. We constructed the corresponding co-expression network and performed Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The results suggested that phytohormone signaling, oxidoreduction, phenylpropanoid biosynthesis, the mitogen-activated protein kinase pathway and ribosome metabolism may play crucial roles in response to salt stress. Conclusions: Our comparative analysis offers a comprehensive understanding of the genes involved in responding to salt stress and maintaining cell homeostasis in soybean. The regulatory gene networks constructed here also provide valuable molecular resources for future functional studies and breeding of soybean with improved tolerance to salinity.

Background: Anastomosis group 1 IA (AG1-IA) of Rhizoctonia solani is the major agent of banded leaf and sheath blight (BLSB) disease that causes severe yield loss in many worldwide crops. MicroRNAs (miRNAs) are ~ 22 nt non-coding RNAs that negatively regulate gene expression levels by mRNA degradation or translation inhibition. A better understanding of miRNA function during AG1-IA infection can expedite to elucidate the molecular mechanisms of fungi-host interactions. Results: In this study, we sequenced three small RNA libraries obtained from the mycelium of AG1-IA isolate, non-infected maize sheath and mixed maize sheath 3 days after inoculation. In total, 137 conserved and 34 novel microRNA-like small RNAs (milRNAs) were identified from the pathogen. Among these, one novel and 17 conserved milRNAs were identified as potential virulence-associated (VA) milRNAs. Subsequently, the prediction of target genes for these milRNAs was performed in both AG1-IA and maize, while functional annotation of these targets suggested a link to pathogenesis-related biological processes. Further, expression patterns of these virulence-associated milRNAs demonstrated that theyparticipate in the virulence of AG1-IA. Finally, regulation of one maize targeting gene, GRMZM2G412674 for Rhi-milRNA-9829-5p, was validated by dual-luciferase assay and identified to play a positive role in BLSB resistance in two maize mutants. These results suggest the global differentially expressed milRNAs of R. solani AG1-IA that participate in the regulation of target genes in both AG1-IA and maize to reinforce its pathogenicity. Conclusions: Our data have provided a comprehensive overview of the VA-milRNAs of R. solani and identified that they are probably the virulence factors by directly interfered in host targeting genes. These results offer new insights on the molecular mechanisms of R.solani-maize interactions during the process of infection.