Rethinking temperature effects on leaf growth, gene expression and metabolism: Diel variation matters

Plants have evolved to grow under prominently fluctuating environmental conditions. In experiments under controlled conditions, temperature is often set to artificial, binary regimes with constant values at day and at night. This study investigated how such a diel (24 hr) temperature regime affects leaf growth, carbohydrate metabolism and gene expression, compared to a temperature regime with a field-like gradual increase and decline throughout 24 hr. Soybean (Glycine max) was grown under two contrasting diel temperature treatments. Leaf growth was measured in high temporal resolution. Periodical measurements were performed of carbohydrate concentrations, carbon isotopes as well as the transcriptome by RNA sequencing. Leaf growth activity peaked at different times under the two treatments, which cannot be explained intuitively. Under field-like temperature conditions, leaf growth followed temperature and peaked in the afternoon, whereas in the binary temperature regime, growth increased at night and decreased during daytime. Differential gene expression data suggest that a synchronization of cell division activity seems to be evoked in the binary temperature regime. Overall, the results show that the coordination of a wide range of metabolic processes is markedly affected by the diel variation of temperature, which emphasizes the importance of realistic environmental settings in controlled condition experiments.

A robust and practical CRISPR/crRNA screening system for soybean cultivar editing using LbCpf1 ribonucleoproteins

KEY MESSAGE

Calli protoplasts isolated from three soybean cultivars are useful tools to evaluate guide RNAs for clustered regularly interspaced short palindromic repeats (CRISPR)-based precise gene editing. A type V CRISPR effector, LbCpf1(Cas12a) from Lachnospiraceae bacterium ND 2006, has been used for precision editing of the plant genome. We report that callus-derived protoplasts from three soybeans, including Glycine Max var. Williams 82 and two Korean cultivars (Kwangan and Daewon) represent efficient systems for the screening of active crRNA for CRISPR/LbCpf1. CRISPR/LbCpf1 ribonucleoproteins (RNPs) were delivered as complexes of purified endonucleases mixed with designed crRNA to simultaneously edit target genes of GlymaFAD2-1A and GlymaFAD2-1B transfected into three soybean protoplasts including genome-sequenced Williams 82 with cultivars, Kwangan and Daewon. Previously, we reported that nine crRNAs designed for LbCpf1 exhibited varying degrees of editing efficacy for two FAD2 genes. Among the nine crRNAs, the LbCpf1-crRNA3 complexes showed the highest efficiency in soybean cotyledon protoplasts. The new screening systems of callus protoplasts from three soybeans have been successfully used to transfect GFP-tagged markers and CRISPR/LbCpf1 RNPs. The callus protoplasts confirm that the LbCpf1-crRNA3 complex is an active crRNA for LbCpf1 to edit two FAD2 genes similar to cotyledon protoplasts. These results demonstrate that soybean callus protoplast-based CRISPR/crRNA selection is a new and practical tool to screen the efficacy of crRNAs and a prerequisite for progressive regeneration of the edited soybean.

Exocyst components promote an incompatible interaction between Glycine max (soybean) and Heterodera glycines (the soybean cyst nematode)

Vesicle and target membrane fusion involves tethering, docking and fusion. The GTPase SECRETORY4 (SEC4) positions the exocyst complex during vesicle membrane tethering, facilitating docking and fusion. Glycine max (soybean) Sec4 functions in the root during its defense against the parasitic nematode Heterodera glycines as it attempts to develop a multinucleate nurse cell (syncytium) serving to nourish the nematode over its 30-day life cycle. Results indicate that other tethering proteins are also important for defense. The G. max exocyst is encoded by 61 genes: 5 EXOC1 (Sec3), 2 EXOC2 (Sec5), 5 EXOC3 (Sec6), 2 EXOC4 (Sec8), 2 EXOC5 (Sec10) 6 EXOC6 (Sec15), 31 EXOC7 (Exo70) and 8 EXOC8 (Exo84) genes. At least one member of each gene family is expressed within the syncytium during the defense response. Syncytium-expressed exocyst genes function in defense while some are under transcriptional regulation by mitogen-activated protein kinases (MAPKs). The exocyst component EXOC7-H4-1 is not expressed within the syncytium but functions in defense and is under MAPK regulation. The tethering stage of vesicle transport has been demonstrated to play an important role in defense in the G. max-H. glycines pathosystem, with some of the spatially and temporally regulated exocyst components under transcriptional control by MAPKs.

Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations

Characterization of the metabolic heterogeneity in cell populations requires the analysis of single cells. Most current methods in single-cell analysis rely on cell manipulation, potentially altering the abundance of metabolites in individual cells. A small sample volume and the chemical diversity of metabolites are additional challenges in single-cell metabolomics. Here, we describe the combination of fiber-based laser ablation electrospray ionization (f-LAESI) with 21 T Fourier transform ion cyclotron resonance mass spectrometry (21TFTICR-MS) for in situ single-cell metabolic profiling in plant tissue. Single plant cells infected by bacteria were selected and sampled directly from the tissue without cell manipulation through mid-infrared ablation with a fine optical fiber tip for ionization by f-LAESI. Ultrahigh performance 21T-FTICR-MS enabled the simultaneous capture of isotopic fine structures (IFSs) for 47 known and 11 unknown compounds, thus elucidating their elemental compositions from single cells and providing information on metabolic heterogeneity in the cell population.

A Post-domestication Mutation, Dt2, Triggers Systemic Modification of Divergent and Convergent Pathways Modulating Multiple Agronomic Traits in Soybean

The semi-determinate stem growth habit in leguminous crops, similar to the "green revolution" semi-dwarf trait in cereals, is a key plant architecture trait that affects several other traits determining grain yield. In soybean semi-determinacy is modulated by a post-domestication gain-of-function mutation in the gene, Dt2, which encodes an MADS-box transcription factor. However, its role in systemic modification of stem growth and other traits is unknown. In this study, we show that Dt2 functions not only as a direct repressor of Dt1, which prevents terminal flowering, but also as a direct activator of putative floral integrator/identity genes including GmSOC1, GmAP1, and GmFUL, which likely promote flowering. We also demonstrate that Dt2 functions as a direct repressor of the putative drought-responsive transcription factor gene GmDREB1D, and as a direct activator of GmSPCH and GmGRP7, which are potentially associated with asymmetric division of young epidermal cells and stomatal opening, respectively, and may affect the plant's water-use efficiency (WUE). Intriguingly, Dt2 was found to be a direct activator or repressor of the precursors of eight microRNAs targeting genes potentially associated with meristem maintenance, flowering time, stomatal density, WUE, and/or stress responses. This study thus reveals the molecular basis of pleiotropy associated with plant productivity, adaptability, and environmental resilience.

Effects of exogenous bisphenol A on the function of mitochondria in root cells of soybean (Glycine max L.) seedlings

Bisphenol A (BPA), a contaminant of emerging concern, can affect plant root growth by changing various physiological processes. Mitochondria are critical organelles that produce energy for growth. However, how BPA affects the function and ultrastructure of mitochondria and then plant root growth remains unclear. Here, we evaluated the lethality of BPA to root tip cells, investigated the energy production process of mitochondria, observed mitochondrial ultrastructure, and measured reactive oxygen species (ROS) and lipid peroxidation levels in mitochondria of soybean seedlings roots exposed to exogenous BPA. We found that low-dose BPA (1.5 mg/L) exposure induced limited toxicity in root tip cells, increased the activities of key enzymes (citrate synthase, succinate dehydrogenase, malate dehydrogenase and cytochrome C oxidase) involved in tricarboxylic acid cycle and oxidative phosphorylation, promoted adenosine triphosphate (ATP) synthesis, and increased ROS production in mitochondria. Higher doses of BPA (6.0, 17.2 mg/L) exposure caused massive cell death in root tips, decreased the above key enzyme activities and ATP production, and destroyed mitochondrial ultrastructure; meanwhile, these doses also significantly increased mitochondrial ROS and membrane lipid peroxidation levels. In conclusion, we found that mitochondria were significant subcellular sites through which BPA can damage plant roots. BPA-induced excessive ROS destroyed mitochondrial ultrastructure and inhibited key enzyme activities in energy production, resulting in decreased ATP synthesis and cell death in root tips. Our results demonstrated the effects of BPA on mitochondrial function and structure in plant root cells, providing new insights into understanding the underlying mechanisms of BPA affecting plant root growth.

