ACS (1-aminocyclopropane-1-carboxylic acid synthase) is a member of the aminotransferase superfamily and a pyridoxal phosphate-dependent enzyme. ACS is also a rate-limiting enzyme for the biosynthesis of ethylene and has been linked with plant development, growth, and stress responses. However, information on ACS genes in the soybean genome is limited. In this study, we identified ACS genes in soybean through phylogenetic trees and conserved motifs and analyzed their cis-acting elements, subcellular localization, and expression patterns. Twenty-two members of the ACS family were identified in soybean, and they were divided into four subfamilies based on phylogenetic relationships. Moreover, the results of Arabidopsis mesophyll protoplasts showed that GmACS1, GmACS8, and GmACS15 were all localized in the nucleus and cell membrane. Cis-regulatory elements and qRT-PCR analyses indicated markedly increased levels of GmACS transcripts under hormone treatments and abiotic stress conditions (drought, alkalinity, and salt). In addition, under different abiotic stresses, the potential functional variations across the GmACS isoforms were mirrored in their differential expression. The analysis of transcriptional response to salinity indicated that salt stress might primarily be mediated by the GmACS15 gene. GmACS15 was also found to reduce salt-induced oxidative damage by modulating the ROS-scavenging system, cellular redox homeostasis, and maintaining intracellular Na⁺/K⁺ balance. The results of this investigation revealed the involvement of the ACS gene family in soybean stress-response pathways, including the identification of a potential target for enhancing salt tolerance in soybean.

Fusarium oxysporum-induced root rot severely threatens global soybean production, yet limited understanding of resistance mechanisms constrains breeding progress. This study conducted comparative transcriptomic analysis between highly resistant (Xiaoheiqi) and susceptible (L83-4752) soybean accessions following pathogen inoculation across four time points (8–17 days post-infection). RNA-seq analysis identified 1496 differentially expressed genes following pathogen challenge. KEGG pathway enrichment analysis revealed significant enrichment in MAPK signaling pathway (12 genes) and plant–pathogen interaction pathway (13 genes). Eight genes co-occurred in both pathways, with GmCML (Glyma.10G178400) exhibiting the most dramatic differential expression among these candidates. This gene encodes a 151-amino acid calmodulin-like protein showing 185-fold higher expression in resistant plants at 17 days post-inoculation, confirmed by qRT-PCR validation. Functional validation through transgenic hairy root overexpression demonstrated that GmCML significantly enhanced disease resistance by coordinately activating antioxidant defense systems. Overexpression of GmCML in transgenic soybean enhanced resistance to F. oxysporum by modulating the activity of antioxidant enzymes (superoxide dismutase, SOD; peroxidase, POD; catalase, CAT) and the accumulation of osmoregulatory substances (proline and soluble sugars). Population genetic analysis of 295 diverse soybean accessions revealed three GmCML haplotypes based on promoter region polymorphisms. Two favorable variants (Hap2 and Hap3) conferred significantly lower disease indices and exhibited evidence of positive selection during domestication, indicating evolutionary importance in disease resistance. This research provides the first comprehensive characterization of GmCML’s role in soybean–Fusarium interactions, establishing this calmodulin-like protein as a regulatory hub linking calcium signaling to coordinated defense responses. The identified natural variants and functional mechanisms offer validated targets for both marker-assisted breeding and genetic engineering approaches to enhance soybean disease resistance.

The soybean cyst nematode (Heterodera glycines, SCN) is the leading pathogen causing economic losses in soybean production worldwide. Using resistant cultivars is the most sustainable control method, yet the molecular basis of this resistance remains unclear. Heinong 531 (HN531), a high-yield soybean variety rich in seed oil, shows broad resistance to multiple SCN races. In this research, we studied HN531’s resistance to SCN races 3 and 5 through phenotypic assessment and comparative transcriptomics. Although initial infection rates were similar between resistant HN531 and the susceptible Dongsheng 1 (DS1), HN531 limited later nematode development inside roots, with fewer progressing to the J2 stage and maturing females. RNA-seq at 5 days post-infection revealed 1459 differentially expressed genes (DEGs) in HN531, mainly involved in secondary metabolite pathways, especially phenylpropanoid biosynthesis. We pinpointed a β-glucosidase gene (Glyma.12G053800, BGLU) upregulated after SCN infection and naturally more expressed in HN531 roots than DS1. Functional tests using Agrobacterium rhizogenes-mediated hairy root transformation showed that overexpressing Glyma.12G053800 in the susceptible DS1 significantly decreased SCN development and adult female counts by around 65%, without affecting initial infection. These findings suggest Glyma.12G053800 contributes to SCN resistance via phenylpropanoid-driven secondary metabolism, offering new insights into nematode resistance pathways and a valuable genetic resource for breeding broad-spectrum resistant soybean varieties.

Soybean root rot, caused by diverse soil-borne pathogens, is a major constraint on production worldwide, with yield losses ranging from 10 to 60% under epidemic conditions. Symptomatic plants were collected from three locations in Harbin, Heilongjiang Province, China, and 23 fungal isolates were recovered using standard tissue isolation procedures. Integrated morphological characterization and rDNA-ITS sequencing identified these isolates as three Fusarium species: F. oxysporum (18 isolates, 78%), F. equiseti (3 isolates, 13%), and F. brachygibbosum (2 isolates, 9%). Pathogenicity assays following Koch’s postulates confirmed F. oxysporum as the predominant and most aggressive pathogen in this region. To identify resistance resources, 200 soybean germplasm accessions adapted to Northeast China were screened using an etiolated seedling hypocotyl inoculation method with Fusarium oxysporum isolate A3 (DSI = 68.5) as the test pathogen. Disease severity indices exhibited a continuous distribution (mean = 52.84, range = 0–100), suggesting quantitative inheritance. Accessions were classified as highly resistant (13, 6.5%), resistant (40, 20%), moderately susceptible (67, 33.5%), susceptible (43, 21.5%), or highly susceptible (37, 18.5%). To explore potential molecular mechanisms underlying resistance, RT-qPCR analysis was performed on two extreme genotypes—a highly resistant line (H9477F5, DSI = 15.3) and a highly susceptible line (HN91, DSI = 88.7) at 1, 3, and 5 days post-inoculation. The resistant line maintained consistently higher expression of positive regulators GmFER and GmSOD1, with GmFER reaching 15.89-fold induction at day 3. Conversely, expression of negative regulators GmJAZ1 and GmTAP1 remained lower in the resistant line, with susceptible plants showing 5.62-fold higher GmJAZ1 expression at day 3. These findings provide characterized pathogen isolates, resistant germplasm resources (53 accessions with HR or R classifications), and preliminary molecular insights that may inform breeding strategies for improving root rot resistance in Northeast China.