Flowering time regulator qFT13-3 involved in soybean adaptation to high latitudes

Soybean is a short-day plant that typically flowers earlier when exposed to short-day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome-wide association studies (GWAS) using two re-sequencing datasets that included 113 wild soybeans (G. soja) and 1192 cultivated soybeans (G. max), respectively, and simultaneously identified a candidate flowering gene, qFT13-3, which encodes a protein homologous to the pseudo-response regulator (PRR) transcription factor. We identified four major haplotypes of qFT13-3 in the natural population, with haplotype H4 (qFT13-3H4) being lost during domestication, while qFT13-3H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13-3H1 were located in high-latitude regions. Knockout of qFT13-3 accelerated flowering and maturity time under long-day conditions, indicating that qFT13-3 functions as a flowering inhibitor. Our results also showed that qFT13-3 directly downregulates the expression of GmELF3b-2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13-3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13-3 can be utilized for the breeding of high-yield cultivars with a short maturity time suitable for high latitudes.

GmMATE100 Is Involved in the Import of Soyasaponins A and B into Vacuoles in Soybean Plants (Glycine max L.)

Triterpenoid saponins, synthesized via the mevalonic acid (MVA) pathway in the cytoplasm, provide protection against pathogens and pests in plants and health benefits for humans. However, the mechanisms by which triterpenoid saponins are transported between cellular compartments remain uncharacterized. Here, we characterize a tonoplast localized multidrug and toxic compound extrusion transporter, GmMATE100 (encoded by Glyma.18G143700), from soybean (Glycine max L.). GmMATE100 is co-expressed with soyasaponin biosynthetic genes, and its expression was induced by MeJA treatment, which also led to soyasaponin accumulation in soybean roots. GmMATE100 efficiently transports multiple type-B soyasaponins as well as type-A soyasaponins with low affinity from the cytosol to the vacuole in a yeast system. The GmMATE100 loss-of-function mutant showed a significant decrease in type-A and type-B soyasaponin contents in soybean roots. This study not only characterized the first soybean triterpenoid saponin transporter but also provided new knowledge for the rational engineering of soyasaponin content and composition in soybean plants to modulate their levels within crop environments.

Functional study of the soybean stamen-preferentially expressed gene GmFLA22a in regulating male fertility

China has a high dependence on soybean imports, yield increase at a faster rate is an urgent problem that need to be solved at present. The application of heterosis is one of the effective ways to significantly increase crop yield. In recent years, the development of an intelligent male sterility system based on recessive nuclear sterile genes has provided a potential solution for rapidly harnessing the heterosis in soybean. However, research on male sterility genes in soybean has been lagged behind. Based on transcriptome data of soybean floral organs in our research group, a soybean stamen-preferentially expressed gene GmFLA22a was identified. It encodes a fasciclin-like arabinogalactan protein with the FAS1 domain, and subcellular localization studies revealed that it may play roles in the endoplasmic reticulum. Take advantage of the gene editing technology, the Gmfla22a mutant was generated in this study. However, there was a significant reduction in the seed-setting rate in the mutant plants at the reproductive growth stage. The pollen viability and germination rate of Gmfla22a mutant plants showed no apparent abnormalities. Histological staining demonstrated that the release of pollen grains in the mutant plants was delayed and incomplete, which may due to the locule wall thickening in the anther development. This could be the reason of the reduced seed-setting rate in Gmfla22a mutants. In summary, our study has preliminarily revealed that GmFLA22a may be involved in regulating soybean male fertility. It provides crucial genetic materials for further uncovering its molecular function and gene resources and theoretical basis for the utilization of heterosis in soybean.

Tradeoffs among root functional traits for phosphorus acquisition in 13 soybean genotypes contrasting in mycorrhizal colonization

BACKGROUND AND AIMS

Plants have adapted to acquire phosphorus (P) primarily through advantageous root morphologies, responsive physiological pathways, and associations with mycorrhizal fungi. Yet, to date, little information exists on how variation in arbuscular mycorrhizal (AM) colonization is coordinated with root morphological and physiological traits to enhance P acquisition.

METHODS

Thirteen root functional traits associated with P acquisition were characterized at full bloom stage in pot cultures under low soil P availability conditions for 13 soybean genotypes contrasting in AM colonization.

KEY RESULTS

Significant variation in root functional traits was observed in response to low P stress among the 13 tested soybean genotypes contrasting in AM colonization. Genotypes with low AM colonization exhibited greater root proliferation but with less advantageous root physiological characteristics for P acquisition. In contrast, genotypes with high AM colonization exhibited less root growth but higher phosphatase activities and carboxylate content in the rhizosheath. Root dry weights, and contents of carbon and P were positively correlated with root morphological traits of different root orders and whole root systems, and were negatively correlated with AM colonization of fine roots and whole root systems, as well as, rhizosheath phosphatase activities and carboxylate contents. These results taken in combination with significant positive correlation between plant P content and root morphological traits indicate that root morphological traits play a primary role in soybean P acquisition.

CONCLUSIONS

The results suggest that efficient P acquisition involves tradeoffs among carbon allocation to root proliferation, mycorrhizal symbiosis, or P-mobilizing exudation. Complementarity and complexity in the selection of P acquisition strategies was notable among soybean genotypes contrasting in AM colonization, which is closely related to plant C budgeting.

Measurement of elements by portable x-ray fluorescence spectrometry for the study of adsorption processes: the case of Pb2+adsorption on soybean straw biochar

This study evaluated the reliability of portable X-ray fluorescence (pXRF) in Pb2+adsorption kinetics and isotherm experiments using soybean straw biochar. The research aimed to compare pXRF results with those obtained through traditional atomic absorption spectrometry (AAS). Soybean straw biochar, produced at 400 °C, was employed as the adsorbent for Pb2+. The efficiency of adsorption was assessed using Langmuir and Freundlich models. The kinetics of Pb2+adsorption was analysed through pseudo-first-order and pseudo-second-order models. The pseudo-second-order model described the kinetics of Pb2+adsorption on biochar better than the pseudo-first order model. Importantly, the pXRF technique demonstrated comparable results to those of AAS, making it a reliable and resource-efficient method for studying Pb2+kinetics. The results of the isotherm analyses fit the Langmuir model, indicating a desirable and irreversible adsorption of Pb2+on biochar. PXRF measurements on biochar allowed simultaneous observations of Pb2+adsorption and K+and Ca2+desorption, highlighting ionic exchange as the primary adsorption mechanism. In conclusion, our results showcased the applicability of pXRF for Pb+2adsorption studies in biochars, offering a valuable alternative to traditional methods. The findings contribute to the understanding of biochar as an effective adsorbent for heavy metals, emphasizing the potential of pXRF for cost-effective and efficient environmental research. In this study, we present a novel and detailed procedure that will allow other researchers to continue their studies on Pb2+adsorption on biochar or similar matrices, significantly reducing the resources and time used and enabling the simultaneous study of the behavior of other ions participating in the process.