Phytophthora sojae Effector PsAvh240 Inhibits Host Aspartic Protease Secretion to Promote Infection

Plants secrete defense molecules into the extracellular space (the apoplast) to combat attacking microbes. However, the mechanisms by which successful pathogens subvert plant apoplastic immunity remain poorly understood. In this study, we show that PsAvh240, a membrane-localized effector of the soybean pathogen Phytophthora sojae, promotes P. sojae infection in soybean hairy roots. We found that PsAvh240 interacts with the soybean-resistant aspartic protease GmAP1 in planta and suppresses the secretion of GmAP1 into the apoplast. By solving its crystal structure we revealed that PsAvh240 contain six α helices and two WY motifs. The first two α helices of PsAvh240 are responsible for its plasma membrane-localization and are required for PsAvh240's interaction with GmAP1. The second WY motifs of two PsAvh240 molecules form a handshake arrangement resulting in a handshake-like dimer. This dimerization is required for the effector's repression of GmAP1 secretion. Taken together, these data reveal that PsAvh240 localizes at the plasma membrane to interfere with GmAP1 secretion, which represents an effective mechanism by which effector proteins suppress plant apoplastic immunity.

iTRAQ-based proteomic analysis reveals changes in response to UV-B treatment in soybean sprouts

It has been shown that 15 μW·cm-2 UV-B radiation has the most pronounced effects on γ-aminobutiric acid (GABA), inositol 1,4,5-trisphosphate (IP3) and abscisic acid (ABA) accumulation in 4-day-old soybean sprouts. Nevertheless, its mechanism of action, from the perspective of protein expression, remains largely unknown. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) were employed to investigate UV-B treatment-induced proteomic changes in soybean sprouts. Results showed that UV-B treatment effectively regulated proteins involved in GABA biosynthesis, such as glutamate synthase, glutamate decarboxylase (GAD), methionine synthetase, 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase, aminoaldehyde dehydrogenase (AMADH) and inositol phosphate metabolism pathways, including phosphoinositide phospholipase C (PI-PLC), purple acid phosphatase (PAP) and inositol polyphosphate 5-phosphatase. In addition, proteins involved in ABA biosynthesis and signal transduction, such as 9-cis-epoxycarotenoid dioxygenase (NCED), abscisic-aldehyde oxidase (AO), SNF1-related protein kinase (SnRK), protein phosphatase 2C (PP2C), guanine nucleotide-binding protein and calreticulin-3, were also modulated under UV-B treatment.

Analysis of OJIP Chlorophyll Fluorescence Kinetics and QA Reoxidation Kinetics by Direct Fast Imaging

Chlorophyll fluorescence kinetic analysis has become an important tool in basic and applied research on plant physiology and agronomy. While early systems recorded the integrated kinetics of a selected spot or plant, later systems enabled imaging of at least the slower parts of the kinetics (20-ms time resolution). For faster events, such as the rise from the basic dark-adapted fluorescence yield to the maximum (OJIP transient), or the fluorescence yield decrease during reoxidation of plastoquinone A after a saturating flash, integrative systems are used because of limiting speed of the available imaging systems. In our new macroscopic and microscopic systems, the OJIP or plastonique A reoxidation fluorescence transients are directly imaged using an ultrafast camera. The advantage of such systems compared to nonimaging measurements is the analysis of heterogeneity of measured parameters, for example between the photosynthetic tissue near the veins and the tissue further away from the veins. Further, in contrast to the pump-and-probe measurement, direct imaging allows for measuring the transition of the plant from the dark-acclimated to a light-acclimated state via a quenching analysis protocol in which every supersaturating flash is coupled to a measurement of the fast fluorescence rise. We show that pump-and-probe measurement of OJIP is prone to artifacts, which are eliminated with the direct measurement. The examples of applications shown here, zinc deficiency and cadmium toxicity, demonstrate that this novel imaging platform can be used for detection and analysis of a range of alterations of the electron flow around PSII.

Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca2+ independent form of the AtCPK1 gene

Calcium-dependent protein kinases (CDPKs) represent a class within a multigene family that plays an important role in biotic and abiotic plant stress responses and is involved in the regulation of secondary metabolite biosynthesis. Our previous study showed that overexpression of the mutant constitutively active Ca2+ independent form of the AtCPK1 gene (AtCPK1-Ca) significantly increased the biosynthesis of anthraquinones and stilbenes in Rubia cordifolia L. and Vitis amurensis Rupr. transgenic cell cultures, respectively. Here, we have established transgenic calli of soybean plants Glycine max (L.) Merr. that express the AtCPK1-Ca gene. Heterologous expression of the AtCPK1-Ca gene provoked a 5.2-fold increase in total isoflavone production up to 208.09 mg/L, along with an increase in isoflavone aglycones production up to 6.60 mg/L, which is 3-fold greater than that of the control culture. The production of prenylated isoflavones significantly increased, reaching 3.78 mg/L, 13-fold higher than in the control culture. The expression levels of 4-coumarate:CoA ligases, isoflavone synthases, 2-hydroxyisoflavanone dehydratase, isoflavone dimethylallyltransferase, and coumestrol 4-dimethylallyltransferase genes in transgenic cell cultures significantly increased. Thus, heterologous expression of the AtCPK1-Ca gene can be used to bioengineer plant cell cultures that produce isoflavonoids.

Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

BACKGROUND

Cytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which play crucial roles in microRNAs (miRNAs) function and post-transcription control. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput deep sequencing coupled with RNase R enrichment strategy was conducted.

RESULTS

CircRNA libraries were constructed from flower buds of NJCMS1A and its maintainer NJCMS1B with three biological replicates. A total of 2867 circRNAs were identified, with 1009 circRNAs differentially expressed between NJCMS1A and NJCMS1B based on analysis of high-throughput sequencing. Of the 12 randomly selected circRNAs with different expression levels, 10 showed consistent expression patterns based on high-throughput sequencing and quantitative real-time PCR analyses. Tissue specific expression patterns were also verified with two circRNAs by quantitative real-time PCR. Most parental genes of differentially expressed circRNAs were mainly involved in biological processes such as metabolic process, biological regulation, and reproductive process. Moreover, 83 miRNAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and male fertility; The functions of miRNA targets were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the target mRNAs were significantly enriched in signal transduction and programmed cell death. Furthermore, a total of 165 soybean circRNAs were predicted to contain at least one internal ribosome entry site (IRES) element and an open reading frame, indicating their potential to encode polypeptides or proteins.

CONCLUSIONS

Our study indicated that the circRNAs might participate in the regulation of flower and pollen development, which could provide a new insight into the molecular mechanisms of CMS in soybean.

Quantitative 3D imaging of cell level auxin and cytokinin response ratios in soybean roots and nodules

Legume-Rhizobium symbiosis results in root nodules where rhizobia fix atmospheric nitrogen into plant usable forms in exchange for plant-derived carbohydrates. The development of these specialized root organs involves a set of carefully orchestrated plant hormone signalling. In particular, a spatio-temporal balance between auxin and cytokinin appears to be crucial for proper nodule development. We put together a construct that carried nuclear localized fluorescence sensors for auxin and cytokinin and used two photon induced fluorescence microscopy for concurrent quantitative 3-dimensional imaging to determine cellular level auxin and cytokinin outputs and ratios in root and nodule tissues of soybean. The use of nuclear localization signals on the markers and nuclei segmentation during image processing enabled accurate monitoring of outputs in 3D image volumes. The ratiometric method used here largely compensates for variations in individual outputs due to sample turbidity and scattering, an inherent issue when imaging thick root and nodule samples typical of many legumes. Overlays of determined auxin/cytokinin ratios on specific root zones and cell types accurately reflected those predicted based on previously reported outputs for each hormone individually. Importantly, distinct auxin/cytokinin ratios corresponded to distinct nodule cell types indicating a key role for these hormones in nodule cell type identity.

Genomic and molecular analysis of conserved and unique features of soybean PIF4

Phytochrome-interacting factor 4 (PIF4) participates in light signaling by interacting with photoreceptors, phytochromes, and cryptochromes. Although well characterized in Arabidopsis, PIF4's role in crop plants is unknown. Here we performed the first integrated genomics, transcriptomics, and molecular characterization of PIF4 in soybean (Glycine max) plants. Fifteen identified Glycine max PIFs (GmPIFs) grouped into PIF3, PIF4, and PIF8 subfamilies based on their phylogenetic relationships. The GmPIF4 subfamily formed two distinct clades (GmPIF4 I and GmPIF4 II) with different amino acid sequences in the conserved bHLH region. Quantitative transcriptional analysis of soybean plants exposed to different photoperiods and temperatures indicated that all PIF4 I clade GmPIF4s conserved PIF4-like expression. Three out of four GmPIF4 transcripts of the GmPIF4 I clade increased at 35 °C compared to 25 °C under short day conditions. RNA sequencing of soybeans undergoing floral transition showed differential regulation of GmPIF4b, and ectopic GmPIF4b expression in wild type Arabidopsis resulted in an early flowering phenotype. Complementation of GmPIF4b in Arabidopsis pif4-101 mutants partially rescued the mutant phenotype. PIF4 protein levels peaked before dawn, and a GmPIF4b protein variant was observed in soybean plants treated at high temperatures.

Occurrence and tolerance mechanisms of seed cracking under low temperatures in soybean (Glycine max)

MAIN CONCLUSION

In soybean, occurrence of, or tolerance to, seed cracking under low temperatures may be related to the presence or absence, respectively, of proanthocyanidin accumulation in the seed coat dorsal region. Soybean seeds sometimes undergo cracking during low temperatures in summer. In this study, we focused on the occurrence and tolerance mechanisms of low-temperature-induced seed cracking in the sensitive yellow soybean cultivar Yukihomare and the tolerant yellow soybean breeding line Toiku 248. Yukihomare exhibited seed cracking when subjected to a 21-day low-temperature treatment from 10 days after flowering. In yellow soybeans, seed coat pigmentation is inhibited, leading to low proanthocyanidin levels in the seed coat. Proanthocyanidins accumulated on the dorsal side of the seed coat in Yukihomare under the 21-day low-temperature treatment. In addition, a straight seed coat split occurred on the dorsal side at the full-sized seed stage, resulting in seed cracking in this cultivar. Conversely, proanthocyanidin accumulation was suppressed throughout the seed coat in low-temperature-treated Toiku 248. We propose the following mechanism of seed cracking: proanthocyanidin accumulation and subsequent lignin deposition under low temperatures affects the physical properties of the seed coat, making it more prone to splitting. Further analyses uncovered differences in the physical properties of the seed coat between Yukihomare and Toiku 248. In particular, seed coat hardness decreased in Yukihomare, but not in Toiku 248, under the low-temperature treatment. Seed coat flexibility was higher in Toiku 248 than in Yukihomare under the low-temperature treatment, suggesting that the seed coat of low-temperature-treated Toiku 248 is more flexible than that of low-temperature-treated Yukihomare. These physical properties of the Toiku 248 seed coat observed under low-temperature conditions may contribute to its seed-cracking tolerance.

GmHMA3 sequesters Cd to the root endoplasmic reticulum to limit translocation to the stems in soybean

A single point-mutation in GmHMA3 (Glycine max heavy metal-associated ATPase; a wild type allele cloned from a low Cd-accumulated soybean) is closely associated with seed cadmium (Cd) concentration. It is linked to Cd transportation in yeast, and is primarily expressed in the roots of plants. We hypothesized that the function of GmHMA3w in soybean would be akin to that of OsHMA3 in rice, which expresses in the root tonoplast and sequestrates Cd into the root vacuole to reduce Cd translocation to the shoots and limit its accumulation in the seeds. In this study, the transient expression of the GmHMA3w-GFP fusion protein in rice mesophyll protoplasts indicated that the subcellular localization of GmHAM3w was in the endoplasmic reticulum (ER). Overexpression of GmHMA3w increased the Cd concentration in the roots, decreased the Cd concentration in the stems, and did not affect the Cd concentration in the leaves. Additionally, its overexpression did not alter the Cd concentration across the whole plant. These findings indicated that GmHMA3w does not influence the Cd uptake, but limits the translocation of Cd from the roots to the stems. GmHMA3w thus acts in metal transportation. Assessment of the subcellular distribution of Cd indicated that GmHMA3w facilitated transport of Cd from the cell wall fraction to the organelle fraction, and then sequestrated Cd into the root ER, thus limiting its translocation to the stems. Additionally, the results also suggested that the ER constitutes a site of particularly high Cd sensitively in plants.

Isolation, Purity Assessment, and Proteomic Analysis of Nuclei

The integrity of a subcellular proteomics is largely dependent on purity of the isolated compartment away from other contaminants. If high-purity nuclei is isolated, nuclear proteomics is a useful approach for investigating the mechanisms underlying plant physiological function. Although the isolation of high-purity nuclei from tissue or organ in plant is a difficult task, successful purification has been achieved through fractionation processes. For purification, there are five protocols such as (1) differential centrifugation, (2) discontinuous Percoll gradients, (3) continuous sucrose gradients, (4) combined continuous Percoll/sucrose gradients, and (5) continuous Percoll gradients. Furthermore, because purity assessment of purified nuclei is an important step, it is also described in this chapter.

Spatiotemporal deep imaging of syncytium induced by the soybean cyst nematode Heterodera glycines

Parasite infections cause dramatic anatomical and ultrastructural changes in host plants. Cyst nematodes are parasites that invade host roots and induce a specific feeding structure called a syncytium. A syncytium is a large multinucleate cell formed by cell wall dissolution-mediated cell fusion. The soybean cyst nematode (SCN), Heterodera glycines, is a major soybean pathogen. To investigate SCN infection and the syncytium structure, we established an in planta deep imaging system using a clearing solution ClearSee and two-photon excitation microscopy (2PEM). Using this system, we found that several cells were incorporated into the syncytium; the nuclei increased in size and the cell wall openings began to be visible at 2 days after inoculation (DAI). Moreover, at 14 DAI, in the syncytium developed in the cortex, there were thickened concave cell wall pillars that resembled "Parthenon pillars." In contrast, there were many thick board-like cell walls and rarely Parthenon pillars in the syncytium developed in the stele. We revealed that the syncytia were classified into two types based on the pattern of the cell wall structures, which appeared to be determined by the position of the syncytium inside roots. Our results provide new insights into the developmental process of syncytium induced by cyst nematode and a better understanding of the three-dimensional structure of the syncytium in host roots.

Genome-wide comparative analysis of DNA methylation between soybean cytoplasmic male-sterile line NJCMS5A and its maintainer NJCMS5B

BACKGROUND

DNA methylation is an important epigenetic modification. It can regulate the expression of many key genes without changing the primary structure of the genomic DNA, and plays a vital role in the growth and development of the organism. The genome-wide DNA methylation profile of the cytoplasmic male sterile (CMS) line in soybean has not been reported so far.

RESULTS

In this study, genome-wide comparative analysis of DNA methylation between soybean CMS line NJCMS5A and its maintainer NJCMS5B was conducted by whole-genome bisulfite sequencing. The results showed 3527 differentially methylated regions (DMRs) and 485 differentially methylated genes (DMGs), including 353 high-credible methylated genes, 56 methylated genes coding unknown protein and 76 novel methylated genes with no known function were identified. Among them, 25 DMRs were further validated that the genome-wide DNA methylation data were reliable through bisulfite treatment, and 9 DMRs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. Finally, 8 key DMGs possibly associated with soybean CMS were identified.

