Soybean NIMA-Related Kinase1 Promotes Plant Growth and Improves Salt and Cold Tolerance

Crosstalk between ethylene and melatonin activates isoflavone biosynthesis and antioxidant systems to produce high-quality soybean sprouts

Isoflavone, which are mainly found in soybeans, are a secondary metabolite with a variety of physiological functions. In recent years, increasing the isoflavone content of soybeans has received widespread attention. Although ethephon treatment significantly increased isoflavone content in soybean sprouts, it also had a certain inhibitory effect on the growth of sprouts. Melatonin (MT), as a new type of plant hormone, not only alleviated the damage caused by abiotic stress to plants, but also promoted the synthesis of secondary metabolites. In this study, we aimed to elucidate the mechanism of exogenous MT in regulating the growth and development, and the metabolism of isoflavone in soybean sprouts under ethephon treatment. The results indicated that MT alleviated the adverse effects of ethephon treatment on soybean sprouts by increasing the activities of superoxide dismutase, peroxidase, catalase, and the expression of their corresponding genes, as well as decreased the content of malondialdehyde and hydrogen peroxide. In addition, MT further increased the isoflavone content by up-regulating the expression level of isoflavone synthesis genes and increased the activities of phenylalanine ammonia-lyase and cinnamic acid 4-hydroxylase under ethephon treatment. This study provided technical support and reference value for the production of high-quality soybean sprouts to a certain extent.

Zinc-finger protein GmZF351 improves both salt and drought stress tolerance in soybean

Abiotic stress is one of the most important factors reducing soybean yield. It is essential to identify regulatory factors contributing to stress responses. A previous study found that the tandem CCCH zinc-finger protein GmZF351 is an oil level regulator. In this study, we discovered that the GmZF351 gene is induced by stress and that the overexpression of GmZF351 confers stress tolerance to transgenic soybean. GmZF351 directly regulates the expression of GmCIPK9 and GmSnRK, leading to stomata closing, by binding to their promoter regions, which carry two CT(G/C)(T/A)AA elements. Stress induction of GmZF351 is mediated through reduction in the H3K27me3 level at the GmZF351 locus. Two JMJ30-demethylase-like genes, GmJMJ30-1 and GmJMJ30-2, are involved in this demethylation process. Overexpression of GmJMJ30-1/2 in transgenic hairy roots enhances GmZF351 expression mediated by histone demethylation and confers stress tolerance to soybean. Yield-related agronomic traits were evaluated in stable GmZF351-transgenic plants under mild drought stress conditions. Our study reveals a new mode of GmJMJ30-GmZF351 action in stress tolerance, in addition to that of GmZF351 in oil accumulation. Manipulation of the components in this pathway is expected to improve soybean traits and adaptation under unfavorable environments.

Progress and Prospects of the Molecular Basis of Soybean Cold Tolerance

Cold stress is a major factor influencing the geographical distribution of soybean growth and causes immense losses in productivity. