Selection on synonymous codon usage in soybean (Glycine max) WRKY genes.

The WRKY transcription factor gene family in soybean [Glycine max (L.) Merr.] (GmWRKY) is critical for the plant's development and stress responses. This study examines the evolutionary dynamics of the GmWRKY gene family, focusing on its synonymous codon usage bias (CUB) in a comprehensive set of 179 coding sequences. CUB was analyzed using various indices, revealing a preference for A/T-ending codons and relatively low codon bias. Codon adaptation index (CAI) analysis suggested that these genes are optimized for efficient translation despite relatively low bias, reflecting a balance between codon diversity and translation efficiency. Neutrality and NC plots indicated that selective forces dominate over mutational forces in shaping codon usage, while selection signature analysis showed purifying selection being prevalent across the gene family. However, episodic positive selection was also detected in certain clades, highlighting potential adaptive diversification in response to environmental stress. Additionally, promoter binding site analysis uncovered correlations between codon usage and transcriptional regulation, indicating a context-dependent relationship between CUB and gene expression. Phylogenetic analysis identified 11 well-supported clades in the modern GmWRKY gene family and ancestral sequence reconstruction revealed more relaxed codon preferences and reduced selection constraints in modern GmWRKY genes, potentially linked to neofunctionalization and adaptation to environmental changes. These findings provide a framework for optimizing gene expression in transgenic soybean crops with resilience. Further functional validation of positively selected genes is recommended to elucidate their role in stress responses.

Assessment of soybean productivity and its changing factors in Japan based on the production cost statistics.

Soybean (Glycine max [L.] Merr.) yields have remained below 2.0 t ha-1 for over 30 years in Asian countries, indicating long-term stagnation in productivity and production technology. This study aimed to measure the total factor productivity (TFP) of soybean production in Japan and to assess the factors affecting TFP and yield. The Färe-Primont index of TFP was measured for two agroclimatic regions using soybean production cost statistics from 1987 to 2015 to analyze the regression of TFP and yield with per-farm land size, time trends, and production-related input variables. The TFP increased by 1.5-2.4 % annually in the two regions, despite an annual decrease of 0.7 % in country's average yield. The TFP in the subarctic Hokkaido region improved by 9-15 % due to the land-size increase and progress of time, i.e., technological progress, during the period. While in the temperate main-island region, a 14 % TFP increase induced by increased land size was largely offset by the time-progress effect (-11 %), i.e., technological retrogression. Similar time-progress effects observed on yield indicated that technological changes occurred, with respect to cultivation methods. The TFP-improving land-size increase adversely resulted in a 9 % yield decrease in the main-island region accounting for 85 % of soybean cultivation area in Japan. The results further showed that TFP improved by saving production inputs, such as fertilizer, per unit area in both regions, and the yield rose with increased inputs in seed, agrochemicals, and rental services, depending on the region. This study revealed continual soybean TFP improvements across Japan due to land-size increases and input saving in addition to the regionally biased progress in cultivation technologies. The implications of the results are discussed from the perspective of improving TFP and yield while increasing the per-farm land size.

Short-term reoxygenation is not enough for the recovery of soybean plants exposed to saline waterlogging.

The ability of plants to recover after stressful events is crucial for resuming growth and development and is a key trait when studying stress tolerance. However, there is a lack of information on the physiological responses and the time required to restore homeostasis after the stress experience. This study aimed to (i) enhance understanding of soybean photosynthesis performance during saline waterlogging and (ii) investigate the effects of this combined stress during the reoxygenation and recovery period. Soybean plants (cultivar PELBR10-6049 RR) were subjected to waterlogging, NaCl, or hypoxia + NaCl for 3 and 6 days. Afterward, plants were drained and allowed to recover for an additional two (short-term) and seven days (long-term). Compared to plants exposed to single stress, the combined hypoxia + NaCl treatment resulted in a lower net CO2 assimilation rate, ФPSII, and levels of photosynthetic pigments during the waterlogging period. Furthermore, hypoxia + NaCl increased foliar electrolyte leakage during waterlogging. In response to short-term reoxygenation, these negative effects were amplified, while prolonged reoxygenation resulted in a slight increase in biomass accumulation. In conclusion, full recovery was not achieved under any condition during the reoxygenation periods tested. Notably, the brief reoxygenation phase imposed greater stress than the initial stress conditions for plants facing combined stress. Although extended recovery increased biomass accumulation, it remained lower in plants previously subjected to saline waterlogging.

Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium.

Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.

Identification of Linalool Disaccharide Glycoside (Linalyl ß-Vicianoside) in Soybean Leaves and Its Implication for Herbivore Resistance.

Linalool is anticipated to have significant ecological roles. In this study, linalyl 6-O-α-arabinopyranosyl-ß-D-glucopyranoside (linalyl ß-vicianoside: LinVic) was synthesized, and a linalool diglycoside purified from soybean leaves was identified as LinVic by using liquid chromatography-mass spectrometry. High levels of LinVic were detected in leaves and sepals during soybean plant growth. The LinVic content did not significantly increase following methyl jasmonate treatment of the leaves, indicating that its synthesis is independent of the jasmonic acid signaling pathway. In addition to LinVic, soybean also contains 1-octen-3-yl primeveroside. We treated soybean leaves with vaporized linalool and 1-octen-3-ol to determine whether the glycosylation system discriminates between these two volatile alcohols. Linalool treatment resulted in the accumulation of LinVic, while 1-octen-3-ol treatment caused little change in the amount of 1-octen-3-yl primeveroside, suggesting discrimination between these compounds. Linalool-treated soybean leaves exhibited increased resistance against common cutworms, indicating that LinVic may contribute to herbivore resistance.

Knockdown of ß-conglycinin α' and α subunits alters seed protein composition and improves salt tolerance in soybean.

Soybean is an important plant source of protein worldwide. Increasing demands for soybean can be met by improving the quality of its seed protein. In this study, GmCG-1, which encodes the ß-conglycinin α' subunit, was identified via combined genome-wide association study and transcriptome analysis. We subsequently knocked down GmCG-1 and its paralogues GmCG-2 and GmCG-3 with CRISPR-Cas9 technology and generated two stable multigene knockdown mutants. As a result, the ß-conglycinin content decreased, whereas the 11S/7S ratio, total protein content and sulfur-containing amino acid content significantly increased. Surprisingly, the globulin mutant exhibited salt tolerance in both the germination and seedling stages. Little is known about the relationship between seed protein composition and the salt stress response in soybean. Metabonomics and RNA-seq analysis indicated that compared with the WT, the mutant was formed through a pathway that was more similar to that of active salicylic acid biosynthesis; however, the synthesis of cytokinin exhibited greater defects, which could lead to increased expression of plant dehydrin-related salt tolerance proteins and cell membrane ion transporters. Population evolution analysis suggested that GmCG-1, GmCG-2, and GmCG-3 were selected during soybean domestication. The soybean accessions harboring GmCG-1Hap1 presented relatively high 11S/7S ratios and relatively high salt tolerance. In conclusion, knockdown of the ß-conglycinin α and α' subunits can improve the nutritional quality of soybean seeds and increase the salt tolerance of soybean plants, providing a strategy for designing soybean varieties with high nutritional value and high salt tolerance.

Genome-wide identification and tissue expression pattern analysis of TPS gene family in soybean (Glycine max).

The terpene synthase (TPS) plays a pivotal roles in plant growth, development, and enhancing resilience against environmental stresses. Despite this, the bioinformatics analysis of the TPS family gene in soybean (Glycine max) is lacking. In this study, we investigated 36 GmTPS members in soybean, exhibiting a diverse range of protein lengths, spanning from 144 to 835 amino acids. A phylogenetic tree was constructed from these GmTPS genes revealed a classification into five distinct subgroups: Group1, Group2, Group3, Group4 and Group5. Notably, within each subgroup, we identified the motifs of GmTPS proteins were similar, although variations existed among different subfamilies. Gene duplication events analysis demonstrated that TPS genes expand differently in G. max, A. thaliana and O. sativa. Among, both tandem duplication and Whole genome duplication contributive to the expansion of TPS genes in G. max, and Whole genome duplication played a major role. Moreover, the cis-element analysis suggested that TPS is related to hormone signals, plant growth and development and environmental stress. Yeast two-hybrid (Y2H) assay results indicated TPS protein may form heterodimer to function, or may form complex with P450 proteins to function. RNA-seq results revealed a higher expression of most GmTPS genes in flowers, suggesting their potential contribution to flower development. Collectively, these findings offer a provide a holistic knowledge of the TPS gene family in soybean and will facilitate further characterization of TPSs effectively.

