The effect of salt damage on plants is mainly caused by the toxic effect of Na⁺. Studies showed that the secretory carrier membrane proteins were associated with the Na⁺ transport. However, the salt tolerance mechanism of secretory carrier protein (SCAMP) in soybean was yet to be defined. In this study, ten potential SCAMP genes distributed in seven soybean chromosomes were identified in the soybean genome. The phylogenetic tree of SCAMP domain sequences of several plants can divide SCAMPs into two groups. Most GmSCAMPs genes contained multiple Box4, MYB and MYC cis-elements indicated they may respond to abiotic stresses. We found that GmSCAMP1, GmSCAMP2 and GmSCAMP4 expressed in several tissues and GmSCAMP5 was significantly induced by salt stress. GmSCAMP5 showed the same expression patterns under NaCl treatment in salt-tolerant and salt-sensitive soybean varieties, but the induced time of GmSCAMP5 in salt-tolerant variety was earlier than that of salt-sensitive variety. To further study the effect of GmSCAMP5 on the salt tolerance of soybean plants, compared to GmSCAMP5-RNAi and EV-Control plants, GmSCAMP5-OE had less wilted leave and higher SPAD value. Compared to empty vector control, less trypan blue staining was observed in GmSCAMP5-OE leaves while more staining in GmSCAMP5-RNAi leaves. The Na⁺ of GmSCAMP5-RNAi plants leaves under NaCl stress were significantly higher than that in EV-Control plants, while significantly lower Na⁺ in GmSCAMP5-OE plants than in that EV-Control plants. The contents of leaves K⁺ of GmSCAMP5-RNAi, EV-Control, and GmSCAMP5-OE plants under NaCl stress were opposite to that of leaves Na⁺ content. Finally, salt stress-related genes NHX1, CLC1, TIP1, SOD1, and SOS1 in transformed hairy root changed significantly compared with the empty control. The research will provide novel information for study the molecular regulation mechanism of soybean salt tolerance.

Nodulation is the most efficient nitrate assimilation system in the ecosystem, while excessive fertilization has an increased nitrate inhibition effect; deciphering the nitrate signal transduction mechanism in the process is of the utmost importance. In this study, genome-wide analyses of the GmCEP genes were applied to identify nodulation-related CEP genes; 22 GmCEP family members were identified, while GmCEP6 was mainly expressed in nodules and significantly responded to nitrate treatment and rhizobium infection, especially in later stages. Overexpression and CRISPR-Cas9 were used to validate its role in nodulation. We found that GmCEP6 overexpression significantly increased the nodule number, while GmCEP6 knock-out significantly decreased the nodule number, which suggests that GmCEP6 functions as a positive regulator in soybean nodulation. qRT-PCR showed that alterations in the expression of GmCEP6 affected the expression of marker genes in the Nod factor signaling pathway. Lastly, the function of GmCEP6 in nitrate inhibition of nodulation was analyzed; nodule numbers in the GmCEP6-overexpressed roots significantly increased under nitrogen treatments, which suggests that GmCEP6 functions in the resistance to nitrate inhibition. The study helps us understand that GmCEP6 promotes nodulation and participates in the regulation of nitrate inhibition of nodulation, which is of great significance for high efficiency utilization of nitrogen in soybeans.

Legume-rhizobial symbiotic nitrogen fixation is the most efficient nitrogen assimilation system in the ecosystem. In the special interaction between organ–root nodules, legumes supply rhizobial carbohydrates for their proliferation, while rhizobials provide host plants with absorbable nitrogen. Nodule initiation and formation require a complex molecular dialogue between legumes and rhizobia, which involves the accurate regulation of a series of legume genes. The CCR4–NOT complex is a conserved multi-subunit complex with functions regulating gene expression in many cellular processes. However, the functions of the CCR4–NOT complex in rhizobia–host interactions remain unclear. In this study, we identified seven members of the NOT4 family in soybean and further classified them into three subgroups. Bioinformatic analysis showed that NOT4s shared relatively conserved motifs and gene structures in each subgroup, while there were significant differences between NOT4s in the different subgroups. Expression profile analysis indicated that NOT4s may be involved in nodulation in soybean, as most of them were induced by Rhizobium infection and highly expressed in nodules. We further selected GmNOT4-1 to clarify the biological function of these genes in soybean nodulation. Interestingly, we found that either GmNOT4-1 overexpression or down-regulation of GmNOT4-1 by RNAi or CRISPR/Cas9 gene editing would suppress the number of nodules in soybean. Intriguingly, alterations in the expression of GmNOT4-1 repressed the expression of genes in the Nod factor signaling pathway. This research provides new insight into the function of the CCR4–NOT family in legumes and reveals GmNOT4-1 to be a potent gene for regulating symbiotic nodulation.

