Soybean mosaic virus (SMV) is the most prevalent soybean viral disease in the world. As a critical enzyme in the secondary metabolism of plants, especially in lignin synthesis, cinnamyl alcohol dehydrogenase (CAD) is widely involved in plant growth and development, and in defense against pathogen infestation. Here, we performed RNAseq-based transcriptome analyses of a highly SMV-resistant accession (BYO-15) of wild soybean (Glycine soja) and a SMV-susceptible soybean cultivar (Williams 82), also sequenced together with a resistant plant and a susceptible plant of their hybrid descendants at the F3 generation at 7 and 14 days post-inoculation with SMV. We found that the expression of GsCAD1 (from G. soja) was significantly up-regulated in the wild soybean and the resistant F3 plant, while the GmCAD1 from the cultivated soybean (G. max) did not show a significant and persistent induction in the soybean cultivar and the susceptible F3 plant, suggesting that GsCAD1 might play an important role in SMV resistance. We cloned GsCAD1 and overexpressed it in the SMV-susceptible cultivar Williams 82, and we found that two independent GsCAD1-overexpression (OE) lines showed significantly enhanced SMV resistance compared with the non-transformed wild-type (WT) control. Intriguingly, the lignin contents in both OE lines were higher than the WT control. Further liquid chromatography (HPLC) analysis showed that the contents of salicylic acid (SA) were significantly more improved in the OE lines than that of the wild-type (WT), coinciding with the up-regulated expression of an SA marker gene. Finally, we observed that GsCAD1-overexpression affected the accumulation of SMV in leaves. Collectively, our results suggest that GsCAD1 enhances resistance to SMV in soybeans, most likely by affecting the contents of lignin and SA.

Soil health reflects the sustained capacity of soil to function as a vital living ecosystem, ensuring support for all forms of life. The evaluation of soil health relies heavily on physicochemical indicators. However, it remains unclear whether and how microbial traits are related to soil health in soil with long-term organic manure amendment. This study aims to examine how detrimental and beneficial microbial traits change with soil health based on physicochemical indicators. This research measures the effects of 9-year manure supplementation on soil health using multiomics techniques. We found that, compared to 100% chemical fertilizers, the soil health index increased by 5.2%, 19.3%, and 72.6% with 25%, 50%, and 100% organic fertilizer amendments, respectively. Correspondingly, the abundance of beneficial microorganisms, including Actinomadura, Actinoplanes, Aeromicrobium, Agromyces, Azospira, Cryobacterium, Dactylosporangium, Devosia, Hyphomicrobium, Kribbella, and Lentzea, increased progressively, while the abundance of the pathogenic fungus Fusarium decreased with the organic manure application rate. In addition, the application of organic manure significantly increased the concentrations of soil metabolites, such as sugars (raffinose, trehalose, maltose, and maltotriose) and lithocholic acid, which promoted plant growth and soil aggregation. Moreover, the abundances of pathogens and beneficial microorganisms and the concentrations of beneficial soil metabolites were significantly correlated with the soil health index based on physicochemical indicators. We conclude that organic fertilizer can enhance soil health by promoting the increase in beneficial microorganisms while suppressing detrimental microorganisms, which can serve as potential indicators for assessing soil health. In agricultural production, substituting 25–50% of chemical fertilizers with organic fertilizers significantly helps improve soil health and promotes crop growth.