Dynamic Landscapes of Long Noncoding RNAs During Early Root Development and Differentiation in Glycine max and Glycine soja.

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.

Identification of potential auxin response candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis.

Introduction: Throughout domestication, crop plants have gone through strong genetic bottlenecks, dramatically reducing the genetic diversity in today's available germplasm. This has also reduced the diversity in traits necessary for breeders to develop improved varieties. Many strategies have been developed to improve both genetic and trait diversity in crops, from backcrossing with wild relatives, to chemical/radiation mutagenesis, to genetic engineering. However, even with recent advances in genetic engineering we still face the rate limiting step of identifying which genes and mutations we should target to generate diversity in specific traits. Methods: Here, we apply a comparative evolutionary approach, pairing phylogenetic and expression analyses to identify potential candidate genes for diversifying soybean (Glycine max) canopy cover development via the nuclear auxin signaling gene families, while minimizing pleiotropic effects in other tissues. In soybean, rapid canopy cover development is correlated with yield and also suppresses weeds in organic cultivation. Results and discussion: We identified genes most specifically expressed during early canopy development from the TIR1/AFB auxin receptor, Aux/IAA auxin co-receptor, and ARF auxin response factor gene families in soybean, using principal component analysis. We defined Arabidopsis thaliana and model legume species orthologs for each soybean gene in these families allowing us to speculate potential soybean phenotypes based on well-characterized mutants in these model species. In future work, we aim to connect genetic and functional diversity in these candidate genes with phenotypic diversity in planta allowing for improvements in soybean rapid canopy cover, yield, and weed suppression. Further development of this and similar algorithms for defining and quantifying tissue- and phenotype-specificity in gene expression may allow expansion of diversity in valuable phenotypes in important crops.

Genetic variability increase by gamma irradiation of soybean seeds.

The increase of genetic variability by the appearance of new genes of agronomic interest may be favored by the use of gamma radiation. The objective of this study was to evaluate different doses of gamma irradiation on dry seeds of VX04-5692 soybean line, aiming to increase the genetic variability and, with this, the identification of possible mutant plants. The doses of 0, 50, 150 and 250 Gy of gamma radiation were applied from a60Co source. The newly irradiated seeds were sown in the field, giving rise to the M1 cycle. Selected plants originated the M2 cycle. The number of seedlings was counted on the 21st day after sowing. Ten plants of each row were identified and evaluated for the various agronomic characteristics and for chemical composition. The data were submitted to analysis of variance. The F test was applied and the results were presented by boxplots and biplot (canonical variables). There was effect of gamma radiation doses at plant height at full bloom and maturity, number of nodes, pods with one seed and seeds per pod. The use of gamma radiation increases the variability in soybean, with consequent increase in the probabilities of identification of new mutants and gains in the chemical composition, useful for breeding programs that aim at better agronomic performance and gains in oil and protein contents. More satisfactory results in the generation of variability are obtained by the application of gamma radiation on soybean dry seeds between 50 and 150 Gy.

Statement complementing the EFSA Scientific Opinion on application (EFSA-GMO-NL-2015-126) for authorisation of food and feed containing, consisting of and produced from genetically modified soybean MON 87705 × MON 87708 × MON 89788.