Knockout of miR396 genes increases seed size and yield in soybean

Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed. miR396 genes have been shown to negatively regulate grain size in rice, but whether miR396 family members may function in a similar manner in soybean is unknown. Here, we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean miR396 genes through genome editing with clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas)12SF01 in the elite soybean cultivar Zhonghuang 302 (ZH302). Four triple mutants (mir396aci, mir396acd, mir396adf, and mir396cdf), two quadruple mutants (mir396abcd and mir396acfi), and two quintuple mutants (mir396abcdf and mir396bcdfi) were characterized. We found that plants of all the mir396 mutants produced larger seeds compared to ZH302 plants. Field tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower latitude. In contrast, mir396abcdf and mir396bcdfi plants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues, but they are suited for low latitude growth zones with increased yield without lodging problems. Taken together, our study demonstrated that loss-of-function of miR396 genes leads to significantly enlarged seed size and increased yield in soybean, providing valuable germplasms for breeding high-yield soybean.

Hopanoid lipids promote soybean-Bradyrhizobium symbiosis

The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote Bradyrhizobium symbioses with tropical legumes. To characterize hopanoids in Bradyrhizobium symbiosis with soybean, we validated a recently published cumate-inducible hopanoid mutant of Bradyrhizobium diazoefficiens USDA110, Pcu-shc::∆shc. GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress. In planta, Pcu-shc::∆shc is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within the host tissue. RNA-seq revealed that hopanoid loss reduces the expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances the expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to B. diazoefficiens in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility.

A major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between Bradyrhizobium diazoefficiens USDA110, an important commercial inoculant strain, and its economically significant host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.

Application of electronic nose and machine learning used to detect soybean gases under water stress and variability throughout the daytime

The development of non-invasive methods and accessible tools for application to plant phenotyping is considered a breakthrough. This work presents the preliminary results using an electronic nose (E-Nose) and machine learning (ML) as affordable tools. An E-Nose is an electronic system used for smell global analysis, which emulates the human nose structure. The soybean (Glycine Max) was used to conduct this experiment under water stress. Commercial E-Nose was used, and a chamber was designed and built to conduct the measurement of the gas sample from the soybean. This experiment was conducted for 22 days, observing the stages of plant growth during this period. This chamber is embedded with relative humidity [RH (%)], temperature (°C), and CO2 concentration (ppm) sensors, as well as the natural light intensity, which was monitored. These systems allowed intermittent monitoring of each parameter to create a database. The soil used was the red-yellow dystrophic type and was covered to avoid evapotranspiration effects. The measurement with the electronic nose was done daily, during the morning and afternoon, and in two phenological situations of the plant (with the healthful soy irrigated with deionized water and underwater stress) until the growth V5 stage to obtain the plant gases emissions. Data mining techniques were used, through the software "Weka™" and the decision tree strategy. From the evaluation of the sensors database, a dynamic variation of plant respiration pattern was observed, with the two distinct behaviors observed in the morning (~9:30 am) and afternoon (3:30 pm). With the initial results obtained with the E-Nose signals and ML, it was possible to distinguish the two situations, i.e., the irrigated plant standard and underwater stress, the influence of the two periods of daylight, and influence of temporal variability of the weather. As a result of this investigation, a classifier was developed that, through a non-invasive analysis of gas samples, can accurately determine the absence of water in soybean plants with a rate of 94.4% accuracy. Future investigations should be carried out under controlled conditions that enable early detection of the stress level.

Comparative Morpho-Physiological, Biochemical, and Gene Expressional Analyses Uncover Mechanisms of Waterlogging Tolerance in Two Soybean Introgression Lines

Waterlogging is one of the key abiotic factors that severely impedes the growth and productivity of soybeans on a global scale. To develop soybean cultivars that are tolerant to waterlogging, it is a prerequisite to unravel the mechanisms governing soybean responses to waterlogging. Hence, we explored the morphological, physiological, biochemical, and transcriptional changes in two contrasting soybean introgression lines, A192 (waterlogging tolerant, WT) and A186 (waterlogging sensitive, WS), under waterlogging. In comparison to the WT line, waterlogging drastically decreased the root length (RL), shoot length (ShL), root fresh weight (RFW), shoot fresh weight (ShFW), root dry weight (RDW), and shoot dry weight (ShDW) of the WS line. Similarly, waterlogging inhibited soybean plant growth by suppressing the plant's photosynthetic capacity, enhancing oxidative damage from reactive oxygen species, and decreasing the chlorophyll content in the WS line but not in the WT line. To counteract the oxidative damage and lipid peroxidation, the WT line exhibited increased activity of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), as well as higher levels of proline content than the WS line. In addition, the expression of antioxidant enzyme genes (POD1, POD2, FeSOD, Cu/ZnSOD, CAT1, and CAT2) and ethylene-related genes (such as ACO1, ACO2, ACS1, and ACS2) were found to be up-regulated in WT line under waterlogging stress conditions. In contrast, these genes showed a down-regulation in their expression levels in the stressed WS line. The integration of morpho-physiological, biochemical, and gene expression analyses provide a comprehensive understanding of the responses of WT and WS lines to waterlogging conditions. These findings would be beneficial for the future development of soybean cultivars that can withstand waterlogging.

Agrobacterium-Mediated Transformation of the Dwarf Soybean MiniMax

This study aims to establish an Agrobacterium-mediated transformation system for use with the 'MiniMax'soybean cultivar. MiniMax is a mutant soybean whose growth cycle is around 90 days, half that of most other soybean varieties, making it an optimal model cultivar to test genes of interest before investing in modification of elite lines. We describe an efficient protocol for Agrobacterium-mediated transformation using MiniMax seeds. It uses a modified 'half seed' regeneration protocol for transgenic soybean production, utilizing the rapid generation MiniMax variety to obtain T1 seeds in approximately 145 days. Addition of phloroglucinol (PG) to the regeneration protocol was key to obtaining high-efficiency rooting of the regenerated shoots. Transfer to soil was accomplished using an organic soil amendment containing nutrients and mycorrhiza for plants to thrive in the greenhouse. This combination of genotype and stimulants provides a transformation protocol to genetically engineer MiniMax seeds with a transgenic lab-to-greenhouse production efficiency of 4.0%. This is the first report of MiniMax soybean whole plant transformation and heritable T1 transmission. This protocol provides an ideal resource for enhancing the genetic transformation of any soybean cultivar.

Long term co-application of biochar and fertilizer could increase soybean yield under continuous cropping: insights from photosynthetic physiology

BACKGROUND

Photosynthesis is the key to crop yield. The effect of biochar on photosynthetic physiology and soybean yield under continuous cropping is unclear. We conducted a long-term field experiment to investigate the effects of co-application of biochar and fertilizer (BCAF) on these parameters. Five treatments were established: F2 (fertilizer), B1F1 (3 t hm-2 biochar plus fertilizer), B1F2 (3 t hm-2 biochar plus reduced fertilizer), B2F1 (6 t hm-2 biochar plus fertilizer), and B2F2 (6 t hm-2 biochar plus reduced fertilizer).