Soybean is a dual-purpose crop for food and oil, playing a crucial role in China’s grain production. Seed size and weight are key agronomic traits directly influencing the yield. Cytokinin oxidases/dehydrogenases (CKXs) specifically degrade certain isoforms of endogenous cytokinins (CKs), thereby modulating plant growth and seed development. However, their role in soybeans remains largely uncharacterized. In a previous genome-wide association study of 250 soybean core germplasms, we identified GmCKX3 as a yield-related gene. To elucidate its function, we developed GmCKX3-deficient mutants using CRISPR/Cas9 gene editing in soybean Williams82 and conducted a three-year phenotypic analysis. Loss of GmCKX3 function significantly enhanced the seed size and weight, which was attributed to an increased cell size and fat accumulation in the endosperm. This enhancement was driven by elevated endogenous CK levels resulting from suppressed GmCKX3 expression. Subcellular localization revealed that GmCKX3 resides in the endoplasmic reticulum and predominantly degrades the isopentenyladenine (iP)-type CK. Integrated transcriptomic and metabolomic analyses uncovered key genes and pathways involved in CK regulation, supporting GmCKX3’s central role in seed-trait modulation. These findings advance our understanding of cytokinin-mediated seed development and offer promising targets for molecular breeding aimed at improving the soybean yield.

Soybean is rich in protein and oil and serves as the most important legume crop globally. Soybean mosaic virus (SMV) is a severe threat to soybean production worldwide. MutMap, a gene-mapping technology based on map-based cloning and whole-genome resequencing, is utilized to clone key regulatory genes for agronomic traits in plants. However, no relevant studies have reported the cloning of genes resistant to SMV. We used an M3 mutant population derived from ethyl methanesulfonate mutagenesis of Williams 82, and conducted field inoculation experiments involving the SMV-SC3 strain. After field validation, two lines with high resistance to SMV were finally identified. Using MutMap, we initially screened candidate genes for SMV resistance and found that the G-to-A transitions of one candidate resistance gene, Glyma.13G194900, were at base positions 122 and 166. These transitions resulted in the substitution of glycine with glutamic acid (GGA→GAA) and valine with aspartic acid (GTT→GAT), respectively. Transgenic functional validation in soybean showed that the mutant allele of Glyma.13G194900 (designated Glyma.13G194900^M) substantially enhanced resistance to SMV-SC3, in contrast to the wild-type allele, which did not enhance resistance. Our results demonstrate that MutMap can rapidly identify SMV resistance-related genes to provide a genetic resource that accelerates the breeding of new SMV-resistant soybean.

The pseudo response regulator (PRR) gene is an important component of the core oscillator involved in plant circadian rhythms and plays an important role in regulating plant growth and development and stress responses. In this study, we investigated the function of GmPRR7b by overexpression and gene editing approaches. It was found that GmPRR7b plays a role in delaying flowering. While GmPRR7b overexpressing plants showed significantly delayed flowering compared to untransformed WT, GmPRR7b edited plants flowered earlier than the control WT. On the basis of previous research results and bioinformatics analysis, we re-identified 14 soybean PRR genes and analysed their rhythmic expression. Based on the rhythmic expression pattern, we found that GmPRR5/9a and GmPRR5/9b interacted with GmPRR7b by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments. Combined with the expression regulatory networks of the GmPRR7b, we inferred a possible regulatory mechanism by which GmPRR7b affects flowering through quit rhythm expression. These research elements provide valuable references for understanding growth, development, and circadian regulation in soybean.

Genome editing is becoming an important tool for crop improvement by enabling precise modification of genetic variation. CRISPR-Cas technologies have expanded beyond nuclease-induced mutations to include base and prime editing, transcriptional and epigenetic regulation, multiplex editing, organelle editing and targeted DNA insertion. These advances support the development of agronomically valuable alleles and extend crop improvement beyond conventional selection, recombination and random mutagenesis. Applications now include plant architecture, yield-related traits, resistance to biotic and abiotic stresses, seed composition and nutritional quality, and extend to de novo domestication, haploid induction and hybrid breeding. Current research is increasingly moving from single-gene modification toward the engineering of promoters, cis-regulatory elements, quantitative alleles and multiple-gene editing, particularly in polyploid crops. Wider breeding applications will depend on efficient delivery and regeneration, recovery of transgene-free and heritable edited germplasm, reliable targeted insertion and validation across relevant environments. Integration with pangenomics, multi-omics, phenomics, artificial intelligence and predictive breeding may further improve target identification, allele design and prediction of editing outcomes, thereby supporting the development of more precise and efficient crop-breeding strategies.