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The wild soybean Glycine soja Sieb. et Zucc. is an ancestor of the cultivated soybean Glycine max (L.) Merr. and a source of many valuable genes missing in the G. max genome, including genes that determine stress resistance to adverse environmental factors. Biochemical parameters (protein, oil, ascorbic acid, carotene, higher fatty acids, and specific activities and multiple forms of enzymes of the oxidoreductase and hydrolase classes) were studied in five G. soja accessions from the collection of the All-Russian Institute of Soybean (КА-1413, КА-342, КBl-29, КBl-24, and Kеl-72). The accessions provide unique natural gene banks. Wild seeds were collected in three districts (Arkharinskii, Blagoveshchensk, and Belogorskii) of Amur Oblast. Based on superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), polyphenol oxidase (PPO), ribonuclease (RNase), acid phosphatase, esterase, and amylase (AML) activities and biochemical parameters of seeds, the G. soja accession KA-1413 was found to have higher contents of protein, oleic acid, and linolenic acid; a lower polyphenol oxidase specific activity; and higher activities of SODs, esterases, and RNases. The accession KA-1413 was therefore recommended to use as a source of dominant genes in breeding to increase the adaptive potential of new soybean varieties. A higher heterogeneity of multiple forms was observed for SOD, AML, RNase, and esterase, which can provide markers of adaptation to environmental conditions. [ABSTRACT FROM AUTHOR]

Various species of rhizobium establish compatible symbiotic relationships with soybean (Glycinemax) leading to the formation of nitrogen-fixing nodules in roots. The formation of functional nodules is mediated through complex developmental and transcriptional reprogramming that involves the activity of thousands of plant genes. However, host transcriptome that differentiate between functional or nonfunctional nodules remain largely unexplored. In this study, we investigated differential compatibilities between rhizobium strains (Bradyrhizobium diazoefficiens USDA110 Bradyrhizobium sp. strain LVM105) and cultivated and wild soybeans. The nodulation assays revealed that both USDA110 and LVM105 strains effectively nodulate G. soja but only USDA110 can form symbiotic relationships with Williams 82. LVM105 formed pseudonodules on Williams 82 that consist of a central nodule-like mass that are devoid of any rhizobia. RNA-seq data revealed that USDA110 and LVM105 induce distinct transcriptome programing in functional mature nodules formed on G. soja roots, where genes involved in nucleosome assembly, DNA replication, regulation of cell cycle, and defense responses play key roles. Transcriptome comparison also suggested that activation of genes associated with cell wall biogenesis and organization and defense responses together with downregulation of genes involved in the biosynthesis of isoprenoids and antioxidant stress are associated with the formation of non-functional nodules on Williams 82 roots. Moreover, our analysis implies that increased activity of genes involved in oxygen binding, amino acid transport, and nitrate transport differentiates between fully-developed nodules in cultivated versus wild soybeans. [ABSTRACT FROM AUTHOR]

Soybean [Glycine max (L.) Merr.] is an annual plant of the legume family that is ancestral to the Glycine bean (Glycine soja Sieb. & Zucc.). Soybeans are a key component of "Japanese cuisine," which has been registered as a UNESCO Heritage of Intangible Differentiation and has become an essential part of the Japanese diet. Despite being an important crop in Japan's food culture, the self-sufficiency rate of Japan's domestically produced soybean crop has declined considerably to ~24 % for use in food products and ~6% for combined nonfood uses. Although domestic consumption of processed soybean products such as tofu has been increasing annually, imported soybeans have been used as raw materials. From the food security perspective, improving the self-sufficiency rate by promoting the development of soybean varieties that are internationally competitive and of superior quality is a prominent issue. Therefore, the Soybean Subcommittee of the 70th Anniversary Meeting of the Japanese Society for Food Science and Technology invited Dr. Yohei Nanjo of the Crops Research Division of the National Institute of Agrobiological Science in 2023 to give a presentation on the current state of soybean breeding and its future outlook. [ABSTRACT FROM AUTHOR]

SUMMARY: Recombination is the primary mechanism underlying genetic improvement in populations and allows plant breeders to create new allelic combinations for agronomic improvement. Soybean [Glycine max (L.) Merr.] has gone through multiple genetic bottlenecks that have significantly affected its genetic diversity, linkage disequilibrium, and altered allele frequencies. To investigate the impact of genetic bottlenecks on recombination hotspots in soybeans, historical recombination was studied in three soybean populations. The populations were wild soybean [Glycine soja (Sieb. and Zucc.)], landraces, and North American elite soybean cultivars that have been genotyped with the SoySNP50K BeadChip. While each population after a genetic bottleneck had an increased average haplotype block size, they did not have a significant difference in the number of hotspots between each population. Instead, the increase in observed haplotype block size is likely due to an elimination of individuals that contained historical recombination at hotspots which decreased the observed rate of recombination for the hotspot after each genetic bottleneck. Conversely, heterochromatic DNA which has an increased haplotype block size compared to euchromatic DNA had a significantly different number of hotspots but not a significant difference in the average hotspot recombination rate. Previously identified genomic motifs associated with hotspots were also associated with hotspots found in the historical populations suggesting a common mechanism. This characterization of historical recombination hotspots in soybeans provides further insights into the effect genetic bottlenecks and selection have on recombination hotspots. Significance Statement: This manuscript provides a first look into soybean recombination hotspots across three diverse soybean populations. The populations used consist of a wild soybean population, landrace population, and North American elite soybean population. Through comparing the characteristics of the hotspots between the populations, this work provides insights into how selection and the genetic bottlenecks of domestication, introduction, and modern plant breeding have affected recombination hotspots and haplotype block structure in soybeans. [ABSTRACT FROM AUTHOR]

Summary: Soybean (Glycine max L. Merr.) is a major crop worldwide, providing essential dietary proteins and edible oils for agriculture, food, animal feed and biofuel industries. However, its limited genetic variation makes it vulnerable to harsh environmental conditions, and its chemical diversity was strongly reduced after long domestication. Wild soybean (Glycine soja Sieb. et Zucc.), the ancestor of the G. max, possesses a high level of genetic diversity and thus present a precious reservoir for improving cultivated soybean. Characterising metabolomes of different G. soja accessions is crucial in exploring metabolite accumulation patterns for developing metabolic breeding strategies. This study successfully revealed the metabolomes of sixty‐four seed lines of G. soja collected throughout Japan by a widely targeted metabolomics approach, therefore, providing a good source of information for further studies to induce the production of bioactive compounds and the defence mechanism to stress. [ABSTRACT FROM AUTHOR]

Wild soybeans retain many substances significantly reduced or lost in cultivars during domestication. This study utilized LC-MS to analyze metabolites in the seed coats and embryos of wild and cultivated soybeans. 866 and 815 metabolites were identified in the seed extracts of both soybean types, with 35 and 10 significantly differing metabolites in the seed coat and embryos, respectively. The upregulated metabolites in wild soybeans are linked to plant defense, stress responses, and nitrogen cycling. MALDI-MSI results further elucidated the distribution of these differential metabolites in the cotyledons, hypocotyls, and radicles. In addition to their role in physiological processes like growth and response to environmental stimuli, the prevalent terpenoids, lipids, and flavonoids present in wild soybeans exhibit beneficial bioactivities, including anti-inflammatory, antibacterial, anticancer, and cardiovascular disease prevention properties. These findings underscore the potential of wild soybeans as a valuable resource for enhancing the nutritional and ecological adaptability of cultivated soybeans.