RESULTS

BCAF increased chlorophyll and leaf area, enhancing soybean photosynthesis. The net photosynthetic rate (Pn ), transpiration rate (Tr ), stomatal conductance (Gs ), water use efficiency (WUE) and intercellular carbon dioxide (CO2 ) concentration (Ci ) were enhanced by BCAF. In addition, BCAF improved soybean photosystem II (PSII) photosynthetic performance, driving force, potential photochemical efficiency (Fv /F0 ), and quantum yield of electron transfer (φE0 ). Furthermore, BCAF enhanced the accumulation of photosynthetic products, such as soluble proteins, soluble sugars and sucrose content, resulting in higher leaf dry weight. Consequently, BCAF increased the soybean yield, with the highest increase of 41.54% in B2F1. The correlation analysis revealed positive relationships between soybean yield and chlorophyll, leaf area, maximal quantum yield of PSII (Fv /Fm ), electron transport flux per cross-section at t = 0 (ET0 /CS0 ), trapped energy flux per cross-section at t = 0 (TR0 /CS0 ), composite blade driving force (DFTotal ), and leaf dry weight.

CONCLUSIONS

We demonstrated that long-term BCAF enhances soybean photosynthesis under continuous planting, reduces fertilizer use and increases yield. This study reveals a novel way and theory to sustainably increase soybean productivity. © 2023 Society of Chemical Industry.

Pigmentation of soybean seed coats via a mutation that abolishes production of multiple-phased siRNAs of chalcone synthase genes

Lack of pigmentation in seed coats of soybean is caused by natural RNA silencing of chalcone synthase (CHS) genes. This phenomenon is an evolutionary consequence of structural changes in DNA that resulted in the production of double-stranded RNAs (dsRNAs) that trigger RNA degradation. Here we determined that a mutant with pigmented seed coats derived from a cultivar that lacked the pigmentation had a deletion between DNA regions ICHS1 and a cytochrome P450 gene; the deletion included GmIRCHS, a candidate gene that triggers CHS RNA silencing via production of CHS dsRNAs. We also characterized CHS short interfering RNAs (siRNAs) produced in the wild-type seed coats that had CHS RNA silencing. Phased 21-nt CHS siRNAs were detected in all 21 phases and were widely distributed in exon 2 of CHS7, which indicates commonality in the pattern of RNA degradation in natural CHS RNA silencing between distantly related species. These results with the similarities in the rearrangements found in spontaneous mutants suggest that the structural organization that generates dsRNAs that trigger phased siRNA production is vulnerable to further structural changes, which eventually abolish the induction of RNA silencing.

Identification of major QTLs for drought tolerance in soybean, together with a novel candidate gene, GmUAA6

Drought tolerance is a complex trait in soybean that is controlled by polygenetic quantitative trait loci (QTLs). In this study, wilting score, days-to-wilting, leaf relative water content, and leaf relative conductivity were used to identify QTLs associated with drought tolerance in recombinant inbred lines derived from a cross between a drought-sensitive variety, Lin, and a drought-tolerant variety, Meng. A total of 33 drought-tolerance QTLs were detected. Of these 17 were major QTLs. In addition, 15 were novel drought-tolerance QTLs. The most predominant QTL was on chromosome 11. This was detected in at least three environments. The overlapped mapping interval of the four measured traits was 0.2 cM in genetic distance (about 220 kb in physical length). Glyma.11g143500 (designated as GmUAA6), which encodes a UDP-N-acetylglucosamine transporter, was identified as the most likely candidate gene. The allele of GmUAA6 from Lin (GmUAA6Lin) was associated with improved soybean drought tolerance. Overexpression of GmUAA6Lin in Arabidopsis and soybean hairy roots enhanced drought tolerance. Furthermore, a 3-bp insertion/deletion (InDel) in the coding sequence of GmUAA6 explained up to 49.9% of the phenotypic variation in drought tolerance-related traits, suggesting that this InDel might be used in future marker-assisted selection of drought-tolerant lines in soybean breeding programs.

Fulvic Acid Promotes Legume-Rhizobium Symbiosis by Stimulating Endogenous Flavonoids Synthesis and Secretion

Fulvic acid (FA) promotes symbiosis between legumes and rhizobia. To elucidate from the aspect of symbiosis, the effects of root irrigation of water-soluble humic materials (WSHM) or foliar spraying of its highly active component, FA, on soybean root exudates and on rhizosphere microorganisms were investigated. As a result, WSHM/FA treatments significantly altered root exudate metabolite composition, and isoflavonoids were identified as key contributors in both treatments compared to the control. Increased expression of genes related to the isoflavonoid biosynthesis were validated by RT-qPCR in both treatments, which notably elevated the synthesis of symbiotic signals genistein, daidzin, coumestrol, and biochanin A. Moreover, the WSHM/FA treatments induced a change in rhizosphere microbial community, coupled with an increase in the relative abundance of rhizobia. Our findings showed that WSHM/FA promotes symbiosis by stimulating the endogenous flavonoid synthesis and leads to rhizobia accumulation in the rhizosphere. This study provides new insights into mechanisms underlying the FA-mediated promotion of symbiosis.

Identification and Genetic Dissection of Resistance to Red Crown Rot Disease in a Diverse Soybean Germplasm Population

Red crown rot (RCR) disease caused by Calonectria ilicicola negatively impacts soybean yield and quality. Unfortunately, the knowledge of the genetic architecture of RCR resistance in soybeans is limited. In this study, 299 diverse soybean accessions were used to explore their genetic diversity and resistance to RCR, and to mine for candidate genes via emergence rate (ER), survival rate (SR), and disease severity (DS) by a multi-locus random-SNP-effect mixed linear model of GWAS. All accessions had brown necrotic lesions on the primary root, with five genotypes identified as resistant. Nine single-nucleotide polymorphism (SNP) markers were detected to underlie RCR response (ER, SR, and DS). Two SNPs colocalized with at least two traits to form a haplotype block which possessed nine genes. Based on their annotation and the qRT-PCR, three genes, namely Glyma.08G074600, Glyma.08G074700, and Glyma.12G043600, are suggested to modulate soybean resistance to RCR. The findings from this study could serve as the foundation for breeding RCR-tolerant soybean varieties, and the candidate genes could be validated to deepen our understanding of soybean response to RCR.

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.

Frontiers of soybean pan-genome studies

Artificial domestication provided the original motivation to the blooming of agriculture, following with the dramatic change of the genetic background of crops and livestock. According to theory and technology upgradation that contributing to the omics, we appreciate using the pan-genome instead of single reference genome for crop study. By comparison and integration of multiple genomes under the guidance of pan-genome theory, we can estimate the genomic information range of a species, leading to a global understanding of its genetic diversity. Combining pan-genome with large size chromosomal structural variations, high throughput population resequencing, and multi-omics data, we can profoundly study the genetic basis behind species traits we focus on. Soybean is one of the most important commercial crops over the world. It is also essential to our food security. Dissecting the formation of genetic diversity and the causal loci of key agricultural traits of soybean will make the modern soybean breeding more efficiently. In this review, we summarize the core idea of pan-genome and clarified the characteristics of construction strategies of pan-genome such as de novo/mapping assembly, iterative assembly and graph-based genome. Then we used the soybean pan-genome work as a case study to introduce the general way to study pan-genome. We highlighted the contribution of structural variation (SV) to the evolution/domestication of soybean and its value in understanding the genetic bases of agronomy traits. By those, we approved the value of graph-based pan-genome for data integration and SV calculation. Future research directions are also discussed for crop genomics and data science.

et Zucc.) and assigning a mini-core collection

Wild soybean (Glycine soja), the ancestor of the cultivated soybean (G. max), is a crucial resource for capturing the genetic diversity of soybean species. In this study, we used a set of 78 genome-wide microsatellite markers to analyze the genetic diversity and geographic differentiation patterns in a global collection of 2,050 G. soja accessions and a mini-core collection of G. max stored in two public seed banks. We observed a notable reduction in the genetic diversity of G. max compared to G. soja and identified a close phylogenetic relationship between G. max and a G. soja subpopulation located in central China. Furthermore, we revealed substantial genetic divergence between northern and southern subpopulations, accompanied by diminished genetic diversity in the northern subpopulations. Two clusters were discovered among the accessions from north-eastern China-one genetically close to those from South Korea and southern Japan, and another close to those from Amur Oblast, Russia. Finally, 192 accessions were assigned to a mini-core collection of G. soja, retaining 73.8% of the alleles detected in the entire collection. This mini-core collection is accessible to those who need it, facilitating efficient evaluation and utilization of G. soja genetic resources in soybean breeding initiatives.

