Soybean is a legume crop rich in protein and oil. Symbiotic nitrogen fixation plays an important role in the growth of soybean. The type-III effectors such as NopT and NopP are the important signaling factors for the establishment of symbiosis in soybean. In this study, the analysis of nodulation in soybean after inoculation with HH103ΩNopT, HH103ΩNopP, and HH103ΩNopT&NopP indicated crosstalking between NopT and NopP. Further, we aimed to identify the genes of soybean involved in the pathway underlying the crosstalk between NopT and NopP using RNA-seq analysis. Five of the identified candidate genes were confirmed to be induced by NopT and NopP. The expression of GmPBS1 significantly increased to a much larger extent than that of the other four genes after soybean was inoculated with HH103ΩNopT, HH103ΩNopP, or HH103ΩNopT&NopP. The interaction between NopT and GmPBS1 was confirmed via bimolecular fluorescence complementation. Finally, nodulation analysis after GmPBS1 overexpression in the hairy roots indicate that GmPBS1 can regulate the negative effect of NopP on the nodulation, and this regulation is related to NopT. Collectively, our results suggested that during the nodulation in soybean, NopT and NopP have a crosstalking network and GmPBS1 is the hub gene.

Soybeans are a major crop that produce the best vegetable oil and protein for use in food and beverage products worldwide. However, one of the most well-known viral infections affecting soybeans is the Soybean Mosaic Virus (SMV), a member of the Potyviridae family. A crucial method for preventing SMV damage is the breeding of resistant soybean cultivars. Adult resistance and resistance of seedcoat mottling are two types of resistance to SMV. Most studies have focused on adult-plant resistance but not on the resistance to seedcoat mottling. In this study, chromosome segment-substituted lines derived from a cross between Suinong14 (cultivated soybean) and ZYD00006 (wild soybean) were used to identify the chromosome region and candidate genes underlying soybean resistance to seed coat mottling. Herein, two quantitative trait loci (QTLs) were found on chromosome 17, and eighteen genes were found in the QTL region. RNA-seq was used to evaluate the differentially expressed genes (DEGs) among the eighteen genes located in the QTLs. According to the obtained data, variations were observed in the expression of five genes following SMV infection. Furthermore, Nicotiana benthamiana was subjected to an Agrobacterium-mediated transient expression assay to investigate the role of the five candidate genes in SMV resistance. It has also been revealed that Glyma.17g238900 encoding a RICE SALT SENSITIVE 3-like protein (RSS3L) can inhibit the multiplication of SMV in N.benthamiana. Moreover, two nonsynonymous single-nucleotide polymorphisms (SNPs) were found in the coding sequence of Glyma.17g238900 derived from the wild soybean ZYD00006 (GsRSS3L), and the two amino acid mutants may be associated with SMV resistance. Hence, it has been suggested that GsRSS3L confers seedcoat mottling resistance, shedding light on the mechanism of soybean resistance to SMV.

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent ‘Suinong14’ (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.

Soybean is a pivotal staple crop worldwide, supplying the main food and feed plant proteins in some countries. In addition to interacting with mutualistic microbes, soybean also needs to protect itself against pathogens. However, to grow inside plant tissues, plant defense mechanisms ranging from passive barriers to induced defense reactions have to be overcome. Pathogenic but also symbiotic micro-organisms effectors can be delivered into the host cell by secretion systems and can interfere with the immunity system and disrupt cellular processes. This review summarizes the latest advances in our understanding of the interaction between secreted effectors and soybean feedback mechanism and uncovers the conserved and special signaling pathway induced by pathogenic soybean cyst nematode, Pseudomonas, Xanthomonas as well as by symbiotic rhizobium.

The SQS_PSY family (Squalene/phytoene synthase family), with squalene synthase (SQS) and phytoene synthase (PSY) as core members, comprises enzymes that catalyze the head-to-head condensation of isoprenoid precursors. These enzymes play pivotal roles in mediating plant responses to both biotic and abiotic stresses; nevertheless, their specific functions in soybean defense against Phytophthora sojae infection remain elusive. In the present study, a comprehensive bioinformatics approach was utilized to identify 12 SQS_PSY family members in the soybean genome, followed by subsequent analyses of chromosomal distribution, phylogenetic relationships, gene structures, conserved motifs, and cis-acting regulatory elements within promoter regions. Notably, multiple cis-elements responsive to biotic and abiotic stresses were detected in the promoter regions of SQS_PSY genes in soybean, implying their potential involvement in stress-responsive pathways. To elucidate their roles in defense, resistant and susceptible soybean cultivars were inoculated with P. sojae, and RNA-seq was conducted on sampled tissues. Integrated with quantitative real-time PCR (qRT-PCR) validation, our findings demonstrated that GmSQS1 exhibited differential expression patterns between resistant and susceptible cultivars at multiple time points post-inoculation. Furthermore, the functional role of GmSQS1 in enhancing soybean resistance to P. sojae was confirmed using a transgenic hairy root system. Collectively, this study preliminarily validated the functions of the SQS_PSY genes in soybean and offers novel insights into their potential application for improving resistance against Phytophthora root rot.

Bacterial and viral diseases significantly reduce soybean (Glycine max) yield and quality. RNA modifications, particularly N⁶-methyladenosine (m⁶A), are increasingly recognized as having a regulatory role in plant–pathogen interactions, but the m⁶A methylome of soybean during viral and bacterial infection has not yet been characterized. Here, we performed transcriptome sequencing and MeRIP-seq (methylated RNA immunoprecipitation followed by high-throughput sequencing) of soybean leaves infected with Soybean mosaic virus (SMV) and/or Pseudomonas syringae pv. glycinea (Psg). In general, m⁶A peaks were highly enriched near stop codons and in 3′-UTR regions of soybean transcripts, and m⁶A methylation was negatively correlated with transcript abundance. Multiple genes showed differential methylation between infected and control plants: 1122 in Psg-infected plants, 539 in SMV-infected plants, and 2269 in co-infected plants; 195 (Psg), 84 (SMV), and 354 (Psg + SMV) of these transcripts were both differentially methylated and differentially expressed. Interestingly, viral infection was predominantly associated with hypermethylation and downregulation, whereas bacterial infection was predominantly associated with hypomethylation and upregulation. GO and KEGG enrichment analysis revealed shared processes likely affected by changes in m⁶A methylation during bacterial and viral infection, including ATP-dependent RNA helicase activity, RNA binding, and endonuclease activity, as well as specific processes affected by only one pathogen. Our findings shed light on the role of m⁶A modifications during pathogen infection and highlight potential targets for epigenetic editing to increase the broad-spectrum disease resistance of soybean.