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Humic substances (HS) are the most important natural biostimulant of plants. However, the relationship between their structure and biological activity in plants is still not well recognized. The objective of this paper was to assess the influence of molecular fractions of humic acids (HA) (HA < 30 kDa and HA > 30 kDa) on reducing negative effects of drought stress in soybean (Glycine max (L.) Merr.) seedlings of Progres and Nawiko cultivars. Drought stress was induced in laboratory conditions by the addition of polyethylene glycol 6000 (PEG 6000) to make a water potential of −0.5 MPa. HA were extracted according to the International Humic Substances Society procedure, and then were separated into two molecular fractions by membrane filtration. The following physiological and biometric parameters were determined: chlorophyll content, photosynthesis activity, electrical conductivity, fresh and dry mass of overground and roots, and plant length. The enzyme activity and ion contents were also measured. Differences in response to drought stress with the addition of HA < 30 kDa and HA > 30 kDa or not to the Hoagland’s solution were observed among studied cultivars. Drought stress caused a decrease in the most physiological parameters and increase in peroxidase activity in the case of both studied cultivars. However, the results of biometric measurements showed that the Progres cultivar appears to have better tolerance to drought stress. The significant influence of water deficit on most macroelement content in dry matter leaves of both studied cultivars was not observed, while its effect on microelement uptake by soybean plants was concluded. In the case of the Progres cultivar, the results showed a significant decrease in microelement content in the dry matter of leaves, whereas in the leaves of Nawiko cultivar there was a significant increase. The influence of HA > 30 kDa and HA < 30 KDa fractions on physiological features of both studied cultivars was varied. HA > 30 kDa fraction better up-regulated the antioxidant defense system. Unfortunately, no effect of either HA fraction on the macro- and micronutrients uptake system of both studied cultivars was observed.

MiRNAs play crucial roles in many aspects of plant development and the response to the environment. The miR172 family has been shown to participate in the control of flowering time and the response to abiotic stress. This family regulates the expression of APETALA2 (AP2)-like transcription factors in Arabidopsis. In the present study, soybean (Glycine max L. Merr.) miR172c, a member of the miR172 family, and its target gene were investigated for abiotic stress responses in transgenic Arabidopsis. gma-miR172c was induced by abscisic acid (ABA) treatments and abiotic stresses, including salt and water deficit. 5′-RACE (5′-rapid amplification of cDNA ends) assays indicated that miR172c directed Glyma01g39520 mRNA cleavage in soybeans. Overexpression of gma-miR172c in Arabidopsis resulted in reduced leaf water loss and increased survival rate under stress conditions. Meanwhile, the root length, germination rate, and cotyledon greening of transgenic plants were improved during both high salt and water deficit conditions. In addition, transgenic plants exhibited hypersensitivity to ABA during both the seed germination and post-germination seedling growth stages. Stress-related physiological indicators and the expression of stress/ABA-responsive genes were affected by abiotic treatments. The overexpression of gma-miR172c in Arabidopsis promoted earlier flowering compared with the wild type through modulation of the expression of flowering genes, such as FT and LFY during long days, especially under drought conditions. Glyma01g39520 weakened ABA sensitivity and reduced the tolerance to drought stress in the snz mutant of Arabidopsis by reducing the expression of ABI3 and ABI5. Overall, the present results demonstrate that gma-miR172c confers tolerance to water deficit and salt stress but increased ABA sensitivity by regulating Glyma01g39520, which also accelerates flowering under abiotic stresses.