CONCLUSIONS

Genome-wide DNA methylation profile of the soybean CMS line NJCMS5A and its maintainer NJCMS5B was obtained for the first time. Several specific DMGs which participated in pollen and flower development were further identified to be probably associated with soybean CMS. This study will contribute to further understanding of the molecular mechanism behind soybean CMS.

A comparative genomic and transcriptomic analysis at the level of isolated root hair cells reveals new conserved root hair regulatory elements

KEY MESSAGE

A comparative transcriptomic and genomic analysis between Arabidopsis thaliana and Glycine max root hair genes reveals the evolution of the expression of plant genes after speciation and whole genome duplication. Our understanding of the conservation and divergence of the expression patterns of genes between plant species is limited by the quality of the genomic and transcriptomic resources available. Specifically, the transcriptomes generated from plant organs are the reflection of the contribution of the different cell types composing the samples weighted by their relative abundances in the sample. These contributions can vary between plant species leading to the generation of datasets which are difficult to compare. To gain a deeper understanding of the evolution of gene transcription in and between plant species, we performed a comparative transcriptomic and genomic analysis at the level of one single plant cell type, the root hair cell, and between two model plants: Arabidopsis (Arabidopsis thaliana) and soybean (Glycine max). These two species, which diverged 90 million years ago, were selected as models based on the large amount of genomic and root hair transcriptomic information currently available. Our analysis revealed in detail the transcriptional divergence and conservation between soybean paralogs (i.e., the soybean genome is the product of two successive whole genome duplications) and between Arabidopsis and soybean orthologs in this single plant cell type. Taking advantage of this evolutionary study, we combined bioinformatics, molecular, cellular and microscopic tools to characterize plant promoter sequences and the discovery of two root hair regulatory elements (RHE1 and RHE2) consistently and specifically active in plant root hair cells.

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs

Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single-cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated than were stripped roots. However, in response to heat stress, both root hairs and stripped roots showed hypomethylation in each context, especially in the CHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes in DNA methylation are directly or indirectly associated with expression of genes and transposons within the context of either specific tissues/cells or stress (heat).

Accumulation of proanthocyanidins and/or lignin deposition in buff-pigmented soybean seed coats may lead to frequent defective cracking

MAIN CONCLUSION

Defective cracking frequently occurs in buff-pigmented soybean seed coats, where proanthocyanidins accumulate and lignin is deposited, suggesting that proanthocyanidins and/or lignin may change physical properties and lead to defective cracking. In the seed production of many yellow soybean (Glycine max) cultivars, very low percentages of self-pigmented seeds are commonly found. This phenomenon is derived from a recessive mutation of the I gene inhibiting seed coat pigmentation. In Japan, most of these self-pigmented seeds are buff-colored, and frequently show multiple defective cracks in the seed coat. However, it is not known why cracking occurs specifically in buff seed coats. In this study, quantitative analysis was performed between yellow and buff soybean seed coats. Compared with yellow soybeans, in which defective cracking rarely occurs, contents of proanthocyanidins (PAs) and lignin were significantly higher in buff seed coats. Histochemical data of PAs and lignin in the seed coats strongly supported this result. Measurements of the physical properties of seed coats using a texture analyzer showed that a hardness value was significantly decreased in the buff seed coats. These results suggest that PA accumulation and/or lignin deposition may affect the physical properties of buff seed coats and lead to the defective cracking. This work contributes to understanding of the mechanism of defective cracking, which decreases the seed quality of soybean and related legumes.

The purple acid phosphatase GmPAP21 enhances internal phosphorus utilization and possibly plays a role in symbiosis with rhizobia in soybean

Induction of secreted and intracellular purple acid phosphatases (PAPs; EC 3.1.3.2) is widely recognized as an adaptation of plants to phosphorus (P) deficiency. The secretion of PAPs plays important roles in P acquisition. However, little is known about the functions of intracellular PAP in plants and nodules. In this study, we identified a novel PAP gene GmPAP21 in soybean. Expression of GmPAP21 was induced by P limitation in nodules, roots and old leaves, and increased in roots with increasing duration of P starvation. Furthermore, the induction of GmPAP21 in nodules and roots was more intensive than in leaves in both P-efficient genotype HN89 and P-inefficient genotype HN112 in response to P starvation, and the relative expression in the leaves and nodules of HN89 was significantly greater than that of HN112 after P deficiency treatment. Further functional analyses showed that over-expressing GmPAP21 significantly enhanced both acid phosphatase activity and growth performance of hairy roots under P starvation condition, indicating that GmPAP21 plays an important role in P utilization. Moreover, GUS expression driven by GmPAP21 promoter was shown in the nodules besides roots. Overexpression of GmPAP21 in transgenic soybean significantly inhibited nodule growth, and thereby affected plant growth after inoculation with rhizobia. This suggests that GmPAP21 is also possibly involved in regulating P metabolism in nodules. Taken together, our results suggest that GmPAP21 is a novel plant PAP that functions in the adaptation of soybean to P starvation, possibly through its involvement in P recycling in plants and P metabolism in nodules.

Cytological behaviour of floral organs and in silico characterization of differentially expressed transcript-derived fragments associated with 'floral bud distortion' in soybean

An attempt was made to understand the 'floral bud distortion' (FBD), an unexplored disorder prevailing in soybean. Cytological behaviour of floral reproductive organs and in silico characterization of differentially expressed transcript-derived fragments (TDFs) in symptomatic and asymptomatic soybean plants were carried out. Pollens in asymptomatic plants do not have defects in number, size, shape and function. However, in symptomatic plant, pollens were found nonviable, abnormal in shape and with reduced germination ability. Here, we employed a computational approach, exploring invaluable resources. The tissue-specific transcript profile of symptomatic and asymptomatic sources was compared to determine differentially expressed TDFs associated with FBD to improve its basic understanding. A total of 60 decamer primers produced 197 scorable amplicons, ranged 162-1130 bp, of which 171 were monomorphic and 26 were differentially regulated. Reproducible TDFs were sequenced and characterized for their homology analysis, annotation, protein-protein interaction, subcellular localization and their physical mapping. Homology-based annotation of TDFs in soybean revealed presence of two characterized and seven uncharacterized hits. Annotation of characterized sequences showed presence of genes, namely auxin response factor 9 (ARF9) and forkhead-associated (FHA) domain, which are directly involved in plant development through various pathways, such as hormonal regulation, plant morphology, embryogenesis and DNA repair.

Overexpression of a Chitinase Gene from Trichoderma asperellum Increases Disease Resistance in Transgenic Soybean

In the present study, a chi gene from Trichoderma asperellum, designated Tachi, was cloned and functionally characterized in soybean. Firstly, the effects of sodium thiosulfate on soybean Agrobacterium-mediated genetic transformation with embryonic tip regeneration system were investigated. The transformation frequency was improved by adding sodium thiosulfate in co-culture medium for three soybean genotypes. Transgenic soybean plants with constitutive expression of Tachi showed increased resistance to Sclerotinia sclerotiorum compared to WT plants. Meanwhile, overexpression of Tachi in soybean exhibited increased reactive oxygen species (ROS) level as well as peroxidase (POD) and catalase (SOD) activities, decreased malondialdehyde (MDA) content, along with diminished electrolytic leakage rate after S. sclerotiorum inoculation. These results suggest that Tachi can improve disease resistance in plants by enhancing ROS accumulation and activities of ROS scavenging enzymes and then diminishing cell death. Therefore, Tachi represents a candidate gene with potential application for increasing disease resistance in plants.

Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli

Soybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state-space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical "external stimulus-induced information loss" model of biological systems.