Various species of rhizobium establish compatible symbiotic relationships with soybean (Glycine max) leading to the formation of nitrogen-fixing nodules in roots. The formation of functional nodules is mediated through complex developmental and transcriptional reprogramming that involves the activity of thousands of plant genes. However, host transcriptome that differentiate between functional or non-functional nodules remain largely unexplored. In this study, we investigated differential compatibilities between rhizobium strains (Bradyrhizobium diazoefficiens USDA110 Bradyrhizobium sp. strain LVM105) and cultivated and wild soybeans. The nodulation assays revealed that both USDA110 and LVM105 strains effectively nodulate G. soja but only USDA110 can form symbiotic relationships with Williams 82. LVM105 formed pseudonodules on Williams 82 that consist of a central nodule-like mass that are devoid of any rhizobia. RNA-seq data revealed that USDA110 and LVM105 induce distinct transcriptome programing in functional mature nodules formed on G. soja roots, where genes involved in nucleosome assembly, DNA replication, regulation of cell cycle, and defense responses play key roles. Transcriptome comparison also suggested that activation of genes associated with cell wall biogenesis and organization and defense responses together with downregulation of genes involved in the biosynthesis of isoprenoids and antioxidant stress are associated with the formation of non-functional nodules on Williams 82 roots. Moreover, our analysis implies that increased activity of genes involved in oxygen binding, amino acid transport, and nitrate transport differentiates between fully-developed nodules in cultivated versus wild soybeans.

Frogeye leaf spot (FLS), caused by Cercospora sojina, is a threat to soybean cultivation, leading to substantial economic losses. Here, an RNA sequencing analysis was conducted to identify genes associated with the response of wild soybean (Glycine soja) to C. sojina. Differentially expressed genes (DEGs) were identified by comparing the gene expression of C. sojina-inoculated plants with that of non-inoculated plants. A total of 1642 DEGs (790 up-regulated and 852 down-regulated) were identified in C. sojina-inoculated wounded leaves compared with non-inoculated wounded leaves. The DEGs were analyzed for gene ontology and the KEGG pathway to identify the key genes responsible for the response to C. sojina and the corresponding pathways. In GO analysis, 'Defense response' was highlighted, while in KEGG analysis, 'Metabolic pathways' and 'Flavonoid biosynthesis' were emphasized. A total of 67 DEGs were categorized within the 'biotic stress' MapMan category, with 'Redox state,' 'Cell wall,' and 'Secondary metabolites' showing the highest abundance of assigned DEGs. DEGs associated with the phenylpropanoid pathway (GsALDH and GsAOMT-like), cell wall remodeling (GsPME12), and reactive oxygen species (GsGSTUs), were identified in plants inoculated with C. sojina compared to non-inoculated plants. Additionally, Gs2MF3OR-like (encodes an enone oxidoreductase) and Gsα-DOX1-like (involved in oxidative stress) also participated in the response of wild soybean to the disease. Our results suggest potential C. sojina-resistant genes that could serve as targets for further functional characterization, as well as for soybean molecular breeding programs aimed at improving FLS resistance. [ABSTRACT FROM AUTHOR]

Glyceollins, a family of phytoalexins elicited in legume species, play crucial roles in environmental stress response (e.g., defending against pathogens) and human health. However, little is known about the genetic basis of glyceollin elicitation. In the present study, we employed a metabolite-based genome-wide association (mGWA) approach to identify candidate genes involved in glyceollin elicitation in genetically diverse and understudied wild soybeans subjected to soybean cyst nematode. In total, eight SNPs on chromosomes 3, 9, 13, 15, and 20 showed significant associations with glyceollin elicitation. Six genes fell into two gene clusters that encode glycosyltransferases in the phenylpropanoid pathway and were physically close to one of the significant SNPs (ss715603454) on chromosome 9. Additionally, transcription factors (TFs) genes such as MYB and WRKY were also found as promising candidate genes within close linkage to significant SNPs on chromosome 9. Notably, four significant SNPs on chromosome 9 show epistasis and a strong signal for selection. The findings describe the genetic foundation of glyceollin biosynthesis in wild soybeans; the identified genes are predicted to play a significant role in glyceollin elicitation regulation in wild soybeans. Additionally, how the epistatic interactions and selection influence glyceollin variation in natural populations deserves further investigation to elucidate the molecular mechanism of glyceollin biosynthesis. [ABSTRACT FROM AUTHOR]

Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource. [ABSTRACT FROM AUTHOR]

Glyceollins, a family of phytoalexins elicited in legume species, play crucial roles in environmental stress response (e.g., defending against pathogens) and human health. However, little is known about the genetic basis of glyceollin elicitation. In the present study, we employed a metabolite-based genome-wide association (mGWA) approach to identify candidate genes involved in glyceollin elicitation in genetically diverse and understudied wild soybeans subjected to soybean cyst nematode. In total, eight SNPs on chromosomes 3, 9, 13, 15, and 20 showed significant associations with glyceollin elicitation. Six genes fell into two gene clusters that encode glycosyltransferases in the phenylpropanoid pathway and were physically close to one of the significant SNPs (ss715603454) on chromosome 9. Additionally, transcription factors (TFs) genes such as MYB and WRKY were also found as promising candidate genes within close linkage to significant SNPs on chromosome 9. Notably, four significant SNPs on chromosome 9 show epistasis and a strong signal for selection. The findings describe the genetic foundation of glyceollin biosynthesis in wild soybeans; the identified genes are predicted to play a significant role in glyceollin elicitation regulation in wild soybeans. Additionally, how the epistatic interactions and selection influence glyceollin variation in natural populations deserves further investigation to elucidate the molecular mechanism of glyceollin biosynthesis.

Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. The results show that the fungal pathogen infection reduced the growth of the root and hypocotyl in most G. soja accessions. The accession PI 507794 displayed the highest level of resistance response to M. phaseolina infection among the tested wild soybean accessions, while PI 487431 and PI 483660B were susceptible to charcoal rot in terms of the reduction in root and hypocotyl growth. The mean values of the root and hypocotyl parameters in PI 507794 were significantly higher (p < 0.05) than those of PI 487431 and PI 483460B. A analysis of the resistance of wild soybean accessions to M. phaseolina using the root and hypocotyl as the assessment parameters at the early seedling stage provides an alternative way to rapidly identify potential resistant genotypes and facilitate breeding for soybean resistance to charcoal rot. [ABSTRACT FROM AUTHOR]

Background: Glycine soja Sieb. & Zucc. is the wild ancestor from which the important crop plant soybean was bred. G. soja provides important germplasm resources for the breeding and improvement of cultivated soybean crops, however the species is threatened by habitat loss and fragmentation, and is experiencing population declines across its natural range. Understanding the patterns of genetic diversity in G. soja populations can help to inform conservation practices. Methods: In this study, we analyzed the genetic diversity and differentiation of G. soja at different sites and investigated the gene flow within the species. We obtained 147 G. soja accessions collected from 16 locations across the natural range of the species from China, Korea and Japan. Samples were analyzed using SLAF-seq (Specific-Locus Amplified Fragment Sequencing). Results: We obtained a total of 56,489 highly consistent SNPs. Our results suggested that G. soja harbors relatively high diversity and that populations of this species are highly differentiated. The populations harboring high genetic diversity, especially KR, should be considered first when devising conservation plans for the protection of G. soja, and in situ protection should be adopted in KR. G. soja populations from the Yangtze River, the Korean peninsula and northeastern China have a close relationship, although these areas are geographically disconnected. Other populations from north China clustered together. Analysis of gene flow suggested that historical migrations of G. soja may have occurred from the south northwards across the East-Asia land-bridge, but not across north China. All G. soja populations could be divided into one of two lineages, and these two lineages should be treated separately when formulating protection policies. [ABSTRACT FROM AUTHOR]

The vine growth habit (VGH) is a notable property of wild soybean plants that also holds a high degree of importance in domestication as it can preclude using these wild cultivars for breeding and improving domesticated soybeans. Here, a bulked segregant analysis (BSA) approach was employed to study the genetic etiology of the VGH in soybean plants by integrating linkage mapping and population sequencing approaches. To develop a recombinant inbred line (RIL) population, the cultivated Zhongdou41 (ZD41) soybean cultivar was bred with ZYD02787, a wild soybean accession. The VGH status of each line in the resultant population was assessed, ultimately leading to the identification of six and nine QTLs from the BSA sequencing of the F4 population and F6-F8 population sequence mapping, respectively. One QTL shared across these analyzed generations was detected on chromosome 19. Three other QTLs detected by BSA-seq were validated and localized to the 90.93 kb, 2.9 Mb, and 602.08 kb regions of chromosomes 6 and 13, harboring 14, 53, and 4 genes, respectively. Three consistent VGH-related QTLs located on chromosomes 2 and 19 were detected in a minimum of three environments, while an additional six loci on chromosomes 2, 10, 13, and 18 were detected in at least two environments via ICIM mapping. Of all the detected loci, five had been reported previously whereas seven represent novel QTLs. Together, these data offer new insights into the genetic basis of the VGH in soybean plants, providing a rational basis to inform the use of wild accessions in future breeding efforts. [ABSTRACT FROM AUTHOR]

SOS2-like protein kinases (PKS/CIPK) family genes are known to be involved in various abiotic stresses in plants. Even though, its functions have been well characterized under salt and drought stresses. The roles of PKS genes associated with alkaline stress response are not fully established yet. In this study, we identified 56 PKS family genes which could be mainly classified into three groups in wild soybean (Glycine soja). PKS family genes transcript profiles revealed different expression patterns under alkali stress. Furthermore, we confirmed the regulatory roles of GsPKS24 in response to NaHCO3, pH and ABA treatments. Overexpression of GsPKS24 enhanced plant tolerance to pH stress in Arabidopsis and soybean hairy roots but conferred suppressed pH tolerance in Arabidopsis atpks mutant. Additionally, Overexpression of GsPKS24 decreased the ABA sensitivity compared to Arabidopsis atpks mutant which displayed more sensitivity towards ABA. Moreover, upregulated expression of stress responsive and ABA signal-related genes were detected in GsPKS24 overexpression lines. In conclusion, we identified the wild soybean PKS family genes, and explored the roles of GsPKS24 in positive response to pH stress tolerance, and in alleviation of ABA sensitivity. [ABSTRACT FROM AUTHOR]

WRKY proteins are a superfamily of transcription factors (TFs) that play multiple roles in plants' growth, development, and environmental stress response. In this study, a novel WRKY gene called GsWRKY23 that is specifically upregulated in salt-tolerant Glycine soja accession BB52 seedlings was identified by transcriptomic analysis under salt stress. How the physiological functions and mechanisms of the GsWRKY23 gene affect salt tolerance was investigated using transformations of soybean hairy roots and Arabidopsis, including wild-type (WT) and atwrky23-mutant plants. The results showed that GsWRKY23 in the roots, stems, and leaves of BB52, along with its promoter in the cotyledons and root tips of GsWRKY23pro::GUS Arabidopsis seedlings, displayed enhanced induction under salt stress. GsWRKY23 localises to the nucleus and shows transcriptional activation ability in yeast cells. Compared to GsWRKY23-RNAi wild soybean hairy-root composite plants under salt stress, obvious improvements, such as superior growth appearance, plant height and fresh weight (FW), and leaf chlorophyll and relative water content (RWC), were displayed by GsWRKY23-overexpressing (OE) composite plants. Moreover, their relative electrolytic leakage (REL) values and malondialdehyde (MDA) contents in the roots and leaves declined significantly. Most of the contents of Na+ and Cl− in the roots, stems, and leaves of GsWRKY23-OE plants decreased significantly, while the content of K+ in the roots increased, and the content of NO3− displayed no obvious change. Ultimately, the Na+/K+ ratios of roots, stems, and leaves, along with the Cl−/NO3− ratios of roots and stems, decreased significantly. In the transgenic WT-GsWRKY23 and atwrky23-GsWRKY23 Arabidopsis seedlings, the salt-induced reduction in seed germination rate and seedling growth was markedly ameliorated; plant FW, leaf chlorophyll content, and RWC increased, and the REL value and MDA content in shoots decreased significantly. In addition, the accumulation of Na+ and Cl− decreased, and the K+ and NO3− levels increased markedly to maintain lower Na+/K+ and Cl−/NO3− ratios in the roots and shoots. Taken together, these results highlight the role of GsWRKY23 in regulating ionic homeostasis in NaCl-stressed overexpressed soybean composite plants and Arabidopsis seedlings to maintain lower Na+/K+ and Cl−/NO3− ratios in the roots and shoots, thus conferring improved salt tolerance. [ABSTRACT FROM AUTHOR]

The work was performed in order to study the morphological and agriculturally important traits and molecular genetic allelic polymorphism of the cultivated varieties and wild forms of soybean using microsatellite DNA with the aim of identification and certification of their genotypes. Unique DNA profiles of the studied soybean cultivars and wild forms were obtained by PCR analysis using six microsatellite loci (Satt1, Satt2, Satt5, Satt9, Sourgr1, and Soyhsp176). Twenty-four alleles have been identified, with the number of alleles per locus ranging from two to ten. For each locus, Polymorphism Information Content (PIC) varied from 0.28 to 0.86 and the average was 0.62; the effective number of alleles varied from 1.38 to 6.92 and the average was 3.30. Cultivated soybean varieties differed by from 1 to 4 loci. The dendrogram constructed for the studied soybean genotypes by the unweighted pair group method with arithmetic mean (UPGMA) with the aid of the POPGENE v. 1.32 software revealed two large clusters. Cluster I included the cultivated soybean varieties, while cluster II included wild soybean forms, which overall pointed to the significant genetic differences between these two groups. The highest morphological differences were revealed between the Topaz and Dauriya varieties, both in the phenotype (pubescence coloration and density and seed and eye color and shape) and in all agriculturally important traits (vegetation period—95 and 112 days; yield—26.8 and 30.9 hundred kg/ha; plant height—64 and 81 cm; lower bean attachment height—13 and 16 cm; weight of 1000 seeds—174.7 and 185.4 g; protein content—40.3 and 38.2%; oil content—19.2 and 19.8%, respectively). For the first time, molecular genetic passports of nine soybean cultivars bred in the All-Russia Soybean Research Institute for their genotype identification have been obtained based on the findings of this study. [ABSTRACT FROM AUTHOR]

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

Abstract Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underlying flowering time in response to AAT especially in wild soybean were rarely reported. In this study, we used 294 wild soybean accessions derived from major soybean production region characterized by different AAT in Northeast of China. Based on genome-wide association study (GWAS), we identified 96 SNPs corresponded to 342 candidate genes that significantly associated with flowering time recorded in two-year experiments. Gene Ontology enrichment analysis suggests that the pathways of photosynthesis light reaction and actin filament binding were significantly enriched. We found three lead SNPs with -log10(p-value) > 32 across the two-year experiments, i.e., Chr02:9490318, Chr04:8545910 and Chr09:49553555. Linkage disequilibrium block analysis shows 28 candidate genes within the genomic region centered on the lead SNPs. Among them, expression levels of three genes (aspartic peptidase 1, serine/threonine-protein kinase and protein SCAR2-like) were significantly differed between two subgroups possessing contrasting flowering time distributed at chromosome 2, 4 and 9, respectively. There are 6, 7 and 3 haplotypes classified on the coding regions of the three genes, respectively. Collectively, accessions with late flowering time phenotype are typically derived from AAT zone 1, which is associated with the haplotypic distribution and expression levels of the three genes. This study provides an insight into a potential mechanism responsible for flowering time in response to AAT in wild soybean, which could promote the understanding of genetic basis for other major crops.

Abstract Background Since the root nodules formation is regulated by specific and complex interactions of legume and rhizobial genes, there are still too many questions to be answered about the role of the genes involved in the regulation of the nodulation signaling pathway. Results The genetic and biological roles of the isoflavone-7-O-beta-glucoside 6″-O-malonyltransferase gene GsIMaT2 from wild soybean (Glycine soja) in the regulation of nodule and root growth in soybean (Glycine max) were examined in this work. The effect of overexpressing GsIMaT2 from G. soja on the soybean nodulation signaling system and strigolactone production was investigated. We discovered that the GsIMaT2 increased nodule numbers, fresh nodule weight, root weight, and root length by boosting strigolactone formation. Furthermore, we examined the isoflavone concentration of transgenic G. max hairy roots 10 and 20 days after rhizobial inoculation. Malonyldaidzin, malonylgenistin, daidzein, and glycitein levels were considerably higher in GsMaT2-OE hairy roots after 10- and 20-days of Bradyrhizobium japonicum infection compared to the control. These findings suggest that isoflavones and their biosynthetic genes play unique functions in the nodulation signaling system in G. max. Conclusions Finally, our results indicate the potential effects of the GsIMaT2 gene on soybean root growth and nodulation. This study provides novel insights for understanding the epistatic relationship between isoflavones, root development, and nodulation in soybean. Highlights * Cloning and Characterization of 7-O-beta-glucoside 6″-O-malonyltransferase (GsIMaT2) gene from wild soybean (G. soja). * The role of GsIMaT2 gene in the regulation of root nodule development. *Overexpression of GsMaT2 gene increases the accumulation of isoflavonoid in transgenic soybean hairy roots. * This gene could be used for metabolic engineering of useful isoflavonoid production.

Black soybean (Glycine soja (L.) Merril) is one of the potential agricultural commodities in Indonesia. The multilocation trial is the primary requirement for variety release before farmers can widely use the new varieties. Various stability measurements on grain yields will provide more accurate information in selecting superior lines. The aims of the study were to: (i) identify the effect of genotype by environment interactions (G×E) on black soybean grain yields; (ii) select the black soybean lines with stable and high grain yields in different agroecosystems; and (iii) determine the best representative environment for testing black soybean lines. The field trials used an augmented design that was applied in three blocks for each location. The research was conducted in West Java, Indonesia, specifically in Sumedang, Indramayu, and Majalengka. The three locations are traditionally soybean production areas in West Java. The results showed that G×E significantly affected grain yields, with a contribution of 38.35%. Based on the results of stability testing using parametric, non-parametric, and genotype plus genotype by environments (GGE) biplot measurements, the G13, G22, G25, and G26 lines were considered the most stable and produced the highest yields in the three agroecosystems. In addition, Sumedang is the most representative location for testing black soybeans in Indonesia. Therefore, the four lines can be proposed as new superior lines for black soybeans with high yields and stability in three environments. Information about the relationship between the yield stability parameters can be used for the most accessible parameter selection.

To study the effect of growth temperature on the nutritional components and metabolites of the wild soybean (Glycine soja), we analyzed the nutritional components and metabolic gases of the wild soybean in six accumulated temperature regions of the Heilongjiang Province, China, by gas chromatography–time-of-flight mass spectrometry (GC-TOF-MS). A total of 430 metabolites, including organic acids, organic oxides, and lipids, were identified and analyzed using multivariate statistical analysis, orthogonal partial least squares discriminant analysis, principal component analysis, and cluster analysis. Eighty-seven metabolites significantly differed in the sixth accumulated temperature region compared with the other five accumulated temperature regions. The 40 metabolites (such as threonine (Thr) and lysine (Lys)) were found to be elevated in soybeans from the sixth accumulated temperature zone compared with the other five accumulated temperature zones. Through analyzing the metabolic pathways of these metabolites, amino acid metabolism had the greatest influence on wild soybean quality. The results of the amino acid analysis were consistent with those of the GC-TOF-MS and showed that amino acids in wild soybeans from the sixth accumulated temperature zone significantly differed from those of the other zones. Threonine and lysine were the main substances driving these differences. The growth temperature affected the type and concentrations of metabolites in wild soybeans, and the GC-TOF-MS analysis of the effect of growth temperature on wild soybean metabolites was shown to be feasible. [ABSTRACT FROM AUTHOR]

Wild soybean, also known as Glycine soja Sieb. et Zucc. (GS), has long been known for its various health benefits. Although various pharmacological effects of G. soja have been studied, the effects of GS leaf and stem (GSLS) on osteoarthritis (OA) have not been evaluated. Here, we examined the anti-inflammatory effects of GSLS in interleukin-1β (IL-1β)-stimulated SW1353 human chondrocytes. GSLS inhibited the expression of inflammatory cytokines and matrix metalloproteinases and ameliorated the degradation of collagen type II in IL-1β-stimulated chondrocytes. Furthermore, GSLS played a protective role in chondrocytes by inhibiting the activation of NF-κB. In addition, our in vivo study demonstrated that GSLS ameliorated pain and reversed cartilage degeneration in joints by inhibiting inflammatory responses in a monosodium iodoacetate (MIA)-induced OA rat model. GSLS remarkably reduced the MIA-induced OA symptoms, such as joint pain, and decreased the serum levels of proinflammatory mediators, cytokines, and matrix metalloproteinases (MMPs). Our findings show that GSLS exerts anti-osteoarthritic effects and reduces pain and cartilage degeneration by downregulating inflammation, suggesting that it is a useful therapeutic candidate for OA. [ABSTRACT FROM AUTHOR]

Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource.