Soybean is a widely cultivated crop, however, its growth and development is very sensitive to light. Shade-tolerance of cultivar is very important in intercropping. The objective of this study was to understand light acclimation of different soybean cultivars grown under different shade treatments and why the photosynthetic capacity of soybean decreased in shade. The chlorophyll content (Chl a , Chl b , and Chl a + b ), apparent quantum efficiency (AQE), the value of electrons produced per photon (α), maximal quantum yield of primary photochemistry ( φ Po ), quantum yield for electron transport ( φ Eo ), efficiency/probability that an electron moves further than Q A − ( ψ Eo ), and performance index on the absorption basis (PI ABS ) of shade treatment increased significantly, while efficiency/probability with which an electron from the intersystem electron carriers is transferred to reduce end electron acceptors at the PSI acceptor side ( δ Ro ), quantum yield for reduction in end electron acceptors at the PSI acceptor side ( φ Ro ), total PI, measuring the performance up to the PSI end electron acceptors (PI total ) dropped significantly. The chlorophyll content, AQE, α, φ Po , φ Eo , ψ Eo and PI ABS of cultivar L32 were higher than those of L29. These results showed that shade increased the light-intercepting and utilization ratio to low light and the activity of PSII of soybean plants, but the energy transport from PSII to PSI was blocked, which was the reason why the photosynthetic capacity was inhibited. Shade-tolerant cultivar L32 had higher PSII activity and energy transport from PSII to PSI than L29 in shade, so shade-tolerant cultivar exhibited higher photosynthetic capacity and yield than shade-sensitive in shade.

A representative sample comprising 366 accessions from the Chinese soybean landrace population (CSLRP) was tested under four growth environments for determination of the whole-genome quantitative trait loci (QTLs) system of the 100-seed weight trait (ranging from 4.59 g to 40.35 g) through genome-wide association study (GWAS). A total of 116 769 single nucleotide polymorphisms (SNPs) were identified and organized into 29 121 SNP linkage disequilibrium blocks (SNPLDBs) to fit the property of multiple alleles/haplotypes per locus in germplasm. An innovative two-stage GWAS was conducted using a single locus model for shrinking the marker number followed by a multiple loci model utilizing a stepwise regression for the whole-genome QTL identification. In total, 98.45% of the phenotypic variance (PV) was accounted for by four large-contribution major QTLs (36.33%), 51 small-contribution major QTLs (43.24%), and a number of unmapped minor QTLs (18.88%), with the QTL×environment variance representing only 1.01% of the PV. The allele numbers of each QTL ranged from two to 10. A total of 263 alleles along with the respective allele effects were estimated and organized into a 263 × 366 matrix, giving the compact genetic constitution of the CSLRP. Differentiations among the ecoregion matrices were found. No landrace had alleles which were all positive or all negative, indicating a hidden potential for recombination. The optimal crosses within and among ecoregions were predicted, and showed great transgressive potential. From the QTL system, 39 candidate genes were annotated, of which 26 were involved with the gene ontology categories of biological process, cellular component, and molecular function, indicating that diverse genes are involved in directing the 100-seed weight.

Understanding the genetic architecture of soybean seed fatty acid (FA) compositions to enhance oil quality is crucial for nutritional value and industrial applications. This study elucidates the genomic determinants of seed FA composition in soybean ( Glycine max [L.] Merr.) through comprehensive genome-wide association study (GWAS) analysis utilizing 1,550 diverse soybean accessions evaluated across five distinct environmental conditions. The phenotypic evaluation revealed significant genetic variability and environmental influences on the biosynthetic process of five essential FAs: palmitic (PA), stearic (SA), oleic (OA), linoleic (LA), and linolenic acid (LNA). High-throughput genomic association mapping identified 110,964 significant SNP-trait associations encompassing 18,841 putative genes. Notable genetic loci included chromosome 5 and 17 harboring GmFATB1A and GmFATB1B for PA biosynthesis; chromosome 2 and 8 containing Glyma.02G161200 and Glyma.08G279700 associated with SA regulation; chromosomes 10, 13, and 20 with GmKCS21 , GmKAS2 , and GmFAD2 affecting OA concentration; chromosomes 10 and 13 with GmKCS21 and GmKAS2 influencing LA content; and chromosome 14 containing GmFAD3 controlling LNA biosynthesis. Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed significant overrepresentation of lipid metabolic processes, particularly glycerolipid metabolic pathways. The haplotype characterization of three key regulatory genes GmKCS21 , GmFAD2 , and GmFAD3 revealed distinct geographic distribution patterns across the northern region, Huang-Huai-Hai region, and southern ecoregions of China, with varying allelic frequencies between improved cultivars and landraces, reflecting adaptive evolution and selection pressure during domestication and enhancement. This study provides a comprehensive genetic resource of 110,964 SNP-trait associations and functionally characterized haplotypes of key regulatory genes ( GmKCS21 , GmFAD2 , and GmFAD3 ) that demonstrate ecoregion-specific allele frequency patterns, enabling marker-assisted selection strategies tailored to those soybean production ecoregions.