Label-free in situ imaging of oil body dynamics and chemistry in germination

Plant oleosomes are uniquely emulsified lipid reservoirs that serve as the primary energy source during seed germination. These oil bodies undergo significant changes regarding their size, composition and structure during normal seedling development; however, a detailed characterization of these oil body dynamics, which critically affect oil body extractability and nutritional value, has remained challenging because of a limited ability to monitor oil body location and composition during germination in situ Here, we demonstrate via in situ, label-free imaging that oil bodies are highly dynamic intracellular organelles that are morphologically and biochemically remodelled extensively during germination. Label-free, coherent Raman microscopy (CRM) combined with bulk biochemical measurements revealed the temporal and spatial regulation of oil bodies in native soya bean cotyledons during the first eight days of germination. Oil bodies undergo a cycle of growth and shrinkage that is paralleled by lipid and protein compositional changes. Specifically, the total protein concentration associated with oil bodies increases in the first phase of germination and subsequently decreases. Lipids contained within the oil bodies change in saturation and chain length during germination. Our results show that CRM is a well-suited platform to monitor in situ lipid dynamics and local chemistry and that oil bodies are actively remodelled during germination. This underscores the dynamic role of lipid reservoirs in plant development.

In silico characterization of 1,2-diacylglycerol cholinephosphotransferase and lysophospha-tidylcholine acyltransferase genes in Glycine max L. Merrill

The enzymes 1,2-diacylglycerol cholinephosphotrans-ferase (CPT) and lysophosphatidylcholine acyltransferase (LPCAT) are important in lipid metabolism in soybean seeds. Thus, understand-ing the genes that encode these enzymes may enable their modification and aid the improvement of soybean oil quality. In soybean, the genes encoding these enzymes have not been completely described; there-fore, this study aimed to identify, characterize, and analyze the in silico expression of these genes in soybean. We identified two gene models encoding CPT and two gene models encoding LPCAT, one of which presented an alternative transcript. The sequences were positioned on the physical map of soybean and the promoter regions were analyzed. Cis-elements responsible for seed-specific expression and responses to biotic and abiotic stresses were identified. Virtual expression analysis of the gene models for CPT and LPCAT indicated that these genes are expressed under different stress conditions, in somatic embryos during differentiation, in immature seeds, root tissues, and calli. Putative ami-no acid sequences revealed the presence of transmembrane domains, and analysis of the cellular localization of these enzymes revealed they are located in the endoplasmic reticulum.

Effector-Triggered Immunity Determines Host Genotype-Specific Incompatibility in Legume-Rhizobium Symbiosis

Symbiosis between legumes and rhizobia leads to the formation of N2-fixing root nodules. In soybean, several host genes, referred to as Rj genes, control nodulation. Soybean cultivars carrying the Rj4 gene restrict nodulation by specific rhizobia such as Bradyrhizobium elkanii We previously reported that the restriction of nodulation was caused by B. elkanii possessing a functional type III secretion system (T3SS), which is known for its delivery of virulence factors by pathogenic bacteria. In the present study, we investigated the molecular basis for the T3SS-dependent nodulation restriction in Rj4 soybean. Inoculation tests revealed that soybean cultivar BARC-2 (Rj4/Rj4) restricted nodulation by B. elkanii USDA61, whereas its nearly isogenic line BARC-3 (rj4/rj4) formed nitrogen-fixing nodules with the same strain. Root-hair curling and infection threads were not observed in the roots of BARC-2 inoculated with USDA61, indicating that Rj4 blocked B. elkanii infection in the early stages. Accumulation of H2O2 and salicylic acid (SA) was observed in the roots of BARC-2 inoculated with USDA61. Transcriptome analyses revealed that inoculation of USDA61, but not its T3SS mutant in BARC-2, induced defense-related genes, including those coding for hypersensitive-induced responsive protein, which act in effector-triggered immunity (ETI) in Arabidopsis. These findings suggest that B. elkanii T3SS triggers the SA-mediated ETI-type response in Rj4 soybean, which consequently blocks symbiotic interactions. This study revealed a common molecular mechanism underlying both plant-pathogen and plant-symbiont interactions, and suggests that establishment of a root nodule symbiosis requires the evasion or suppression of plant immune responses triggered by rhizobial effectors.

Environmental and Historical Determinants of Patterns of Genetic Differentiation in Wild Soybean (Glycine soja Sieb. et Zucc)

Wild soybean, the direct progenitor of cultivated soybean, inhabits a wide distribution range across the mainland of East Asia and the Japanese archipelago. A multidisciplinary approach combining analyses of population genetics based on 20 nuclear microsatellites and one plastid locus were applied to reveal the genetic variation of wild soybean, and the contributions of geographical, environmental factors and historic climatic change on its patterns of genetic differentiation. High genetic diversity and significant genetic differentiation were revealed in wild soybean. Wild soybean was inferred to be limited to southern and central China during the Last Glacial Maximum (LGM) and experienced large-scale post-LGM range expansion into northern East Asia. A substantial northward range shift has been predicted to occur by the 2080s. A stronger effect of isolation by environment (IBE) versus isolation by geographical distance (IBD) was found for genetic differentiation in wild soybean, which suggested that environmental factors were responsible for the adaptive eco-geographical differentiation. This study indicated that IBE and historical climatic change together shaped patterns of genetic variation and differentiation of wild soybean. Different conservation measures should be implemented on different populations according to their adaptive potential to future changes in climate and human-induced environmental changes.

Comparisons of the Effects of Elevated Vapor Pressure Deficit on Gene Expression in Leaves among Two Fast-Wilting and a Slow-Wilting Soybean

Limiting the transpiration rate (TR) of a plant under high vapor pressure deficit (VPD) has the potential to improve crop yield under drought conditions. The effects of elevated VPD on the expression of genes in the leaves of three soybean accessions, Plant Introduction (PI) 416937, PI 471938 and Hutcheson (PI 518664) were investigated because these accessions have contrasting responses to VPD changes. Hutcheson, a fast-wilting soybean, and PI 471938, a slow-wilting soybean, respond to increased VPD with a linear increase in TR. TR of the slow-wilting PI 416937 is limited when VPD increases to greater than about 2 kPa. The objective of this study was to identify the response of the transcriptome of these accessions to elevated VPD under well-watered conditions and identify responses that are unique to the slow-wilting accessions. Gene expression analysis in leaves of genotypes PI 471938 and Hutcheson showed that 22 and 1 genes, respectively, were differentially expressed under high VPD. In contrast, there were 944 genes differentially expressed in PI 416937 with the same increase in VPD. The increased alteration of the transcriptome of PI 416937 in response to elevated VPD clearly distinguished it from the other slow-wilting PI 471938 and the fast-wilting Hutcheson. The inventory and analysis of differentially expressed genes in PI 416937 in response to VPD is a foundation for further investigation to extend the current understanding of plant hydraulic conductivity in drought environments.

Effects of bisphenol A on key enzymes in cellular respiration of soybean seedling roots

The environmental endocrine disrupter bisphenol A (BPA) is ubiquitous in the environment, with potential toxic effects on plants. Previous studies have found a significant effect of BPA on levels of mineral nutrients in plant roots, but the underlying mechanism remains unknown. To determine how BPA influences root mineral nutrients, the effects of BPA (1.5 mg L(-1) , 3.0 mg L(-1) , 6.0 mg L(-1) , 12.0 mg L(-1) , 24.0 mg L(-1) , 48.0 mg L(-1) , and 96.0 mg L(-1) ) on activities of critical respiratory enzymes (hexokinase, phosphofructokinase, pyruvate kinase, isocitrate dehydrogenase, and cytochrome c oxidase) were investigated in soybean seedling roots. After BPA exposure for 7 d, the low concentrations of BPA increased the activities of critical respiratory enzymes in roots, whereas opposite effects were observed in roots exposed to high concentrations of BPA, and the inhibitory effect was greater for higher BPA concentrations. In addition, evident morphological anomalies and decreases in root lengths and volumes were induced by high concentrations of BPA. Following withdrawal of BPA exposure after 7 d, the activities of respiratory enzymes and visible signs of toxicity recovered, and the extent of recovery depended on the type of enzyme and the BPA concentration. Furthermore, correlation analysis showed that the disturbance by BPA to activities of respiratory enzymes, which led to interference in the energy metabolism in roots, might be an effect mechanism of BPA on mineral element accumulation in plant roots.