Following a request from the European Commission, the GMO Panel assessed additional information related to the application for authorisation of food and feed containing, consisting of and produced from genetically modified soybean MON × MON 87708 × MON 89788 (EFSA-GMO-NL-2015-126). The applicant conducted a 90-day feeding study on GM soybean MON 87705 and provided a proposal for post-market monitoring considering the altered fatty acid profile of GM soybean MON 87705 × MON 87708 × MON 89788, to fulfil the deficiencies identified by EFSA GMO Panel, addressing elements that remained inconclusive from a previous EFSA scientific opinion issued in 2020. The GMO Panel concludes that the 90-day feeding study on GM soybean MON 87705 is in line with the requirements of Regulation (EU) No 503/2013 and that no treatment-related adverse effects were observed in rats after feeding diets containing soybean MON 87705 meals at 30% or 15% for 90 days. The GMO Panel reiterates the recommendation for a PMM for food in accordance with Regulation (EC) No 1829/2003 and Regulation (EU) No 503/2013 and concludes that the proposal provided by the applicant is in line with the recommendations described for the PMM plan of soybean MON 87705 × MON 87708 × MON 89788 in the adopted scientific opinion. Taking into account the previous assessment and the new information, the GMO Panel concludes that soybean MON 87705 × MON 87708 × MON 89788, as assessed in the scientific opinion on application EFSA-GMO-NL-2015-126 and in the supplementary toxicity study, is as safe as its non-GM comparator and the non-GM reference varieties tested and does not represent a nutritional concern in humans and animals, within the scope of this application.

High-throughput phenotyping in maize and soybean genotypes using vegetation indices and computational intelligence.

Building models that allow phenotypic evaluation of complex agronomic traits in crops of global economic interest, such as grain yield (GY) in soybean and maize, is essential for improving the efficiency of breeding programs. In this sense, understanding the relationships between agronomic variables and those obtained by high-throughput phenotyping (HTP) is crucial to this goal. Our hypothesis is that vegetation indices (VIs) obtained from HTP can be used to indirectly measure agronomic variables in annual crops. The objectives were to study the association between agronomic variables in maize and soybean genotypes with VIs obtained from remote sensing and to identify computational intelligence for predicting GY of these crops from VIs as input in the models. Comparative trials were carried out with 30 maize genotypes in the 2020/2021, 2021/2022 and 2022/2023 crop seasons, and with 32 soybean genotypes in the 2021/2022 and 2022/2023 seasons. In all trials, an overflight was performed at R1 stage using the UAV Sensefly eBee equipped with a multispectral sensor for acquiring canopy reflectance in the green (550 nm), red (660 nm), near-infrared (735 nm) and infrared (790 nm) wavelengths, which were used to calculate the VIs assessed. Agronomic traits evaluated in maize crop were: leaf nitrogen content, plant height, first ear insertion height, and GY, while agronomic traits evaluated in soybean were: days to maturity, plant height, first pod insertion height, and GY. The association between the variables were expressed by a correlation network, and to identify which indices are best associated with each of the traits evaluated, a path analysis was performed. Lastly, VIs with a cause-and-effect association on each variable in maize and soybean trials were adopted as independent explanatory variables in multiple regression model (MLR) and artificial neural network (ANN), in which the 10 best topologies able to simultaneously predict all the agronomic variables evaluated in each crop were selected. Our findings reveal that VIs can be used to predict agronomic variables in maize and soybean. Soil-adjusted Vegetation Index (SAVI) and Green Normalized Dif-ference Vegetation Index (GNDVI) have a positive and high direct effect on all agronomic variables evaluated in maize, while Normalized Difference Vegetation Index (NDVI) and Normalized Difference Red Edge Index (NDRE) have a positive cause-and-effect association with all soybean variables. ANN outperformed MLR, providing higher accuracy when predicting agronomic variables using the VIs select by path analysis as input. Future studies should evaluate other plant traits, such as physiological or nutritional ones, as well as different spectral variables from those evaluated here, with a view to contributing to an in-depth understanding about cause-and-effect relationships between plant traits and spectral variables. Such studies could contribute to more specific HTP at the level of traits of interest in each crop, helping to develop genetic materials that meet the future demands of population growth and climate change.

Morphological, physiological, and biochemical responses of three different soybean (Glycine max L.) varieties under salinity stress conditions.