Phytophthora root rot (PRR) is a destructive disease of soybeans (Glycine max (L.) Merr) caused by Phytophthora sojae (P. sojae). The most effective way to prevent the disease is growing resistant or tolerant varieties. Partial resistance provides a more durable resistance against the pathogen compared to complete resistance. Wild soybean (Glycine soja Sieb. & Zucc.) seems to be an extraordinarily important gene pool for soybean improvement due to its high level of genetic variation. In this study, 242 wild soybean germplasms originating from different regions of Heilongjiang province were used to identify resistance genes to P. sojae race 1 using a genome-wide association study (GWAS). A total of nine significant SNPs were detected, repeatedly associated with P. sojae resistance and located on chromosomes 1, 10, 12, 15, 17, 19 and 20. Among them, seven favorable allelic variations associated with P. sojae resistance were evaluated by a t-test. Eight candidate genes were predicted to explore the mechanistic hypotheses of partial resistance, including Glysoja.19G051583, which encodes an LRR receptor-like serine/threonine protein kinase protein, Glysoja.19G051581, which encodes a receptor-like cytosolic serine/threonine protein kinase protein. These findings will provide additional insights into the genetic architecture of P. sojae resistance in a large sample of wild soybeans and P. sojae-resistant breeding through marker-assisted selection.

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Sybeans have been grown by plant breeding for decades. As soybeans have very limited genetic variation, it is difficult for soybean breeders to find new genetic resources for abiotic stressors. Recently, soybeans have been exposed to flooding stress from intensive summer rainfall owing to climate change. Glycine soja, a wild soybean, is known to have greater genetic variation and greater resistance to a variety of biotic and abiotic stresses than ordinary soybeans. In this study, high-throughput transcriptome analysis was performed using flood-treated Glycine soja. Differentially expressed genes (DEGs) were analyzed using reads mapped to reference sequences, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using selected DEGs. In addition, RT-qPCR analysis was performed to further analyze the expression of specific candidate genes. Several novel genes that could explain various mechanisms related to water stress were identified as related transcripts and adaptation mechanisms through cell wall expansion, alcoholic fermentation under anaerobic conditions, and structural changes. In addition, most of the isoflavonoid daidzein pathway genes exhibited upregulated expression under flooding stress. Interestingly, expression of the DIR (dirigent protein 1-like) gene, which is known to decrease in response to flooding stress in soybeans (Glycine max), was upregulated in Glycine soja. The expression of DIR revealed that DIR may play a key role in conferring flooding stress resistance in Glycine soja. This study provides useful information regarding the genes and comprehensive adaptation mechanisms related to flooding stress tolerance that can be utilized for cultivated soybeans through the Korean wild soybean. [ABSTRACT FROM AUTHOR]

Rhizobia are common symbiotic microorganisms in the root system of leguminous plants that can usually provide nitrogen to the host through nitrogen fixation. Studies have shown that rhizobium-preinoculated soybean plants usually exhibit improved salt tolerance, but the underlying mechanism is not fully understood. In this paper, transcriptome sequencing (RNA-seq) revealed that preinoculation with rhizobia affected polyamine (PA) metabolism in soybean roots. The assay of PA contents showed that preinoculation with rhizobia significantly increased the putrescine (Put) content in roots and leaves during short-term salt treatment (0–5 d). Long-term salt treatment (5–7 d) resulted in a high Put content and significantly increased Spm and Spd contents, resulting in a rapid increase in the Put/(Spd + Spm) ratio (0–5 d) and subsequent decrease. Moreover, rhizobium preinoculation of soybean plants resulted in increased contents of conjugated and bound PAs under salt stress. Further transcriptome sequencing, PA contents, PA synthase expression and activity analysis revealed that GmADC may be a key gene related to salt tolerance in rhizobium-preinoculated soybean plants, and the GmADC -overexpressing soybean hairy-root composite plants exhibited less ROS damage, lower Cl−/NO 3 − ratios and Na+/K+ ratios, and stabilized ion homeostasis. Taken together, preinoculation with rhizobia increased the expression level and enzyme activity of arginine decarboxylase (ADC) in soybean roots, increased the content of Put in roots and leaves, and increased the content of conjugated and bound PAs in soybean plants, thereby alleviating the oxidative and ionic injuries of soybean plants and enhancing the salt tolerance. • Pre-inoculation with rhizobia conferred soybean salt tolerance via affecting the gene expressions related to PAs metabolism. • Lower Put/(Spd + Spm) ratio attributed to the enhanced salt tolerance of soybean seedlings pre-inoculated with rhizobia. • GmADC- OE hairy-root soybean composite plants exhibited enhanced salt tolerance. [ABSTRACT FROM AUTHOR]

Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. The results show that the fungal pathogen infection reduced the growth of the root and hypocotyl in most G. soja accessions. The accession PI 507794 displayed the highest level of resistance response to M. phaseolina infection among the tested wild soybean accessions, while PI 487431 and PI 483660B were susceptible to charcoal rot in terms of the reduction in root and hypocotyl growth. The mean values of the root and hypocotyl parameters in PI 507794 were significantly higher (p < 0.05) than those of PI 487431 and PI 483460B. A analysis of the resistance of wild soybean accessions to M. phaseolina using the root and hypocotyl as the assessment parameters at the early seedling stage provides an alternative way to rapidly identify potential resistant genotypes and facilitate breeding for soybean resistance to charcoal rot.

The vine growth habit (VGH) is a notable property of wild soybean plants that also holds a high degree of importance in domestication as it can preclude using these wild cultivars for breeding and improving domesticated soybeans. Here, a bulked segregant analysis (BSA) approach was employed to study the genetic etiology of the VGH in soybean plants by integrating linkage mapping and population sequencing approaches. To develop a recombinant inbred line (RIL) population, the cultivated Zhongdou41 (ZD41) soybean cultivar was bred with ZYD02787, a wild soybean accession. The VGH status of each line in the resultant population was assessed, ultimately leading to the identification of six and nine QTLs from the BSA sequencing of the F4 population and F6-F8 population sequence mapping, respectively. One QTL shared across these analyzed generations was detected on chromosome 19. Three other QTLs detected by BSA-seq were validated and localized to the 90.93 kb, 2.9 Mb, and 602.08 kb regions of chromosomes 6 and 13, harboring 14, 53, and 4 genes, respectively. Three consistent VGH-related QTLs located on chromosomes 2 and 19 were detected in a minimum of three environments, while an additional six loci on chromosomes 2, 10, 13, and 18 were detected in at least two environments via ICIM mapping. Of all the detected loci, five had been reported previously whereas seven represent novel QTLs. Together, these data offer new insights into the genetic basis of the VGH in soybean plants, providing a rational basis to inform the use of wild accessions in future breeding efforts.