The beneficial effects of  Bacillus on crop growth have been confirmed in various contexts. However, the impact of exogenous Bacillus application on the rhizosphere microbial community throughout the entire growth cycle of soybean remains unclear. This study investigated the soybean cultivar ‘Qihuang 34’ under three gradient treatments: Control, no Bacillus application, 0 kg/ha(CK), low Bacillus application, 15 kg/ha(BL), and high Bacillus application, 30 kg/ha(BH), analyzing the dynamic changes in rhizosphere soil microbial community structure and their effects on yield across different growth stages (vegetative(V2), flowering(R2), fruiting(R4) and pod-filling(R6)). The results showed that bacterial α-diversity indices were generally higher at the vegetative stage than at flowering, pod-setting, and seed-filling stages, with inconsistent variation patterns across growth periods. The relative abundance of dominant bacterial phyla and genera varied over time. In the BL treatment, the relative abundances of Rhizobiaceae , Sphingomonadaceae , and Pseudomonadaceae significantly increased at the R4 and R6 stages ( p  < 0.05). In the BH treatment, the relative abundance of Fusarium decreased by 16.16% (R4) and 65.21% (R6) compared to CK. Correlation analysis between soil physicochemical properties and microbial phylum-level composition revealed that total nitrogen (TN) and total sulfur (TS) were the primary drivers of rhizosphere bacterial communities, while TS played a key role in shaping fungal communities. Additionally, the BH treatment significantly increased soybean yield by 4.50–13.84% ( p  < 0.05). This study provides foundational insights into how Bacillus influences the composition and diversity of soybean rhizosphere microbial communities, supporting the development of sustainable agricultural practices through rhizosphere microbiome management.

Salinization of cultivated soils may result in either high salt levels or alkaline conditions, both of which stress crops and reduce performance. We sampled genotypes included in the Northeast China soybean germplasm population (NECSGP) to identify possible genes that affect tolerance to alkaline soil conditions. In this study, 361 soybean accessions collected in Northeast China were tested under 220 mM NaHCO3:Na2CO3 = 9:1 (pH = 9.8) to evaluate the alkali-tolerance (ATI) at the seedling stage in Mudanjiang, Heilongjiang, China. The restricted two-stage multi-locus model genome-wide association study (RTM-GWAS) with gene–allele sequences as markers (6503 GASMs) based on simplified genome resequencing (RAD-sequencing) was accomplished. From this analysis, 132 main effect candidate genes with 359 alleles and 35 Gene × Environment genes with 103 alleles were identified, explaining 90.93% and 2.80% of the seedling alkali-tolerance phenotypic variation, respectively. Genetic variability of ATI in NECSGP was observed primarily within subpopulations, especially in ecoregion B, from which 80% of ATI-tolerant accessions were screened out. The biological functions of 132 candidate genes were classified into eight functional categories (defense response, substance transport, regulation, metabolism-related, substance synthesis, biological process, plant development, and unknown function). From the ATI gene–allele system, six key genes–alleles were identified as starting points for further study on understanding the ATI gene network.