Effect of Growth Stage on Nutrition, Fermentation Quality, and Microbial Community of Semidry Silage from Forage Soybean

Soybean (Glycine max (Linn.) Merr.) is highly suitable as animal feed. The silage quality and microbial characteristics of soybean silage are still unclear. Forage soybean (HN389), at six different growth stages (R2-R7), were used as experimental materials to investigate the changes in fermentation, nutritional quality, and microbial characteristics of semidry silage after 0, 7, 14, 30, and 45 d. As the growth period extended, the content of crude protein (CP) and crude fat (EE) gradually increased, while the neutral detergent fiber (NDF) and the acid detergent fiber (ADF) content decreased. The pH value also decreased gradually with fermentation time, accompanied by increases in the proportion of ammonia-N and the content of lactic acid (LA) and acetic acid (AA). In addition, competitive inhibition was observed in the microbial fermentation. With the process of ensiling, Lactobacillus became the dominant bacterial species. The results indicate that the most active stage of fermentation during ensiling occurred within the first 7 days, the fermentation and nutritional quality of the soybean forage were improved, and the optimal mowing stage was the grain stage. Comparison of the microbial abundance showed that all microorganisms entered a stable stage at 30 days of silage. After storage, the dominant bacteria were Lactobacillus, Enterobacter, and Pantoea.

Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean

Soybean is a photoperiod-sensitive short-day crop whose reproductive period and yield are markedly affected by day-length changes. Seed weight is one of the key traits determining the soybean yield; however, the prominent genes that control the final seed weight of soybean and the mechanisms underlying the photoperiod's effect on this trait remain poorly understood. In this study, we identify SW19 as a major locus controlling soybean seed weight by QTL mapping and determine Dt1, an orthologous gene of Arabidopsis TFL1 that is known to govern the soybean growth habit, as the causal gene of the SW19 locus. We showed that Dt1 is highly expressed in developing seeds and regulates photoperiod-dependent seed weight in soybean. Further analyses revealed that the Dt1 protein physically interacts with the sucrose transporter GmSWEET10a to negatively regulate the import of sucrose from seed coat to the embryo, thus modulating seed weight under long days. However, Dt1 does not function in seed development under short days due to its very low expression. Importantly, we discovered a novel natural allelic variant of Dt1 (H4 haplotype) that decouples its pleiotropic effects on seed size and growth habit; i.e., this variant remains functional in seed development but fails to regulate the stem growth habit of soybean. Collectively, our findings provide new insights into how soybean seed development responds to photoperiod at different latitudes, offering an ideal genetic component for improving soybean's yield by manipulating its seed weight and growth habit.

Critical period for yield determination across grain crops

Studies across different crops demonstrated that grain or seed number per unit area (GN m-2) is the dominant yield component. Although grains or seeds derive from floret or flower production and survival, the timing of the critical period for GN m-2 determination is known to vary noticeably, from mainly pre-flowering to strongly post-flowering, across major grain crops. Here, we demonstrate that discrepancy between crops in the timing of their critical period is related to the flowering phase duration and the proportion of the whole cycle allocated to pre-flowering development. Changing the perspective, positioning the critical period at the end of the phase when grain abortion occurs instead of flowering, results in the critical period virtually coinciding among contrasting grain crops.

Identification of nectar sources foraged by female mosquitoes in Canada

For many mosquito species, the females must obtain vertebrate blood to complete a gonotrophic cycle. These blood meals are frequently supplemented by feeding on sugary plant nectar, which sustains energy reserves needed for flight, mating, and overall fitness. Our understanding of mosquito nectar foraging behaviors is mostly limited to laboratory experiments and direct field observations, with little research into natural mosquito-host plant relationships done in North America. In this study, we collected nectar-fed female mosquitoes over a 2-year period in Manitoba, Canada, and amplified a fragment of the chloroplast rbcL gene to identify the plant species fed upon. We found that mosquitoes foraged from diverse plant families (e.g., grasses, trees, ornamentals, and legumes), but preferred certain species, most notably soybean and Kentucky blue grass. Moreover, there appeared to be some associations between plant feeding preferences and mosquito species, date of collection, landscape, and geographical region. Overall, this study implemented DNA barcoding to identify nectar sources forage by mosquitoes in the Canadian Prairies.

Construction of Genetic Map and QTL Mapping for Seed Size and Quality Traits in Soybean (Glycine max L.)

Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Soybean yield and quality traits are mostly quantitative traits controlled by multiple genes. The quantitative trait loci (QTL) mapping for yield and quality traits, as well as for the identification of mining-related candidate genes, is of great significance for the molecular breeding and understanding the genetic mechanism. In this study, 186 individual plants of the F2 generation derived from crosses between Changjiangchun 2 and Yushuxian 2 were selected as the mapping population to construct a molecular genetic linkage map. A genetic map containing 445 SSR markers with an average distance of 5.3 cM and a total length of 2375.6 cM was obtained. Based on constructed genetic map, 11 traits including hundred-seed weight (HSW), seed length (SL), seed width (SW), seed length-to-width ratio (SLW), oil content (OIL), protein content (PRO), oleic acid (OA), linoleic acid (LA), linolenic acid (LNA), palmitic acid (PA), stearic acid (SA) of yield and quality were detected by the multiple- d size traits and 113 QTLs related to quality were detected by the multiple QTL model (MQM) mapping method across generations F2, F2:3, F2:4, and F2:5. A total of 71 QTLs related to seed size traits and 113 QTLs related to quality traits were obtained in four generations. With those QTLs, 19 clusters for seed size traits and 20 QTL clusters for quality traits were summarized. Two promising clusters, one related to seed size traits and the other to quality traits, have been identified. The cluster associated with seed size traits spans from position 27876712 to 29009783 on Chromosome 16, while the cluster linked to quality traits spans from position 12575403 to 13875138 on Chromosome 6. Within these intervals, a reference genome of William82 was used for gene searching. A total of 36 candidate genes that may be involved in the regulation of soybean seed size and quality were screened by gene functional annotation and GO enrichment analysis. The results will lay the theoretical and technical foundation for molecularly assisted breeding in soybean.