A Phytophthora sojae Glycoside Hydrolase 12 Protein Is a Major Virulence Factor during Soybean Infection and Is Recognized as a PAMP

We identified a glycoside hydrolase family 12 (GH12) protein, XEG1, produced by the soybean pathogen Phytophthora sojae that exhibits xyloglucanase and β-glucanase activity. It acts as an important virulence factor during P. sojae infection but also acts as a pathogen-associated molecular pattern (PAMP) in soybean (Glycine max) and solanaceous species, where it can trigger defense responses including cell death. GH12 proteins occur widely across microbial taxa, and many of these GH12 proteins induce cell death in Nicotiana benthamiana. The PAMP activity of XEG1 is independent of its xyloglucanase activity. XEG1 can induce plant defense responses in a BAK1-dependent manner. The perception of XEG1 occurs independently of the perception of ethylene-inducing xylanase. XEG1 is strongly induced in P. sojae within 30 min of infection of soybean and then slowly declines. Both silencing and overexpression of XEG1 in P. sojae severely reduced virulence. Many P. sojae RXLR effectors could suppress defense responses induced by XEG1, including several that are expressed within 30 min of infection. Therefore, our data suggest that PsXEG1 contributes to P. sojae virulence, but soybean recognizes PsXEG1 to induce immune responses, which in turn can be suppressed by RXLR effectors. XEG1 thus represents an apoplastic effector that is recognized via the plant's PAMP recognition machinery.

Charge, size, and cellular selectivity for multiwall carbon nanotubes by maize and soybean

Maize (Zea mays) and soybean (Glycine max) were used as model food-chain plants to explore vegetative uptake of differently charged multiwall carbon nanotubes (MWCNTs). Three types of MWCNTs, including neutral pristine MWCNT (p-MWCNT), positively charged MWCNT-NH2, and negatively charged MWCNT-COOH, were directly taken-up and translocated from hydroponic solution to roots, stems, and leaves of maize and soybean plants at the MWCNT concentrations ranging from 10.0 to 50.0 mg/L during 18-day exposures. MWCNTs accumulated in the xylem and phloem cells and within specific intracellular sites like the cytoplasm, cell wall, cell membrane, chloroplast, and mitochondria, which was observed by transmission electron microscopy. MWCNTs stimulated the growth of maize and inhibited the growth of soybean at the exposed doses. The cumulative transpiration of water in maize exposed to 50 mg/L of MWCNT-COOHs was almost twice as much as that in the maize control. Dry biomass of maize exposed to MWCNTs was greater than that of maize control. In addition, the uptake and translocation of these MWCNTs clearly exhibited cellular, charge, and size selectivity in maize and soybean, which could be important properties for nanotransporters. This is the first report of cellular, charge, and size selectivity on the uptake by whole food plants for three differently charged MWCNTs.

Identification and characterization of a novel group of legume-specific, Golgi apparatus-localized WRKY and Exo70 proteins from soybean

Many plant genes belong to families that arise from extensive proliferation and diversification allowing the evolution of functionally new proteins. Here we report the characterization of a group of proteins evolved from WRKY and exocyst complex subunit Exo70 proteins through fusion with a novel transmembrane (TM) domain in soybean (Glycine max). From the soybean genome, we identified a novel WRKY-related protein (GmWRP1) that contains a WRKY domain with no binding activity for W-box sequences. GFP fusion revealed that GmWRP1 was targeted to the Golgi apparatus through its N-terminal TM domain. Similar Golgi-targeting TM domains were also identified in members of a new subfamily of Exo70J proteins involved in vesicle trafficking. The novel TM domains are structurally most similar to the endosomal cytochrome b561 from birds and close homologues of GmWRP1 and GmEx070J proteins with the novel TM domain have only been identified in legumes. Transient expression of some GmExo70J proteins or the Golgi-targeting TM domain in tobacco altered the subcellular structures labelled by a fluorescent Golgi marker. GmWRP1 transcripts were detected at high levels in roots, flowers, pods, and seeds, and the expression levels of GmWRP1 and GmExo70J genes were elevated with increased age in leaves. The legume-specific, Golgi apparatus-localized GmWRP1 and GmExo70J proteins are probably involved in Golgi-mediated vesicle trafficking of biological molecules that are uniquely important to legumes.

Identification of the primary lesion of toxic aluminum in plant roots

Despite the rhizotoxicity of aluminum (Al) being identified over 100 years ago, there is still no consensus regarding the mechanisms whereby root elongation rate is initially reduced in the approximately 40% of arable soils worldwide that are acidic. We used high-resolution kinematic analyses, molecular biology, rheology, and advanced imaging techniques to examine soybean (Glycine max) roots exposed to Al. Using this multidisciplinary approach, we have conclusively shown that the primary lesion of Al is apoplastic. In particular, it was found that 75 µm Al reduced root growth after only 5 min (or 30 min at 30 µm Al), with Al being toxic by binding to the walls of outer cells, which directly inhibited their loosening in the elongation zone. An alteration in the biosynthesis and distribution of ethylene and auxin was a second, slower effect, causing both a transient decrease in the rate of cell elongation after 1.5 h but also a longer term gradual reduction in the length of the elongation zone. These findings show the importance of focusing on traits related to cell wall composition as well as mechanisms involved in wall loosening to overcome the deleterious effects of soluble Al.

Phytophthora suppressor of RNA silencing 2 is a conserved RxLR effector that promotes infection in soybean and Arabidopsis thaliana

The genus Phytophthora consists of notorious and emerging pathogens of economically important crops. Each Phytophthora genome encodes several hundreds of cytoplasmic effectors, which are believed to manipulate plant immune response inside the host cells. However, the majority of Phytophthora effectors remain functionally uncharacterized. We recently discovered two effectors from the soybean stem and root rot pathogen Phytophthora sojae with the activity to suppress RNA silencing in plants. These effectors are designated Phytophthora suppressor of RNA silencing (PSRs). Here, we report that the P. sojae PSR2 (PsPSR2) belongs to a conserved and widespread effector family in Phytophthora. A PsPSR2-like effector produced by P. infestans (PiPSR2) can also suppress RNA silencing in plants and promote Phytophthora infection, suggesting that the PSR2 family effectors have conserved functions in plant hosts. Using Agrobacterium rhizogenes-mediated hairy roots induction, we demonstrated that the expression of PsPSR2 rendered hypersusceptibility of soybean to P. sojae. Enhanced susceptibility was also observed in PsPSR2-expressing Arabidopsis thaliana plants during Phytophthora but not bacterial infection. These experiments provide strong evidence that PSR2 is a conserved Phytophthora effector family that performs important virulence functions specifically during Phytophthora infection of various plant hosts.

The acetyl bromide method is faster, simpler and presents best recovery of lignin in different herbaceous tissues than Klason and thioglycolic acid methods

We compared the amount of lignin as determined by the three most traditional methods for lignin measurement in three tissues (sugarcane bagasse, soybean roots and soybean seed coat) contrasting for lignin amount and composition. Although all methods presented high reproducibility, major inconsistencies among them were found. The amount of lignin determined by thioglycolic acid method was severely lower than that provided by the other methods (up to 95%) in all tissues analyzed. Klason method was quite similar to acetyl bromide in tissues containing higher amounts of lignin, but presented lower recovery of lignin in the less lignified tissue. To investigate the causes of the inconsistencies observed, we determined the monomer composition of all plant materials, but found no correlation. We found that the low recovery of lignin presented by the thioglycolic acid method were due losses of lignin in the residues disposed throughout the procedures. The production of furfurals by acetyl bromide method does not explain the differences observed. The acetyl bromide method is the simplest and fastest among the methods evaluated presenting similar or best recovery of lignin in all the tissues assessed.