Key messageTwo homologous, chloroplast located CAAX proteases were identified to be functional redundancy in determining soybean leaf color, and they probably play essential roles in regulating light harvesting and absorption during photosynthesis process.Leaf color mutants are ideal materials for studying photosynthesis and chlorophyll metabolism. The soybean [Glycine max (L.) Merr.] yellowing leaf (yl) variation is a recombinant mutant characterized by yellow foliage, which derived from the specific cross between green seed-coated and yellow seed-coated soybean varieties. Molecular cloning and subsequent gene silencing revealed that the yellow leaf trait of yl was controlled by two recessive nuclear genes, glyma11g04660 and glyma01g40650, named as YL1 and YL2 respectively, and the latter was confirmed to be same as the earlier reported green seed-coat gene G. Both YL1 and YL2 belonged to chloroplast-located proteases possessing Abi domain, and these genes were expressed in various tissues, especially in young leaves. In yl, the expression of YL1 and YL2 were suppressed in most tissues, and the young leaf of yl presented an increased maximal photochemical efficiency (Fv/Fm) as well as enhanced net photosynthesis activity (Pn), indicating that YL1 and YL2 are involved in light absorption regulation during photosynthesis process. Collectively, the identification and description of YL1 and YL2 in our study provides insights for the regulatory mechanism of photosynthesis process, and these findings will further assist to clarify the close relationship between photosynthesis and chlorophyll metabolism.

Background To continue to meet the increasing demands of soybean worldwide, it is crucial to identify key genes regulating flowering and maturity to expand the cultivated regions into short season areas. Although four soybean genes have been successfully utilized in early maturity breeding programs, new genes governing maturity are continuously being identified suggesting that there remains as yet undiscovered loci governing agronomic traits of interest. The objective of this study was to identify novel loci and genes involved in a diverse set of early soybean maturity using genome-wide association (GWA) analyses to identify loci governing days to maturity (DTM), flowering (DTF) and pod filling (DTPF), as well as yield and 100 seed weight in Canadian environments. To do so, soybean plant introduction lines varying significantly for maturity, but classified as early varieties, were used. Plants were phenotyped for the five agronomic traits for five site-years and GWA approaches used to identify candidate loci and genes affecting each trait. Results Genotyping using genotyping-by-sequencing and microarray methods identified 67,594 single nucleotide polymorphisms, of which 31,283 had a linkage disequilibrium < 1 and minor allele frequency > 0.05 and were used for GWA analyses. A total of 9, 6, 4, 5 and 2 loci were detected for GWA analyses for DTM, DTF, DTPF, 100 seed weight and yield, respectively. Regions of interest, including a region surrounding the E1 gene for flowering and maturity, and several novel loci, were identified, with several loci having pleiotropic effects. Novel loci affecting maturity were identified on chromosomes five and 13 and reduced maturity by 7.2 and 3.3 days, respectively. Novel loci for maturity and flowering contained genes orthologous to known Arabidopsis flowering genes, while loci affecting yield and 100 seed weight contained genes known to cause dwarfism. Conclusions This study demonstrated substantial variation in soybean agronomic traits of interest, including maturity and flowering dates as well as yield, and the utility of GWA analyses in identifying novel genetic factors underlying important agronomic traits. The loci and candidate genes identified serve as promising targets for future studies examining the mechanisms underlying the related soybean traits.

Black soybeans have a long history in China, with rich nutrition and efficacy. The extraction of its active ingredients is mostly focused on methods such as ultrasound, microwave, Soxhlet extraction, and distillation. These methods rely heavily on solvents, which are not environmentally friendly and healthy, and limit the development and utilization of their functional compositions. This study utilized supercritical fluid extraction technology to prepare functional components of black soybeans and optimized the supercritical CO 2 fluid extraction process of black soybean components through response surface methodology. The qualitative and quantitative analyses of fatty acids in black soybean extracts were mainly conducted, and the free radical scavenging ability of the extracts was studied. The results showed that the black soybean compositions extracted by supercritical fluid were rich, mainly including unsaturated fatty acids and terpenes and had a certain scavenging ability for DPPH and hydroxyl radicals. This study provides a theoretical reference for the industrial preparation of black soybean extractions and also provides ideas for the preparation of functional compositions of other medicinal and edible homologous substances.