A novel miR160a-GmARF16-GmMYC2 module determines soybean salt tolerance and adaptation

Salt stress is a major challenge that has a negative impact on soybean growth and productivity. Therefore, it is important to understand the regulatory mechanism of salt response to ensure soybean yield under such conditions. In this study, we identified and characterized a miR160a-GmARF16-GmMYC2 module and its regulation during the salt-stress response in soybean. miR160a promotes salt tolerance by cleaving GmARF16 transcripts, members of the Auxin Response Factor (ARF) family, which negatively regulates salt tolerance. In turn, GmARF16 activates GmMYC2, encoding a bHLH transcription factor that reduces salinity tolerance by down-regulating proline biosynthesis. Genomic analysis among wild and cultivated soybean accessions identified four distinct GmARF16 haplotypes. Among them, the GmARF16H3 haplotype is preferentially enriched in localities with relatively saline soils, suggesting GmARF16H3 was artificially selected to improve salt tolerance. Our findings therefore provide insights into the molecular mechanisms underlying salt response in soybean and provide valuable genetic targets for the molecular breeding of salt tolerance.

Development of an NLR-ID Toolkit and Identification of Novel Disease-Resistance Genes in Soybean

The recognition of pathogen effectors through the nucleotide-binding leucine-rich repeat receptor (NLR) family is an important component of plant immunity. In addition to typical domains such as TIR, CC, NBS, and LRR, NLR proteins also contain some atypical integrated domains (IDs), the roles of which are rarely investigated. Here, we carefully screened the soybean (Glycine max) genome and identified the IDs that appeared in the soybean TNL-like proteins. Our results show that multiple IDs (36) are widely present in soybean TNL-like proteins. A total of 27 Gm-TNL-ID genes (soybean TNL-like gene encoding ID) were cloned and their antiviral activity towards the soybean mosaic virus (SMV)/tobacco mosaic virus (TMV) was verified. Two resistance (R) genes, SRA2 (SMV resistance gene contains AAA_22 domain) and SRZ4 (SMV resistance gene contains zf-RVT domain), were identified to possess broad-spectrum resistance characteristics towards six viruses including SMV, TMV, plum pox virus (PPV), cabbage leaf curl virus (CaLCuV), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV). The effects of Gm-TNL-IDX (the domain of the Gm-TNL-ID gene after the TN domain) on the antiviral activity of a R protein SRC7TN (we previously reported the TN domain of the soybean broad-spectrum resistance gene SRC7) were validated, and most of Gm-TNL-IDX inhibits antiviral activity mediated by SRC7TN, possibly through intramolecular interactions. Yeast-two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that seven Gm-TNL-IDX interacted with SMV-component proteins. Truncation analysis on a broad-spectrum antiviral protein SRZ4 indicated that SRZ4TIR is sufficient to mediate antiviral activity against SMV. Soybean cDNA library screening on SRZ4 identified 48 interacting proteins. In summary, our results indicate that the integration of IDs in soybean is widespread and frequent. The NLR-ID toolkit we provide is expected to be valuable for elucidating the functions of atypical NLR proteins in the plant immune system and lay the foundation for the development of engineering NLR for plant-disease control in the future.

Characterization of SsHog1 and Shk1 Using Efficient Gene Knockout Systems through Repeated Protoplasting and CRISPR/Cas9 Ribonucleoprotein Approaches in Sclerotinia sclerotiorum

Sclerotinia sclerotiorum is the causal agent of sclerotinia stem rot in over 400 plant species. In a previous study, the group III histidine kinase gene of S. sclerotiorum (Shk1) revealed its involvement in iprodione and fludioxonil sensitivity and osmotic stress. To further investigate the fungicide sensitivity associated with the high-osmolarity glycerol (HOG) pathway, we functionally characterized SsHog1, which is the downstream kinase of Shk1. To generate knockout mutants, split marker transformation combined with a newly developed repeated protoplasting method and CRISPR/Cas9 ribonucleoprotein (RNP) delivery approach were used. The pure SsHog1 and Shk1 knockout mutants showed reduced sensitivity to fungicides and increased sensitivity to osmotic stress. In addition, the SsHog1 knockout mutants demonstrated reduced virulence compared to Shk1 knockout mutants and wild-type. Our results indicate that the repeated protoplasting method and RNP approach can generate genetically pure homokaryotic mutants and SsHog1 is involved in osmotic adaptation, fungicide sensitivity, and virulence in S. sclerotiorum.

Phytopathogenic Curtobacterium flaccumfaciens Strains Circulating on Leguminous Plants, Alternative Hosts and Weeds in Russia

Many bacterial plant pathogens have a broad host range important for their life cycle. Alternate hosts from plant families other than the main (primary) host support the survival and dissemination of the pathogen population even in absence of main host plants. Metabolic peculiarities of main and alternative host plants can affect genetic diversity within and between the pathogen populations isolated from those plants. Strains of Gram-positive bacterium Curtobacterium flaccumfaciens were identified as being causal agents of bacterial spot and wilt diseases on leguminous plants, and other crop and weed plants, collected in different regions of Russia. Their biochemical properties and susceptibility to copper compounds have been found to be relatively uniform. According to conventional PCR assays, all of the isolates studied were categorised as pathovar Curtobacterim flaccumfaciens pv. flaccumfaciens, a pathogen of legumes. However, the strains demonstrated a substantial diversity in terms of virulence on several tested host plants and different phylogenetic relationships were revealed by BOX-PCR and alanine synthase gene (alaS) sequencing.

GmGLU1 and GmRR4 contribute to iron deficiency tolerance in soybean

Iron deficiency chlorosis (IDC) is a form of abiotic stress that negatively impacts soybean yield. In a previous study, we demonstrated that the historical IDC quantitative trait locus (QTL) on soybean chromosome Gm03 was composed of four distinct linkage blocks, each containing candidate genes for IDC tolerance. Here, we take advantage of virus-induced gene silencing (VIGS) to validate the function of three high-priority candidate genes, each corresponding to a different linkage block in the Gm03 IDC QTL. We built three single-gene constructs to target GmGLU1 (GLUTAMATE SYNTHASE 1, Glyma.03G128300), GmRR4 (RESPONSE REGULATOR 4, Glyma.03G130000), and GmbHLH38 (beta Helix Loop Helix 38, Glyma.03G130400 and Glyma.03G130600). Given the polygenic nature of the iron stress tolerance trait, we also silenced the genes in combination. We built two constructs targeting GmRR4+GmGLU1 and GmbHLH38+GmGLU1. All constructs were tested on the iron-efficient soybean genotype Clark grown in iron-sufficient conditions. We observed significant decreases in soil plant analysis development (SPAD) measurements using the GmGLU1 construct and both double constructs, with potential additive effects in the GmRR4+GmGLU1 construct. Whole genome expression analyses (RNA-seq) revealed a wide range of affected processes including known iron stress responses, defense and hormone signaling, photosynthesis, and cell wall structure. These findings highlight the importance of GmGLU1 in soybean iron stress responses and provide evidence that IDC is truly a polygenic trait, with multiple genes within the QTL contributing to IDC tolerance. Finally, we conducted BLAST analyses to demonstrate that the Gm03 IDC QTL is syntenic across a broad range of plant species.