Salinity is one of the most detrimental factors for the growth performance and productivity of crops worldwide. Therefore, understanding crop responses or growth potentials and their effectiveness in salinity mitigation is highly important for the selection of salinity-tolerant plant varieties. In this study, the effects of salinity at various stress levels (0 mM, 50 mM, 100 mM, and 150 mM NaCl) on the morphological, physiological, and biochemical parameters of three soybean varieties ('Afigat', 'Gishama', and 'Pawi-2') were investigated. The results showed that salinity significantly reduced morphological traits including plant height, number of leaves per plant, stem thickness, shoot and root length, and fresh and dry weight. This reduction was more prominent in the 'Afigat' variety for all of these traits except shoot and root length. The concentrations of chlorophyll a and b decreased with increasing salinity. In addition, salinity significantly increased leaf electrolyte leakage (EL), lipid peroxidation, proline accumulation, and phenol and flavonoid content. The 'Pawi-2' variety was more tolerant than the other studied varieties in terms of membrane stability (less EL and a low malondialdehyde content) and proline, phenol, and flavonoid accumulation. Therefore, 'Pawi-2' may be considered as the most salt-tolerant variety in comparison with the other studied soybean varieties. Further complementary studies in field conditions including anatomical parameters are needed to confirm these findings.

Detection and validation of QTLs for green stem disorder of soybean (Glycine max (L.) Merr.).

In mechanically harvested soybean, green stem disorder (GSD) is an undesirable trait that causes green-stained seeds, which are graded lower in Japan. To obtain DNA markers for reduced GSD, we conducted a quantitative trait locus (QTL) analysis for 2 years using F4 and F5 lines from a cross between 'Suzuotome' (less GSD) and 'Fukuyutaka' (more GSD). We validated the effect of a detected QTL for GSD by first identifying F4 or F5 plants in which one or more markers in the QTL region were heterozygous. The F5 or F6 progeny of each plant was used to form a pair consisting of two groups in which the QTL region was homozygous for either the 'Suzuotome' or 'Fukuyutaka' allele in a similar genetic background, and the two groups within each pair were compared for GSD. Over 3 years of testing, the 'Suzuotome' allele of a QTL on chromosome 6 was found to reduce the level of GSD. This novel QTL was mapped to the region around DNA marker W06_0130, and was not closely linked to QTLs for important agronomic traits including yield components. Using this marker, the low level of GSD from 'Suzuotome' could be conferred to 'Fukuyutaka' or other high-GSD cultivars.

Beneficial or detrimental? How nickel application alters the ionome of soybean plants.

The use of nickel (Ni) in agriculture may represent one of the most significant cases of plant hormesis ever reported, as plants exhibit both positive and negative responses depending on the level of exposure to this element. For a more comprehensive understanding of this effect, the next step is to conduct studies on the dynamics of pre-existing chemical elements in the system (ionomic profile), especially when introducing Ni as a novel nutrient for the plants. This micronutrient is of particular interest to the fertilization of leguminous plants, such as the soybean, due to its additional effects on the biological nitrogen fixation process. This study thus evaluated the influence of five doses of Ni (0.0, 0.5, 1.0, 3.0, and 9.0 mg of Ni kg-1) on the ionomic profile of soybean genotypes using modern quantification techniques. The results revealed that the addition of Ni reduced the concentration of cationic micronutrients manganese (Mn), iron (Fe), zinc (Zn), and copper (Cu), while it increased the concentration of macronutrients nitrogen (N) and magnesium (Mg). The application of Ni also resulted in a reduction of the potentially toxic element aluminum (Al). Correlations were also observed for these elements, indicating that Ni could be a controlling agent in elemental absorption and translocation. The ionome of the leaf tissues exhibited the most significant alterations, followed by the grains, nodules, and roots. Exogenous agronomic doses of Ni proved beneficial for the growth and production of soybean plants, although a genotypic effect was observed. The treatment with 9.0 mg of Ni kg-1, resulted in a new ionomic profile related to toxicity, demonstrating suboptimal plant development. Thus, the application of Ni in appropriate doses had a significant impact on the ionomic profile of soybeans, improving plant development and implying resistance to potentially toxic elements such as Al.

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean.

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (>20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the 'Williams' haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of 'Fiskeby III,' a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

Contextualized Metabolic Modelling Revealed Factors Affecting Isoflavone Accumulation in Soybean Seeds.

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.

Piriformospora indica alleviates soda saline-alkaline stress in Glycine max by modulating plant metabolism.