Sugarcane is a primary sugar crop and an important source of bioenergy. Pathogens are the major factors affecting sugarcane yield and sugar content. However, the mechanisms of sugarcane defense regulation remain largely unknown, and research on prospective genetic targets for modification is scarce. As the main class of calcium sensors, calcium-dependent protein kinases (CDPKs/CPKs) play a crucial role in the immune regulatory network. Using sugarcane genomic data, we identified 229 putative ScCDPKs in primordial specie Saccharum officinarum. Searching the putative CDPKs in sugarcane cultivars from National Center for Biotechnology Information (NCBI), 12 putative ScCDPKs in cultivars were identified. Phylogenetic analysis revealed evolutionary relationships among these CDPKs in sugarcane cultivars and those in S. officinarum, Arabidopsis thaliana, and rice. Truncation mutants of ScCDPKs were introduced into the reporter system and examined for activity in inducing Sugarcane Pathogenesis Related Protein 1 (ScPR1). The results showed that truncated ScCDPK1 and ScCDPK8 induce higher expression of ScPR1 than full-length ScCDPK1 and ScCDPK8. Additionally, transient expression of truncated ScCDPK1 and ScCDPK8 exhibit stronger activity in sugarcane protoplasts for activation of ScPR1 and sugarcane Serine Protease Inhibitor (ScSPI). These results demonstrate that ScCDPK1 and ScCDPK8 possess auto-inhibitory activity. The findings of this study provide a basis for an in-depth study of the sugarcane CDPK gene family and lay the foundation for further genetic improvement.

Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil‐borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three‐dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high‐resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high‐throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive cis‐interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase‐accessible chromatin with high‐throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation‐related genes. Notably, novel TADs and long‐range chromatin loops are detected in peanut nodules, including an H3K27me3 modification‐mediated loop that may regulate the expression of Nodule Inception. Another altered chromatin loop highlights the nodule highly expressed AhMsrA gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.

Drought is a significant abiotic stressor affecting crops globally. Beneficial microorganisms, such as rhizobia, have been shown to enhance crop resilience to such stresses. In this study, we isolated a highly efficient rhizobacterial strain (Rhizobium sp. PV-6) from the root system of Phaseolus vulgaris and systematically investigated the phenotypic and physiological responses of the plants across seven growth stages under four treatments: W-NO (watering without inoculation of rhizobium), W-RHI (watering with inoculation of rhizobium), D-NO (drought without inoculation of rhizobium), and D-RHI (drought with inoculation of rhizobium). We also examined the variation in microbial communities in rhizosphere and root compartments. Physiological analyses revealed that rhizobium inoculation significantly enhanced plant height, fresh weight and dry weight, root length, lateral root number, and nodule number of red kidney beans. Alpha diversity analysis suggested that the microbial communities in the roots and rhizosphere of red kidney beans show different variant distributions. Beta diversity and species difference analysis revealed that drought treatments (D-NO, D-RHI) recruit Shinella, Nocardioides, Agromyces, Pseudomonas, and Ensifer at rhizosphere compartments, while D-RHI enrich Pseudomonas, Sphingobacterium, Paenibacillus, Bacillus, Massilia, and Lysobacter at root compartments in the T5 stage. Further, transcriptomic analysis revealed that PV-6 enhances drought tolerance in red kidney beans by modulating the expression of genes associated with abiotic stress-related genes. Our findings highlight the potential of Rhizobium sp. PV-6 as a bioinoculant for improving drought tolerance in red kidney beans (Phaseolus vulgaris), providing a foundation for designing synthetic microbial communities for crop stress resilience.