Autofluorescence-spectral imaging for rapid and invasive characterization of soybean for pre-germination anaerobic stress tolerance

The autofluorescence-spectral imaging (ASI) technique is based on the light-emitting ability of natural fluorophores. Soybean genotypes showing contrasting tolerance to pre-germination anaerobic stress can be characterized using the photon absorption and fluorescence emission of natural fluorophores occurring in seed coats. In this study, tolerant seeds were efficiently distinguished from susceptible genotypes at 405 nm and 638 nm excitation wavelengths. ASI approach can be employed as a new marker for the detection of photon-emitting compounds in the tolerant and susceptible soybean seed coats. Furthermore, the accuracy of rapid characterization of genotypes using this technique can provide novel insights into soybean breeding.

Overexpression of cry1c* Enhances Resistance against to Soybean Pod Borer (Leguminivora glycinivorella) in Soybean

Soybean [Glycine max (L.) Merr.], an essential staple food and oil crop worldwide, boasts abundant vegetable proteins and fats beneficial for both human and animal consumption. However, the soybean pod borer (Leguminivora glycinivorella) (SPB) stands as the most destructive soybean insect pest in northeast China and other northeastern Asian regions, leading to significant annual losses in soybean yield and economic burden. Therefore, this study aims to investigate the introduction of a previously tested codon-optimized cry1c gene, cry1c*, into the soybean genome and assess its effect on the SPB infestation by generating and characterizing stable transgenic soybeans overexpressing cry1c*. The transgenic soybean lines that constitutively overexpressed cry1c* exhibited a significant reduction in the percentage of damaged seeds, reaching as low as 5% in plants under field conditions. Additionally, feeding transgenic leaves to the larvae of S. exigua, S. litura, and M. separta resulted in inhibited larval growth, decreased larval body weight, and lower survival rates compared to larvae fed on wild-type leaves. These findings showed that the transgenic lines maintained their resistance to SPB and other lepidopteran pests, especially the transgenic line KC1. Southern blotting and genome-wide resequencing analysis revealed that T-DNA integration occurred as a single copy between loci 50,868,122 and 50,868,123 of chromosome 10 in the transgenic line KC1. Therefore, the transgenic line KC1, overexpressing high levels of cry1c* in leaves and seeds, holds strong potential for commercial use in the integrated management of SPB and other lepidopteran pests.

Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean

Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement.

Genome-Wide Association Study and Identification of Candidate Genes Associated with Seed Number per Pod in Soybean

Soybean (Glycine max [L.] Merr.) is one of the primary sources of plant protein and oil for human foods, animal feed, and industrial processing. The seed number per pod generally varies from one to four and is an important component of seed number per unit area and seed yield. We used natural variation in 264 landraces and improved cultivars or lines to identify candidate genes involved in the regulation of seed number per pod in soybean. Genome-wide association tests revealed 65 loci that are associated with seed number per pod trait. Among them, 11 could be detected in multiple environments. Candidate genes were identified for seed number per pod phenotype from the most significantly associated loci, including a gene encoding protein argonaute 4, a gene encoding histone acetyltransferase of the MYST family 1, a gene encoding chromosome segregation protein SMC-1 and a gene encoding exocyst complex component EXO84A. In addition, plant hormones were found to be involved in ovule and seed development and the regulation of seed number per pod in soybean. This study facilitates the dissection of genetic networks underlying seed number per pod in soybean, which will be useful for the genetic improvement of seed yield in soybean.

Differentially Expressed Genes Related to Isoflavone Biosynthesis in a Soybean Mutant Revealed by a Comparative Transcriptomic Analysis

Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein-protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds.

Soybean-mediated suppression of BjaI/BjaR1 quorum sensing in Bradyrhizobium diazoefficiens impacts symbiotic nitrogen fixation

The acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR quorum sensing (QS) system orchestrates diverse bacterial behaviors in response to changes in population density. The role of the BjaI/BjaR1 QS system in Bradyrhizobium diazoefficiens USDA 110, which shares homology with LuxI/LuxR, remains elusive during symbiotic interaction with soybean. Here this genetic system in wild-type (WT) bacteria residing inside nodules exhibited significantly reduced activity compared to free-living cells, potentially attributed to soybean-mediated suppression. The deletion mutant strain ΔbjaR1 showed significantly enhanced nodulation induction and nitrogen fixation ability. Nevertheless, its ultimate symbiotic outcome (plant dry weight) in soybeans was compromised. Furthermore, comparative analysis of the transcriptome, proteome, and promoter activity revealed that the inactivation of BjaR1 systematically activated and inhibited genomic modules associated with nodulation and nitrogen metabolism. The former appeared to be linked to a significant decrease in the expression of NodD2, a key cell-density-dependent repressor of nodulation genes, while the latter conferred bacterial growth and nitrogen fixation insensitivity to environmental nitrogen. In addition, BjaR1 exerted a positive influence on the transcription of multiple genes involved in a so-called central intermediate metabolism within the nodule. In conclusion, our findings highlight the crucial role of the BjaI/BjaR1 QS circuit in positively regulating bacterial nitrogen metabolism and emphasize the significance of the soybean-mediated suppression of this genetic system for promoting efficient symbiotic nitrogen fixation by B. diazoefficiens.IMPORTANCEThe present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing the activity of this QS circuit by the soybean host plant in establishing an efficient mutual relationship between the two symbiotic partners. This research expands our understanding of legumes' role in modulating symbiotic nitrogen fixation through rhizobial QS-mediated metabolic functioning, thereby deepening our comprehension of symbiotic coevolution theory. In addition, these findings may hold great promise for developing quorum quenching technology in agriculture.

Assessment of the long-term stability of pesticide residues under freezing conditions in brown rice and soybean certified reference materials

The objective of this study was to assess the long-term stability of pesticide residues in brown rice and soybean. The long-term stability of pesticide residues in brown rice and soybean was assessed for 5415 days (over 14 years) and 1801 days (about 5 years), respectively. The samples-certified reference materials (CRMs) 7504-a (brown rice) and 7509-a (soybean) -were prepared by freeze-pulverization. Two target pesticides (etofenprox and fenitrothion) were selected for brown rice and four (chlorpyrifos, diazinon, fenitrothion, and permethrin) for soybean. Our analytical results for long-term stability based on highly reliable isotope dilution mass spectrometry were in the range of expanded uncertainty (k=2) for the certified values of each CRM. The concentration showed a decreasing trend in none of the target pesticides when the samples were stored at temperatures between -20 °C and -30 °C, which indicated that the target pesticides were stable for the tested long terms.

Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean

Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.

Expression Patterns and Molecular Mechanisms Regulating Drought Tolerance of Soybean [Glycine max (L.) Merr.] Conferred by Transcription Factor Gene GmNAC19

NAC transcription factors are commonly involved in the plant response to drought stress. A transcriptome analysis of root samples of the soybean variety 'Jiyu47' under drought stress revealed the evidently up-regulated expression of GmNAC19, consistent with the expression pattern revealed by quantitative real-time PCR analysis. The overexpression of GmNAC19 enhanced drought tolerance in Saccharomyces cerevisiae INVSc1. The seed germination percentage and root growth of transgenic Arabidopsis thaliana were improved in comparison with those of the wild type, while the transgenic soybean composite line showed improved chlorophyll content. The altered contents of physiological and biochemical indices (i.e., soluble protein, soluble sugar, proline, and malondialdehyde) related to drought stress and the activities of three antioxidant enzymes (i.e., superoxide dismutase, peroxidase, and catalase) revealed enhanced drought tolerance in both transgenic Arabidopsis and soybean. The expressions of three genes (i.e., P5CS, OAT, and P5CR) involved in proline synthesis were decreased in the transgenic soybean hairy roots, while the expression of ProDH involved in the breakdown of proline was increased. This study revealed the molecular mechanisms underlying drought tolerance enhanced by GmNAC19 via regulation of the contents of soluble protein and soluble sugar and the activities of antioxidant enzymes, providing a candidate gene for the molecular breeding of drought-tolerant crop plants.