Soybean cyst nematode (SCN) is the most economically damaging pathogen of soybean and host resistance is a core management strategy. The SCN resistance quantitative trait locus cqSCN-006, introgressed from the wild relative Glycine soja, provides intermediate resistance against nematode populations, including those with increased virulence on the heavily used rhg1-b resistance locus. cqSCN-006 was previously fine-mapped to a genome interval on chromosome 15. The present study determined that Glyma.15G191200 at cqSCN-006, encoding a γ-SNAP, contributes to SCN resistance. CRISPR/Cas9-mediated disruption of the cqSCN-006 allele reduced SCN resistance in transgenic roots. There are no encoded amino acid polymorphisms between resistant and susceptible alleles. However, other cqSCN-006-specific DNA polymorphisms in the Glyma.15G191200 promoter and gene body were identified, and we observed differing induction of γ-SNAP protein abundance at SCN infection sites between resistant and susceptible roots. We identified alternative RNA splice forms transcribed from the Glyma.15G191200 γ-SNAP gene and observed differential expression of the splice forms 2 days after SCN infection. Heterologous overexpression of γ-SNAPs in plant leaves caused moderate necrosis, suggesting that careful regulation of this protein is required for cellular homeostasis. Apparently, certain G. soja evolved quantitative SCN resistance through altered regulation of γ-SNAP. Previous work has demonstrated SCN resistance impacts of the soybean α-SNAP proteins encoded by Glyma.18G022500 (Rhg1) and Glyma.11G234500. The present study shows that a different type of SNAP protein can also impact SCN resistance. Little is known about γ-SNAPs in any system, but the present work suggests a role for γ-SNAPs during susceptible responses to cyst nematodes.[Graphic: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underlying flowering time in response to AAT especially in wild soybean were rarely reported. In this study, we used 294 wild soybean accessions derived from major soybean production region characterized by different AAT in Northeast of China. Based on genome-wide association study (GWAS), we identified 96 SNPs corresponded to 342 candidate genes that significantly associated with flowering time recorded in two-year experiments. Gene Ontology enrichment analysis suggests that the pathways of photosynthesis light reaction and actin filament binding were significantly enriched. We found three lead SNPs with -log10(p-value) > 32 across the two-year experiments, i.e., Chr02:9490318, Chr04:8545910 and Chr09:49553555. Linkage disequilibrium block analysis shows 28 candidate genes within the genomic region centered on the lead SNPs. Among them, expression levels of three genes (aspartic peptidase 1, serine/threonine-protein kinase and protein SCAR2-like) were significantly differed between two subgroups possessing contrasting flowering time distributed at chromosome 2, 4 and 9, respectively. There are 6, 7 and 3 haplotypes classified on the coding regions of the three genes, respectively. Collectively, accessions with late flowering time phenotype are typically derived from AAT zone 1, which is associated with the haplotypic distribution and expression levels of the three genes. This study provides an insight into a potential mechanism responsible for flowering time in response to AAT in wild soybean, which could promote the understanding of genetic basis for other major crops. [ABSTRACT FROM AUTHOR]

Background: Since the root nodules formation is regulated by specific and complex interactions of legume and rhizobial genes, there are still too many questions to be answered about the role of the genes involved in the regulation of the nodulation signaling pathway. Results: The genetic and biological roles of the isoflavone-7-O-beta-glucoside 6″-O-malonyltransferase gene GsIMaT2 from wild soybean (Glycine soja) in the regulation of nodule and root growth in soybean (Glycine max) were examined in this work. The effect of overexpressing GsIMaT2 from G. soja on the soybean nodulation signaling system and strigolactone production was investigated. We discovered that the GsIMaT2 increased nodule numbers, fresh nodule weight, root weight, and root length by boosting strigolactone formation. Furthermore, we examined the isoflavone concentration of transgenic G. max hairy roots 10 and 20 days after rhizobial inoculation. Malonyldaidzin, malonylgenistin, daidzein, and glycitein levels were considerably higher in GsMaT2-OE hairy roots after 10- and 20-days of Bradyrhizobium japonicum infection compared to the control. These findings suggest that isoflavones and their biosynthetic genes play unique functions in the nodulation signaling system in G. max. Conclusions: Finally, our results indicate the potential effects of the GsIMaT2 gene on soybean root growth and nodulation. This study provides novel insights for understanding the epistatic relationship between isoflavones, root development, and nodulation in soybean. Highlights: * Cloning and Characterization of 7-O-beta-glucoside 6″-O-malonyltransferase (GsIMaT2) gene from wild soybean (G. soja). * The role of GsIMaT2 gene in the regulation of root nodule development. *Overexpression of GsMaT2 gene increases the accumulation of isoflavonoid in transgenic soybean hairy roots. * This gene could be used for metabolic engineering of useful isoflavonoid production. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max) is an important crop for its nutritional value. Its wild relative, Glycine soja, provides a valuable genetic resource for improving soybean productivity. Root development and differentiation are essential for soybean plants to take up water and nutrients, store energy and anchor themselves. Long noncoding RNAs (lncRNAs) have been reported to play critical roles in various biological processes. However, the spatiotemporal landscape of lncRNAs during early root development and differentiation in soybeans is scarcely characterized. Using RNA sequencing and transcriptome assembly, we identified 1578 lncRNAs in G. max and 1454 in G. soja, spanning various root portions and time points. Differential expression analysis revealed 82 and 69 lncRNAs exhibiting spatiotemporally differential expression patterns in G. max and G. soja, respectively, indicating their involvement in the early stage of root architecture formation. By elucidating multiple competitive endogenous RNA (ceRNA) networks involving lncRNAs, microRNAs and protein-coding RNAs, we unveiled intricate regulatory mechanisms of lncRNA in early root development and differentiation. Our efforts significantly expand the transcriptome annotations of soybeans, unravel the dynamic landscapes of lncRNAs during early root development and differentiation, and provide valuable resources into the field of soybean root research., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Isoflavones, secondary metabolites with numerous health benefits, are predominantly found in legume seeds, especially soybean; however, their contents in domesticated soybean seeds are highly variable. Wild soybeans are known for higher seed isoflavone contents than cultivars. Here we used experimental and modelling approaches on wild soybean (W05) and cultivated soybean (C08) to delineate factors influencing isoflavone accumulation. We found imported nutrients were converted into storage compounds, with isoflavone accumulation in W05 seeds being faster than in C08 ones. The isoflavone accumulation during seed development was simulated using context-specific cotyledon metabolic models of four developmental stages on cultivar C08, and the metabolic burden imposed by increasing biomass was evaluated. Trade-off analyses between biomass and isoflavone suggest that high biomass requirement in cultivars could limit the reallocation of resources for secondary metabolite production. Isoflavone production in mature seeds was also influenced by biomass compositions. Seeds with higher carbohydrate contents favour isoflavone production, while those with highest protein and oil contents had lowest isoflavone contents. Although seeds could synthesize isoflavones on their own, the predicted fluxes from biosynthesis alone were lower than the empirical levels. Shadow price analyses indicated that isoflavone accumulation depended on both intrinsic biosynthesis and direct contribution from the plant., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

WRKY proteins are a superfamily of transcription factors (TFs) that play multiple roles in plants’ growth, development, and environmental stress response. In this study, a novel WRKY gene called GsWRKY23 that is specifically upregulated in salt-tolerant Glycine soja accession BB52 seedlings was identified by transcriptomic analysis under salt stress. How the physiological functions and mechanisms of the GsWRKY23 gene affect salt tolerance was investigated using transformations of soybean hairy roots and Arabidopsis, including wild-type (WT) and atwrky23-mutant plants. The results showed that GsWRKY23 in the roots, stems, and leaves of BB52, along with its promoter in the cotyledons and root tips of GsWRKY23pro::GUS Arabidopsis seedlings, displayed enhanced induction under salt stress. GsWRKY23 localises to the nucleus and shows transcriptional activation ability in yeast cells. Compared to GsWRKY23-RNAi wild soybean hairy-root composite plants under salt stress, obvious improvements, such as superior growth appearance, plant height and fresh weight (FW), and leaf chlorophyll and relative water content (RWC), were displayed by GsWRKY23-overexpressing (OE) composite plants. Moreover, their relative electrolytic leakage (REL) values and malondialdehyde (MDA) contents in the roots and leaves declined significantly. Most of the contents of Na+ and Cl− in the roots, stems, and leaves of GsWRKY23-OE plants decreased significantly, while the content of K+ in the roots increased, and the content of NO3− displayed no obvious change. Ultimately, the Na+/K+ ratios of roots, stems, and leaves, along with the Cl−/NO3− ratios of roots and stems, decreased significantly. In the transgenic WT-GsWRKY23 and atwrky23-GsWRKY23 Arabidopsis seedlings, the salt-induced reduction in seed germination rate and seedling growth was markedly ameliorated; plant FW, leaf chlorophyll content, and RWC increased, and the REL value and MDA content in shoots decreased significantly. In addition, the accumulation of Na+ and Cl− decreased, and the K+ and NO3− levels increased markedly to maintain lower Na+/K+ and Cl−/NO3− ratios in the roots and shoots. Taken together, these results highlight the role of GsWRKY23 in regulating ionic homeostasis in NaCl-stressed overexpressed soybean composite plants and Arabidopsis seedlings to maintain lower Na+/K+ and Cl−/NO3− ratios in the roots and shoots, thus conferring improved salt tolerance.