Soil salinization is one of the major factors limiting agricultural production. Utilizing beneficial microorganisms like Piriformospora indica (P. indica) to enhance plant tolerance to abiotic stresses is a highly effective method, but the influence of P. indica on the growth of soybean in natural saline-alkaline soil remains unclear. Therefore, we investigated the effects of non-inoculation, P. indica inoculation, and fertilization on the growth, antioxidant defense, osmotic adjustment, and photosynthetic gas exchange parameters of soybean under two different levels of saline-alkaline stress in non-sterilized natural saline-alkaline soil. The study found that: 1) P. indica inoculation significantly promoted soybean growth, increasing plant height, root length, and biomass. Under mildly saline-alkaline stress, the increases were 11.5%, 16.0%, and 14.8%, respectively, compared to non-inoculated treatment. Under higher stress, P. indica inoculation achieved the same level of biomass increase as fertilization, while fertilization only significantly improved stem diameter. 2) Under saline-alkaline stress, P. indica inoculation significantly increased antioxidant enzyme activities and reduced malondialdehyde (MDA) content. Under mildly stress, MDA content was reduced by 47.1% and 43.3% compared to non-inoculated and fertilized treatments, respectively. Under moderate stress, the MDA content in the inoculated group was reduced by 29.9% and 36.6% compared to non-inoculated and fertilized treatments, respectively. Fertilization only had a positive effect on peroxidase (POD) activity. 3) P. indica inoculation induced plants to produce more osmotic adjustment substances. Under mildly stress, proline, soluble sugars, and soluble proteins were increased by 345.7%, 104.4%, and 6.9%, respectively, compared to non-inoculated treatment. Under higher stress, the increases were 75.4%, 179.7%, and 12.6%, respectively. Fertilization had no significant positive effect on proline content. 4) With increasing stress, soybean photosynthetic capacity in the P. indica-inoculated treatment was significantly higher than in the non-inoculated treatment, with net photosynthetic rate increased by 14.8% and 37.0% under different stress levels. These results indicate that P. indica can enhance soybean's adaptive ability to saline-alkaline stress by regulating ROS scavenging capacity, osmotic adjustment substance content, and photosynthetic capacity, thereby promoting plant growth. This suggests that P. indica has great potential in improving soybean productivity in natural saline-alkaline soils.

Differential symbiotic compatibilities between rhizobium strains and cultivated and wild soybeans revealed by anatomical and transcriptome analyses.

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.

Formulation of nutritious and functional meal-based biscuits from mixture of soybean, papaya fruit pulp, and baobab fruit pulp flours.

Background and objective: The current trend in the formulation of convenience foods like biscuits is directed towards using local ingredients endowed with health benefits effects. The present study aimed at valorizing local crops and fruits as substitutes for wheat flour (WF) and sugar in the formulation of healthy, nutritious and functional meal-based biscuits. Methods: Soybean (Glycine max L.), papaya fruit pulp (Carica papaya L.) and baobab fruit pulp (Adansonia digitata L.) flours were produced, characterized, and used to formulate biscuits following a simplex centroid mixing design. The physicochemical, microbiological, sensory and antioxidant properties of the biscuits were assessed. Results: The results showed that protein and lipid contents of the biscuits increased significantly (p < 0.05) with the proportion of soybean flour (SF) in the formulation. The significant increase (p < 0.05) in the mineral content of the biscuits was proportional to the incorporation of papaya fruit pulp (PFPF) and baobab fruit pulp (BFPF) flours in the formulation. The energetic value of the formulated biscuits was higher than those made with 100 % WF. The incorporation of SF and BFPF contributed to a significant increase (p < 0.05) in the crude fibres' content of biscuits. Biscuits made with SF, PFPF and BFPF were safe for human consumption. They were accepted by the panelists; rich in bioactive compounds (total phenolic, flavonoids), and displayed high antioxidant activities. The optimization procedure revealed that the optimum formulation (with the highest desirability of 0.81) was WF 25 g, SF 51.86 g, PFPF 8.06 g and BFPF 15.06 g. Conclusion: This study indicates that baobab fruit pulp, papaya fruit pulp and soybean flours can be used as a substitute for WF in the formulation of functional biscuits. Significance of the research: This study suggests that the formulated meal-based biscuits might have the potential to be used to fight/prevent malnutrition and cardiometabolic diseases, and to boost the immune system while reducing the dependence on wheat.