Discrepancy of Growth Toxicity of Polystyrene Nanoplastics on Soybean (Glycine max) and Mung Bean (Vigna radiata)

Nanoplastics, as a hot topic of novel contaminants, lack extensive concern in higher plants; especially the potential impact and mechanism of nanoplastics on legume crops remains elusive. In this study, the toxicity of polystyrene nanoplastics (PS-NPs, 200 nm) with diverse doses (control, 10, 50, 100, 200, 500 mg/L) to soybean and mung bean plants grown hydroponically for 7 d was investigated at both the macroscopic and molecular levels. The results demonstrated that the root length of both plants was markedly suppressed to varying degrees. Similarly, mineral elements (Fe, Zn) were notably decreased in soybean roots, consistent with Cu alteration in mung bean. Moreover, PS-NPs considerably elevated malondialdehyde (MDA) levels only in soybean roots. Enzyme activity data indicated mung bean exhibited significant damage only at higher doses of PS-NPs stress than soybean, implying mung bean is more resilient. Transcriptome analysis showed that PS-NPs stimulated the expression of genes associated with the antioxidant system in plant roots. Furthermore, starch and sucrose metabolism might play a key role in coping with PS-NPs to enhance soybean resistance, but the MAPK pathway was enriched in mung bean. Our findings provide valuable perspectives for an in-depth understanding of the performance of plants growing in waters contaminated by nanoplastics.

Development of KASP markers assisted with soybean drought tolerance in the germination stage based on GWAS

Soybean [Glycine max(L.)Merr.] is a leading oil-bearing crop and cultivated globally over a vast scale. The agricultural landscape in China faces a formidable challenge with drought significantly impacting soybean production. In this study, we treated a natural population of 264 Chinese soybean accessions using 15% PEG-6000 and used GR, GE, GI, RGR, RGE, RGI and ASFV as evaluation index. Using the ASFV, we screened 17 strong drought-tolerant soybean germplasm in the germination stage. Leveraging 2,597,425 high-density SNP markers, we conducted Genome-Wide Association Studies (GWAS) and identified 92 SNPs and 9 candidate genes significantly associated with drought tolerance. Furthermore, we developed two KASP markers for S14_5147797 and S18_53902767, which closely linked to drought tolerance. This research not only enriches the pool of soybean germplasm resources but also establishes a robust foundation for the molecular breeding of drought tolerance soybean varieties.

Multiomics Analyses Reveal the Dual Role of Flavonoids in Pigmentation and Abiotic Stress Tolerance of Soybean Seeds

The color of the seed coat has great diversity and is regarded as a biomarker of metabolic variations. Here we isolated a soybean variant (BLK) from a population of recombinant inbred lines with a black seed coat, while its sibling plants have yellow seed coats (YL). The BLK and YL plants showed no obvious differences in vegetative growth and seed weight. However, the BLK seeds had higher anthocyanins and flavonoids level and showed tolerance to various abiotic stresses including herbicide, oxidation, salt, and alkalinity during germination. Integrated metabolomic and transcriptomic analyses revealed that the upregulation of biosynthetic genes probably contributed to the overaccumulation of flavonoids in BLK seeds. The transient expression of those biosynthetic genes in soybean root hairs increased the levels of total flavonoids or anthocyanins. Our study revealed the molecular basis of flavonoid accumulation in soybean seeds, leveraging genetic engineering for both nutritious and stress-tolerant soybean germplasm.

The GmSTF1/2-GmBBX4 negative feedback loop acts downstream of blue-light photoreceptors to regulate isoflavonoid biosynthesis in soybean

Isoflavonoids, secondary metabolites derived from the phenylalanine pathway, are predominantly biosynthesized in legumes, especially soybean (Glycine max). They are not only essential for plant responses to biotic and abiotic stresses but also beneficial to human health. In this study, we report that light signaling controls isoflavonoid biosynthesis in soybean. Blue-light photoreceptors (GmCRY1s, GmCRY2s, GmPHOT1s, and GmPHOT2s) and the transcription factors GmSTF1 and GmSTF2 promote isoflavonoid accumulation, whereas the E3 ubiquitin ligase GmCOP1b negatively regulates isoflavonoid biosynthesis. GmPHOT1s and GmPHOT2s stabilize GmSTF1/2, whereas GmCOP1b promotes the degradation of these two proteins in soybean. GmSTF1/2 regulate the expression of approximately 27.9% of the genes involved in soybean isoflavonoid biosynthesis, including GmPAL2.1, GmPAL2.3, and GmUGT2. They also repress the expression of GmBBX4, a negative regulator of isoflavonoid biosynthesis in soybean. In addition, GmBBX4 physically interacts with GmSTF1 and GmSTF2 to inhibit their transcriptional activation activity toward target genes related to isoflavonoid biosynthesis. Thus, GmSTF1/2 and GmBBX4 form a negative feedback loop that acts downstream of photoreceptors in the regulation of isoflavonoid biosynthesis. Our study provides novel insights into the control of isoflavonoid biosynthesis by light signaling in soybean and will contribute to the breeding of soybean cultivars with high isoflavonoid content through genetic and metabolic engineering.

Combining machine learning and remote sensing-integrated crop modeling for rice and soybean crop simulation

Machine learning (ML) techniques offer a promising avenue for improving the integration of remote sensing data into mathematical crop models, thereby enhancing crop growth prediction accuracy. A critical variable for this integration is the leaf area index (LAI), which can be accurately assessed using proximal or remote sensing data based on plant canopies. This study aimed to (1) develop a machine learning-based method for estimating the LAI in rice and soybean crops using proximal sensing data and (2) evaluate the performance of a Remote Sensing-Integrated Crop Model (RSCM) when integrated with the ML algorithms. To achieve these objectives, we analyzed rice and soybean datasets to identify the most effective ML algorithms for modeling the relationship between LAI and vegetation indices derived from canopy reflectance measurements. Our analyses employed a variety of ML regression models, including ridge, lasso, support vector machine, random forest, and extra trees. Among these, the extra trees regression model demonstrated the best performance, achieving test scores of 0.86 and 0.89 for rice and soybean crops, respectively. This model closely replicated observed LAI values under different nitrogen treatments, achieving Nash-Sutcliffe efficiencies of 0.93 for rice and 0.97 for soybean. Our findings show that incorporating ML techniques into RSCM effectively captures seasonal LAI variations across diverse field management practices, offering significant potential for improving crop growth and productivity monitoring.

Dissection of the E8 locus in two early maturing Canadian soybean populations

Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.