We obtained new hybrid soybeans (Hybrid) with different seed coat colors such as green (Hybrid-GR), brown (Hybrid-BR), yellow (Hybrid-YE), and black (Hybrid-BL), by hybridizing β-carotene-enhanced soybeans (BCE; Glycine max L.) containing the phytoene synthase-2A-carotene desaturase gene and wild soybeans (Wild; Glycine soja). This study aimed to analyze metabolic changes between Hybrids using comprehensive metabolite profiling of BCE, Wild, and four Hybrids. The composition and content of metabolites varied based on the type of soybeans. Multivariate and metabolic pathway analyses showed distinct differences among the six soybeans. Hybrid-GR showed accumulation of isoflavones and tocopherols, whereas Hybrid-BL had higher contents of anthocyanins and carotenoids than other Hybrids. The projection to latent structure analysis showed that the most important contributors in enhanced free radical scavenging activity were phenolic compounds such as anthocyanins and flavonoids and isoprenoids such as carotenoids, tocopherols, and phytosterols, assessed using 2,2-diphenyl-1-picrylhydrazyl and 2,2´-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assays, respectively. Based on these results, Hybrid-GR and Hybrid-BL comprising significant quantities of functional compounds such as isoflavones, carotenoids, and anthocyanins are proposed as new breeding candidates. [ABSTRACT FROM AUTHOR]

Modern soybean [Glycine max (L.) Merr] cultivars have low overall genetic variation due to repeated bottleneck events that arose during domestication and from selection strategies typical of many soybean breeding programs. In both public and private soybean breeding programs, the introgression of wild soybean (Glycine soja Siebold and Zucc.) alleles is a viable option to increase genetic diversity and identify new sources for traits of value. The objectives of our study were to examine the genetic architecture responsible for seed protein and oil using a recombinant inbred line (RIL) population derived from hybridizing a G. max line (‘Osage’) with a G. soja accession (PI 593983). Linkage mapping identified a total of seven significant quantitative trait loci on chromosomes 14 and 20 for seed protein and on chromosome 8 for seed oil with LOD scores ranging from 5.3 to 31.7 for seed protein content and from 9.8 to 25.9 for seed oil content. We analyzed 3,015 single F4:9 soybean plants to develop two residual heterozygotes derived near isogenic lines (RHD-NIL) populations by targeting nine SNP markers from genotype-by-sequencing, which corresponded to two novel quantitative trait loci (QTL) derived from G. soja: one for a novel seed oil QTL on chromosome 8 and another for a novel protein QTL on chromosome 14. Single marker analysis and linkage analysis using 50 RHD-NILs validated the chromosome 14 protein QTL, and whole genome sequencing of RHD-NILs allowed us to reduce the QTL interval from ˜16.5 to ˜4.6 Mbp. We identified two genomic regions based on recombination events which had significant increases of 0.65 and 0.72% in seed protein content without a significant decrease in seed oil content. A new Kompetitive allele-specific polymerase chain reaction (KASP) assay, which will be useful for introgression of this trait into modern elite G. max cultivars was developed in one region. Within the significantly associated genomic regions, a total of eight genes are considered as candidate genes, based on the presence of gene annotations associated with the protein or amino acid metabolism/movement. Our results provide better insights into utilizing wild soybean as a source of genetic diversity for soybean cultivar improvement utilizing native traits. [ABSTRACT FROM AUTHOR]

To study the effect of growth temperature on the nutritional components and metabolites of the wild soybean (Glycine soja), we analyzed the nutritional components and metabolic gases of the wild soybean in six accumulated temperature regions of the Heilongjiang Province, China, by gas chromatography–time-of-flight mass spectrometry (GC-TOF-MS). A total of 430 metabolites, including organic acids, organic oxides, and lipids, were identified and analyzed using multivariate statistical analysis, orthogonal partial least squares discriminant analysis, principal component analysis, and cluster analysis. Eighty-seven metabolites significantly differed in the sixth accumulated temperature region compared with the other five accumulated temperature regions. The 40 metabolites (such as threonine (Thr) and lysine (Lys)) were found to be elevated in soybeans from the sixth accumulated temperature zone compared with the other five accumulated temperature zones. Through analyzing the metabolic pathways of these metabolites, amino acid metabolism had the greatest influence on wild soybean quality. The results of the amino acid analysis were consistent with those of the GC-TOF-MS and showed that amino acids in wild soybeans from the sixth accumulated temperature zone significantly differed from those of the other zones. Threonine and lysine were the main substances driving these differences. The growth temperature affected the type and concentrations of metabolites in wild soybeans, and the GC-TOF-MS analysis of the effect of growth temperature on wild soybean metabolites was shown to be feasible.

Wild soybean, also known as Glycine soja Sieb. et Zucc. (GS), has long been known for its various health benefits. Although various pharmacological effects of G. soja have been studied, the effects of GS leaf and stem (GSLS) on osteoarthritis (OA) have not been evaluated. Here, we examined the anti-inflammatory effects of GSLS in interleukin-1β (IL-1β)-stimulated SW1353 human chondrocytes. GSLS inhibited the expression of inflammatory cytokines and matrix metalloproteinases and ameliorated the degradation of collagen type II in IL-1β-stimulated chondrocytes. Furthermore, GSLS played a protective role in chondrocytes by inhibiting the activation of NF-κB. In addition, our in vivo study demonstrated that GSLS ameliorated pain and reversed cartilage degeneration in joints by inhibiting inflammatory responses in a monosodium iodoacetate (MIA)-induced OA rat model. GSLS remarkably reduced the MIA-induced OA symptoms, such as joint pain, and decreased the serum levels of proinflammatory mediators, cytokines, and matrix metalloproteinases (MMPs). Our findings show that GSLS exerts anti-osteoarthritic effects and reduces pain and cartilage degeneration by downregulating inflammation, suggesting that it is a useful therapeutic candidate for OA.