Anatomical response and infection of soybean during latent and pathogenic infection by type A and B of Phialophora gregata

Growth and anatomical responses of plants during latent and pathogenic infection by fungal pathogens are not well understood. The interactions between soybean (Glycine max) and two types of the pathogen Phialophora gregata were investigated to determine how plants respond during latent and pathogenic infection. Stems of soybean cultivars with different or no genes for resistance to infection by P. gregata were inoculated with wildtype or GFP and RFP-labeled strains of types A or B of P. gregata. Plants were sectioned during latent and pathogenic infection, examined with transmitted light or fluorescent microscopy, and quantitative differences in vessels and qualitative differences in infection were assessed using captured images. During latent infection, the number of vessels was similar in resistant and susceptible plants infected with type A or B compared to the control, and fungal infection was rarely observed in vessels. During pathogenic infection, the resistant cultivars had 20 to 25% more vessels than the uninfected plants, and fungal hyphae were readily observed in the vessels. Furthermore, during the pathogenic phase in a resistant cultivar, P. gregata type A-GFP was limited to outside of the primary xylem, while P. gregata type B-RFP was observed in the primary xylem. The opposite occurred with the susceptible cultivar, where PgA-GFP was observed in the primary xylem and PgB-RFP was limited to the interfascicular region. In summary, soybean cultivars with resistance to BSR produced more vessels and can restrict or exclude P. gregata from the vascular system compared to susceptible cultivars. Structural resistance mechanisms potentially compensate for loss of vessel function and disrupted water movement.

A soybean acyl carrier protein, GmACP, is important for root nodule symbiosis

Legumes (members of family Fabaceae) establish a symbiotic relationship with nitrogen-fixing soil bacteria (rhizobia) to overcome nitrogen source limitation. Single root hair epidermal cells serve as the entry point for bacteria to infect the host root, leading to development of a new organ, the nodule, which the bacteria colonize. In the present study, the putative role of a soybean acyl carrier protein (ACP), GmACP (Glyma18g47950), was examined in nodulation. ACP represent an essential cofactor protein in fatty acid biosynthesis. Phylogenetic analysis of plant ACP protein sequences showed that GmACP was classified in a legume-specific clade. Quantitative reverse-transcription polymerase chain reaction analysis demonstrated that GmACP was expressed in all soybean tissues but showed higher transcript accumulation in nodule tissue. RNA interference-mediated gene silencing of GmACP resulted in a significant reduction in nodule numbers on soybean transgenic roots. Fluorescent protein-labeled GmACP was localized to plastids in planta, the site of de novo fatty acid biosynthesis in plants. Analysis of the fatty acid content of root tissue silenced for GmACP expression, as determined by gas chromatography-mass spectrometry, showed an approximately 22% reduction, specifically in palmitic and stearic acid. Taken together, our data provide evidence that GmACP plays an important role in nodulation.

The endoplasmic reticulum binding protein BiP displays dual function in modulating cell death events

The binding protein (BiP) has been demonstrated to participate in innate immunity and attenuate endoplasmic reticulum- and osmotic stress-induced cell death. Here, we employed transgenic plants with manipulated levels of BiP to assess whether BiP also controlled developmental and hypersensitive programmed cell death (PCD). Under normal conditions, the BiP-induced transcriptome revealed a robust down-regulation of developmental PCD genes and an up-regulation of the genes involved in hypersensitive PCD triggered by nonhost-pathogen interactions. Accordingly, the BiP-overexpressing line displayed delayed leaf senescence under normal conditions and accelerated hypersensitive response triggered by Pseudomonas syringae pv tomato in soybean (Glycine max) and tobacco (Nicotiana tabacum), as monitored by measuring hallmarks of PCD in plants. The BiP-mediated delay of leaf senescence correlated with the attenuation of N-rich protein (NRP)-mediated cell death signaling and the inhibition of the senescence-associated activation of the unfolded protein response (UPR). By contrast, under biological activation of salicylic acid (SA) signaling and hypersensitive PCD, BiP overexpression further induced NRP-mediated cell death signaling and antagonistically inhibited the UPR. Thus, the SA-mediated induction of NRP cell death signaling occurs via a pathway distinct from UPR. Our data indicate that during the hypersensitive PCD, BiP positively regulates the NRP cell death signaling through a yet undefined mechanism that is activated by SA signaling and related to ER functioning. By contrast, BiP's negative regulation of leaf senescence may be linked to its capacity to attenuate the UPR activation and NRP cell death signaling. Therefore, BiP can function either as a negative or positive modulator of PCD events.

Enhanced lignin monomer production caused by cinnamic Acid and its hydroxylated derivatives inhibits soybean root growth

Cinnamic acid and its hydroxylated derivatives (p-coumaric, caffeic, ferulic and sinapic acids) are known allelochemicals that affect the seed germination and root growth of many plant species. Recent studies have indicated that the reduction of root growth by these allelochemicals is associated with premature cell wall lignification. We hypothesized that an influx of these compounds into the phenylpropanoid pathway increases the lignin monomer content and reduces the root growth. To confirm this hypothesis, we evaluated the effects of cinnamic, p-coumaric, caffeic, ferulic and sinapic acids on soybean root growth, lignin and the composition of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) monomers. To this end, three-day-old seedlings were cultivated in nutrient solution with or without allelochemical (or selective enzymatic inhibitors of the phenylpropanoid pathway) in a growth chamber for 24 h. In general, the results showed that 1) cinnamic, p-coumaric, caffeic and ferulic acids reduced root growth and increased lignin content; 2) cinnamic and p-coumaric acids increased p-hydroxyphenyl (H) monomer content, whereas p-coumaric, caffeic and ferulic acids increased guaiacyl (G) content, and sinapic acid increased sinapyl (S) content; 3) when applied in conjunction with piperonylic acid (PIP, an inhibitor of the cinnamate 4-hydroxylase, C4H), cinnamic acid reduced H, G and S contents; and 4) when applied in conjunction with 3,4-(methylenedioxy)cinnamic acid (MDCA, an inhibitor of the 4-coumarate:CoA ligase, 4CL), p-coumaric acid reduced H, G and S contents, whereas caffeic, ferulic and sinapic acids reduced G and S contents. These results confirm our hypothesis that exogenously applied allelochemicals are channeled into the phenylpropanoid pathway causing excessive production of lignin and its main monomers. By consequence, an enhanced stiffening of the cell wall restricts soybean root growth.

Specific subunits of heterotrimeric G proteins play important roles during nodulation in soybean

Heterotrimeric G proteins comprising Gα, Gβ, and Gγ subunits regulate many fundamental growth and development processes in all eukaryotes. Plants possess a relatively limited number of G-protein components compared with mammalian systems, and their detailed functional characterization has been performed mostly in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). However, the presence of single Gα and Gβ proteins in both these species has significantly undermined the complexity and specificity of response regulation in plant G-protein signaling. There is ample pharmacological evidence for the role of G proteins in regulation of legume-specific processes such as nodulation, but the lack of genetic data from a leguminous species has restricted its direct assessment. Our recent identification and characterization of an elaborate G-protein family in soybean (Glycine max) and the availability of appropriate molecular-genetic resources have allowed us to directly evaluate the role of G-protein subunits during nodulation. We demonstrate that all G-protein genes are expressed in nodules and exhibit significant changes in their expression in response to Bradyrhizobium japonicum infection and in representative supernodulating and nonnodulating soybean mutants. RNA interference suppression and overexpression of specific G-protein components results in lower and higher nodule numbers, respectively, validating their roles as positive regulators of nodule formation. Our data further show preferential usage of distinct G-protein subunits in the presence of an additional signal during nodulation. Interestingly, the Gα proteins directly interact with the soybean nodulation factor receptors NFR1α and NFR1β, suggesting that the plant G proteins may couple with receptors other than the canonical heptahelical receptors common in metazoans to modulate signaling.