[Effects of Combined Stress of High Density Polyethylene Microplastics and Chlorimuron-ethyl on Soybean Growth and Rhizosphere Bacterial Community]

With the vigorous development of agriculture in China， plastic mulch film and pesticides are widely used in agricultural production. However， the accumulation of microplastics （formed by the degradation of plastic mulch film） and pesticides in soil has also caused many environmental problems. At present， the environmental biological effects of microplastics or pesticides have been reported， but there are few studies on the combined effects on crop growth and the rhizosphere soil bacterial community. Therefore， in this study， the high density polyethylene microplastics （HDPE， 500 mesh） were designed to be co-treated with sulfonylurea herbicide chlorimuron-ethyl to study their effects on soybean growth. In addition， the effects of the combined stress of HDPE and chlorimuron-ethyl on soybean rhizosphere soil bacterial community diversity， structure composition， microbial community network， and soil function were investigated using high-throughput sequencing technology， interaction network， and PICRUSt2 function analysis to clarify the combined toxicity of HDPE and chlorimuron-ethyl to soybean. The results showed that the half-life of chlorimuron-ethyl in soil was prolonged by the 1% HDPE treatment （from 11.5 d to 14.3 d）， and the combined stress of HDPE and chlorimuron-ethyl had more obvious inhibition effects on soybean growth than that of the single pollutant or control. The HiSeq 2 500 sequencing showed that the rhizosphere bacterial community of soybean was composed of 20 phyla and 312 genera under combined stress， the number of phyla and genera was significantly less than that of the control and single pollutant treatment， and the relative abundances of bacteria with potential biological control and plant growth-promoting characteristics （such as Nocardioides and Sphingomonas） were reduced. Alpha diversity analysis showed that the combined stress significantly reduced the richness and diversity of the soybean rhizosphere bacterial community， and Beta diversity analysis showed that the combined stress significantly changed the structure of the bacterial community. The dominant flora of the rhizosphere bacterial community were regulated， and the abundances of secondary functional layers such as amino acid metabolism， energy metabolism， and lipid metabolism were reduced under combined stress by the analysis of LEfSe and PICRUSt2. It was inferred from the network analysis that the combined stress of HDPE and chlorimuron-ethyl reduced the total number of connections and network density of soil bacteria， simplified the network structure， and changed the important flora species to maintain the stability of the network. The results above indicated that the combined stress of HDPE and chlorimuron-ethyl significantly affected the growth of soybean and changed the rhizosphere bacterial community structure， soil function， and network structure. Compared with that of the single pollutant treatment， the potential risk of combined stress was greater. The results of this study can provide guidance for evaluating the ecological risks of polyethylene microplastics and chlorimuron-ethyl and for the remediation of contaminated soil.

Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO2

Introduction

With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2).

Methods

We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding.

Results

Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts.

Conclusion

This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.

The Resistance of Soybean Variety Heinong 84 to Apple Latent Spherical Virus Is Controlled by Two Genetic Loci

Apple latent spherical virus (ALSV) is widely used as a virus-induced gene silencing (VIGS) vector for function genome study. However, the application of ALSV to soybeans is limited by the resistance of many varieties. In this study, the genetic locus linked to the resistance of a resistant soybean variety Heinong 84 was mapped by high-throughput sequencing-based bulk segregation analysis (HTS-BSA) using a hybrid population crossed from Heinong 84 and a susceptible variety, Zhonghuang 13. The results showed that the resistance of Heinong 84 to ALSV is controlled by two genetic loci located on chromosomes 2 and 11, respectively. Cleaved amplified polymorphic sequence (CAPS) markers were developed for identification and genotyping. Inheritance and biochemical analyses suggest that the resistance locus on chromosome 2 plays a dominant dose-dependent role, while the other locus contributes a secondary role in resisting ALSV. The resistance locus on chromosome 2 might encode a protein that can directly inhibit viral proliferation, while the secondary resistance locus on chromosome 11 may encode a host factor required for viral proliferation. Together, these data reveal novel insights on the resistance mechanism of Heinong 84 to ALSV, which will benefit the application of ALSV as a VIGS vector.

A genome-wide association analysis for salt tolerance during the soybean germination stage and development of KASP markers

Salt stress poses a significant challenge to crop productivity, and understanding the genetic basis of salt tolerance is paramount for breeding resilient soybean varieties. In this study, a soybean natural population was evaluated for salt tolerance during the germination stage, focusing on key germination traits, including germination rate (GR), germination energy (GE), and germination index (GI). It was seen that under salt stress, obvious inhibitions were found on these traits, with GR, GE, and GI diminishing by 32% to 54% when compared to normal conditions. These traits displayed a coefficient of variation (31.81% to 50.6%) and a substantial generalized heritability (63.87% to 86.48%). Through GWAS, a total of 1841 significant single-nucleotide polymorphisms (SNPs) were identified to be associated with these traits, distributed across chromosome 2, 5, 6, and 20. Leveraging these significant association loci, 12 candidate genes were identified to be associated with essential functions in coordinating cellular responses, regulating osmotic stress, mitigating oxidative stress, clearing reactive oxygen species (ROS), and facilitating heavy metal ion transport - all of which are pivotal for plant development and stress tolerance. To validate the candidate genes, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was conducted, revealing three highly expressed genes (Glyma.02G067700, Glyma.02G068900, and Glyma.02G070000) that play pivotal roles in plant growth, development, and osmoregulation. In addition, based on these SNPs related with salt tolerance, KASP (Kompetitive Allele-Specific PCR)markers were successfully designed to genotype soybean accessions. These findings provide insight into the genetic base of soybean salt tolerance and candidate genes for enhancing soybean breeding programs in this study.

Optimization of soybean physiochemical, agronomic, and genetic responses under varying regimes of day and night temperatures

Soybean is an important oilseed crop worldwide; however, it has a high sensitivity to temperature variation, particularly at the vegetative stage to the pod-filling stage. Temperature change affects physiochemical and genetic traits regulating the soybean agronomic yield. In this regard, the current study aimed to comparatively evaluate the effects of varying regimes of day and night temperatures (T1 = 20°C/12°C, T2 = 25°C/17°C, T3 = 30°C/22°C, T4 = 35°C/27°C, and T5 = 40°C/32°C) on physiological (chlorophyll, photosynthesis, stomatal conductance, transpiration, and membrane damage) biochemical (proline and antioxidant enzymes), genetic (GmDNJ1, GmDREB1G;1, GmHSF-34, GmPYL21, GmPIF4b, GmPIP1;6, GmGBP1, GmHsp90A2, GmTIP2;6, and GmEF8), and agronomic traits (pods per plant, seeds per plant, pod weight per plant, and seed yield per plant) of soybean cultivars (Swat-84 and NARC-1). The experiment was performed in soil plant atmosphere research (SPAR) units using two factorial arrangements with cultivars as one factor and temperature treatments as another factor. A significant increase in physiological, biochemical, and agronomic traits with increased gene expression was observed in both soybean cultivars at T4 (35°C/27°C) as compared to below and above regimes of temperatures. Additionally, it was established by correlation, principal component analysis (PCA), and heatmap analysis that the nature of soybean cultivars and the type of temperature treatments have a significant impact on the paired association of agronomic and biochemical traits, which in turn affects agronomic productivity. Furthermore, at corresponding temperature regimes, the expression of the genes matched the expression of physiochemical traits. The current study has demonstrated through extensive physiochemical, genetic, and biochemical analyses that the ideal day and night temperature for soybeans is T4 (35°C/27°C), with a small variation having a significant impact on productivity from the vegetative stage to the grain-filling stage.