Featured Application: The β-galactosidase enzyme identified in this study can be used to convert isoflavone glycosides to aglycones in wild soybeans. Isoflavone glycosides are commonly biotransformed into isoflavone aglycones due to the superior biological activities of the latter. Wild soybeans contain a higher isoflavone content than domesticated soybeans due to their high level of genetic diversity. In this study, we cloned and characterized a thermostable β-galactosidase from the extreme thermophile Thermoproteus uzoniensis for potential application in isoflavone conversion in Korean wild soybeans. The purified recombinant enzyme exhibited a maximum specific activity of 1103 μmol/min/mg at pH 5.0 and 90 °C with a half-life of 46 h and exists as a homodimer of 113 kDa. The enzyme exhibited the highest activity for p-nitrophenyl (pNP)-β-D-galactopyranoside among aryl glycosides and it hydrolyzed isoflavone glycosides in the order genistin > daidzin > ononin > glycitin. The enzyme completely hydrolyzed 2.77 mM daidzin and 3.85 mM genistin in the seed extract of wild soybean after 80 and 70 min with productivities of 1.86 and 3.30 mM/h, respectively, and 9.89 mM daidzin and 1.67 mM genistin in the root extract after 180 and 30 min, with the highest productivities of 3.30 and 3.36 mM/h, respectively, compared to other glycosidases. Our results will contribute to the industrial production of isoflavone aglycone using wild soybean and this is the first report on the enzymatic production of isoflavone aglycones from isoflavone glycosides in wild soybeans. [ABSTRACT FROM AUTHOR]

Wild soybeans retain many substances significantly reduced or lost in cultivars during domestication. This study utilized LC-MS to analyze metabolites in the seed coats and embryos of wild and cultivated soybeans. 866 and 815 metabolites were identified in the seed extracts of both soybean types, with 35 and 10 significantly differing metabolites in the seed coat and embryos, respectively. The upregulated metabolites in wild soybeans are linked to plant defense, stress responses, and nitrogen cycling. MALDI-MSI results further elucidated the distribution of these differential metabolites in the cotyledons, hypocotyls, and radicles. In addition to their role in physiological processes like growth and response to environmental stimuli, the prevalent terpenoids, lipids, and flavonoids present in wild soybeans exhibit beneficial bioactivities, including anti-inflammatory, antibacterial, anticancer, and cardiovascular disease prevention properties. These findings underscore the potential of wild soybeans as a valuable resource for enhancing the nutritional and ecological adaptability of cultivated soybeans., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Salinity is an important abiotic stress factor that affects growth and yield of soybean. NY36-87 is a wild soybean germplasm with high salt tolerance. In this study, two F2:3 mapping populations derived from NY36-87 and two salt-sensitive soybean cultivars, Zhonghuang39 and Peking, were used to map salt tolerance-related genes. The two populations segregated as 1 (tolerant):2 (heterozygous):1 (sensitive), indicating a Mendelian segregation model. Using simple sequence repeat (SSR) markers together with the bulked segregant analysis (BSA) mapping strategy, we mapped a salt tolerance locus on chromosome 03 in F2:3 population Zhonghuang39×NY36-87 to a 98-kb interval, in which the known gene GmSALT3 co-segregated with the salt tolerance locus. In the F2:3 population of Peking×NY36-87, the dominant salt tolerance-associated gene was detected and mapped on chromosome 18. We named this gene GmSALT18 and fine mapped it to a 241-kb region. Time course analysis and a grafting experiment confirmed that Peking accumulated more Na+ in the shoot via a root-based mechanism. These findings reveal that the tolerant wild soybean line NY36-87 contains salt tolerance-related genes GmSALT3 and GmSALT18 , providing genetic material and a novel locus for breeding salt-tolerant soybean. [ABSTRACT FROM AUTHOR]

Salinity is an important abiotic stress factor that affects growth and yield of soybean. NY36-87 is a wild soybean germplasm with high salt tolerance. In this study, two F2:3 mapping populations derived from NY36-87 and two salt-sensitive soybean cultivars, Zhonghuang39 and Peking, were used to map salt tolerance-related genes. The two populations segregated as 1 (tolerant):2 (heterozygous):1 (sensitive), indicating a Mendelian segregation model. Using simple sequence repeat (SSR) markers together with the bulked segregant analysis (BSA) mapping strategy, we mapped a salt tolerance locus on chromosome 03 in F2:3 population Zhonghuang39×NY36-87 to a 98-kb interval, in which the known gene GmSALT3 co-segregated with the salt tolerance locus. In the F2:3 population of Peking×NY36-87, the dominant salt tolerance-associated gene was detected and mapped on chromosome 18. We named this gene GmSALT18 and fine mapped it to a 241-kb region. Time course analysis and a grafting experiment confirmed that Peking accumulated more Na+ in the shoot via a root-based mechanism. These findings reveal that the tolerant wild soybean line NY36-87 contains salt tolerance-related genes GmSALT3 and GmSALT18, providing genetic material and a novel locus for breeding salt-tolerant soybean.

Cultivation of transgenic soybean lines [Glycine max (L.) Merr.] and the international trade of their seeds has led to an increased focus on the potential risk of gene flow from transgenic to wild soybean (Glycine soja Sieb. & Zucc.) in countries such as China, Russia, Korea, and Japan, which are the centers of soybean domestication. The degree of natural hybridization between three wild soybean accessions and three transgenic soybean lines that produce recombinant proteins (EGF, IGF-1, and TRX) for use in the skin care industry was estimated under field conditions over 2 years. The wild soybean accessions were sown earlier than the transgenic soybean lines to synchronize the flowering periods. One single hybrid was detected among 16,343 progenies in 2017 and 12 among 333,243 progenies, in 2018. The rate of gene flow from the three transgenic soybean lines to the three wild soybean accessions ranged between 0% and 0.0519% in the 2 years of study. Further studies are required to determine whether the transfer of transgenes (egf, igf-1, and trx) from transgenic to wild soybean alters the ecological fitness of hybrid progenies and the consequences of transgene flow. [ABSTRACT FROM AUTHOR]

Water shortage is one of the most important environmental factors limiting crop yield. In this study, we used wild soybean (Glycine soja Sieb. et Zucc.) and soybean (Glycine max (L.) Merr.) seedlings as experimental materials, simulated drought stress using soil gravimetry, measured growth and physiological parameters, and analyzed differentially expressed genes and metabolites in the leaves of seedling by integrated transcriptomics and metabolomics techniques. The results indicate that under water deficit, Glycine soja maintained stable photosynthate by accumulating Mg2+, Fe3+, Mn2+, Zn2+ and B3+, and improved water absorption by increasing root growth. Notably, Glycine soja enhanced linoleic acid metabolism and plasma membrane intrinsic protein (PIP1) gene expression to maintain membrane fluidity, and increased pentose, glucuronate and galactose metabolism and thaumatin protein genes expression to remodel the cell wall, thereby increasing water-absorption to better tolerate to drought stress. In addition, it was found that secondary phenolic metabolism, such as phenylpropane biosynthesis, flavonoid biosynthesis and ascobate and aldarate metabolism were weakened, resulting in the collapse of the antioxidant system, which was the main reason for the sensitivity of Glycine max to drought stress. These results provide new insights into plant adaptation to water deficit and offer a theoretical basis for breeding soybean varieties with drought tolerance. • Maintain stable photosynthetic assimilation function of leaves are important for Glycine soja growth and survival under drought. • Glycine soja tends to maintain membrane fluidity and remodel cell wall composition and structure to cope with drought stress. • The collapse of antioxidant system was the main reason for the sensitivity of Glycine max to drought stress. [ABSTRACT FROM AUTHOR]