The mitochondrial genome of soybean reveals complex genome structures and gene evolution at intercellular and phylogenetic levels

Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.

Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation

BACKGROUND

Phosphorus (P) plays important roles in plant growth and development. MicroRNAs involved in P signaling have been identified in Arabidopsis and rice, but P-responsive microRNAs and their targets in soybean leaves and roots are poorly understood.

RESULTS

Using high-throughput sequencing-by-synthesis (SBS) technology, we sequenced four small RNA libraries from leaves and roots grown under phosphate (Pi)-sufficient (+Pi) and Pi-depleted (-Pi) conditions, respectively, and one RNA degradome library from Pi-depleted roots at the genome-wide level. Each library generated ~21.45-28.63 million short sequences, resulting in ~20.56-27.08 million clean reads. From those sequences, a total of 126 miRNAs, with 154 gene targets were computationally predicted. This included 92 new miRNA candidates with 20-23 nucleotides that were perfectly matched to the Glycine max genome 1.0, 70 of which belong to 21 miRNA families and the remaining 22 miRNA unassigned into any existing miRNA family in miRBase 18.0. Under both +Pi and -Pi conditions, 112 of 126 total miRNAs (89%) were expressed in both leaves and roots. Under +Pi conditions, 12 leaf- and 2 root-specific miRNAs were detected; while under -Pi conditions, 10 leaf- and 4 root-specific miRNAs were identified. Collectively, 25 miRNAs were induced and 11 miRNAs were repressed by Pi starvation in soybean. Then, stem-loop real-time PCR confirmed expression of four selected P-responsive miRNAs, and RLM-5' RACE confirmed that a PHO2 and GmPT5, a kelch-domain containing protein, and a Myb transcription factor, respectively are targets of miR399, miR2111, and miR159e-3p. Finally, P-responsive cis-elements in the promoter regions of soybean miRNA genes were analyzed at the genome-wide scale.

CONCLUSIONS

Leaf- and root-specific miRNAs, and P-responsive miRNAs in soybean were identified genome-wide. A total of 154 target genes of miRNAs were predicted via degradome sequencing and computational analyses. The targets of miR399, miR2111, and miR159e-3p were confirmed. Taken together, our study implies the important roles of miRNAs in P signaling and provides clues for deciphering the functions for microRNA/target modules in soybean.

Plant cell suspension cultures

Plant cell suspension cultures are widely used in plant biology as a convenient tool for the investigation of a wide range of phenomena, bypassing the structural complexity of the plant organism in toto. The homogeneity of an in vitro cell population, the large availability of material, the high rate of cell growth and the good reproducibility of conditions make suspension-cultured cells suitable for the analysis of complex physiological processes at the cellular and molecular levels. Moreover, plant cell cultures provide a valuable platform for the production of high-value secondary metabolites and other substances of commercial interest. Here we describe how to initiate and maintain plant cell cultures starting from explants obtained from in vitro germinated seedlings. Isolation of protoplasts from plant cell suspension cultures and regeneration of plants via organogenesis and somatic embryogenesis are also presented.

Regulation of soybean seed germination through ethylene production in response to reactive oxygen species

BACKGROUND AND AIMS

Despite their toxicity, reactive oxygen species (ROS) play important roles in plant cell signalling pathways, such as mediating responses to stress or infection and in programmed cell death, at lower levels. Although studies have indicated that hydrogen peroxide (H(2)O(2)) promotes seed germination of several plants such as Arabidopsis, barley, wheat, rice and sunflower, the role of H(2)O(2) in soybean seed germination is not well known. The aim of this study therefore was to investigate the relationships between ROS, plant hormones and soybean seed germination.

METHODS

An examination was made of soybean seed germination, the expression of genes related to ethylene biosynthesis, endogenous ethylene contents, and the number and area of cells in the root tip, using N-acetylcysteine, an antioxidant, to counteract the effect of ROS.

KEY RESULTS

H(2)O(2) promoted germination, which N-acetylcysteine suppressed, suggesting that ROS are involved in the regulation of soybean germination. H(2)O(2) was produced in the embryonic axis after imbibition. N-Acetylcysteine suppressed the expression of genes related to ethylene biosynthesis and the production of endogenous ethylene. Interestingly, ethephon, which is converted to ethylene, and H(2)O(2) reversed the suppression of seed germination by N-acetylcysteine. Furthermore, morphological analysis revealed that N-acetylcysteine suppressed cell elongation at the root tip, and this suppression was also reversed by ethephon or H(2)O(2) treatments, as was the case in germination.

CONCLUSIONS

In soybean seeds, ROS produced in the embryonic axis after imbibition induce the production of endogenous ethylene, which promotes cell elongation in the root tip. This appears to be how ROS regulate soybean seed germination.

Defense responses of soybean roots during exposure to cadmium, excess of nitrogen supply and combinations of these stressors

Heavy metal pollution is a serious environmental problem in agricultural soils since the uptake of heavy metals by plants represents an entry point into the food chain and is influenced by the form and amount of nitrogen (N) fertilization. Here we studied the defense responses in soybean roots exposed to ions of cadmium (applied as 50 mg l(-1) Cd(2+)) when combined with an excessive dose of N in form of NH(4)NO(3). Our data indicate that despite of stunted root growth, several stress symptoms typically observed upon cadmium treatment, e.g. peroxidation of lipid membranes or activation of chitinase isoforms, become suppressed at highly excessive N. At the same time, other defense mechanisms such as catalases and proline accumulation were elevated. Most importantly, the interplay of ongoing responses resulted in a decreased uptake of the metal into the root tissue. This report points to the complexity of plant defense responses under conditions of heavy metal pollution combined with intensive fertilization in agriculture.

Comparative proteomic analyses reveal the changes of metabolic features in soybean (Glycine max) pistils upon pollination

Siphonogamy is a critical process in plant reproductive growth, during which numerous cell-cell interaction events occur between pistil and pollen. Previous studies in Solanaceae, Papaveraceae, and Brassicaceae focusing on pollen-stigma recognition in self-incompatible systems have provided many important views. In this study, we profiled the proteome in soybean mature pistils before and after pollination. Comparative analyses of two-dimensional gel electrophoresis maps from un-pollinated and pollinated pistils were conducted. The results showed that 22 proteins were increased and 36 proteins decreased after pollination. Functional categorization showed that most of them were metabolism- and redox-related proteins. The enhancement of primary metabolism, biosynthesis of pollen tube guidance compounds, and adjustment of redox homeostasis system might be helpful for a successful pollination. Quantitative reverse transcript-polymerase chain reaction analysis implied that the regulation of gene expression might happen at both transcriptional and posttranscriptional levels during pollination. This study will enhance our understanding of pollen-stigma interaction in plant sexual reproductive growth.

Effects of pulsed magnetic field treatment of soybean seeds on calli growth, cell damage, and biochemical changes under salt stress

The effects of magnetic field (MF) treatments of soybean seeds on calli growth, cell damage, and biochemical changes under salt stress were investigated under controlled conditions. Soybean seeds were exposed to a 1.0 Hz sinusoidal uniform pulsed magnetic field (PMF) of 1.5 µT for 5 h/day for 20 days. Non-treated seeds were considered as controls. For callus regeneration, the embryonic axis explants were taken from seeds and inoculated in a saline medium with a concentration of 10 mM NaCl for calli growth analysis and biochemical changes. The combined treatment of MF and salt stress was found to significantly increase calli fresh weight, total soluble sugar, total protein, and total phenol contents, but it decreased the ascorbic acid, lipid peroxidation, and catalase activity of calli from magnetically exposed seeds compared to the control calli. PMF treatment significantly improved calli tolerance to salt stress in terms of an increase in flavonoid, flavone, flavonole, alkaloid, saponin, total polyphenol, genistein, and daidzein contents under salt stress. The results suggest that PMF treatment of soybean seeds has the potential to counteract the adverse effects of salt stress on calli growth by improving primary and secondary metabolites under salt stress conditions.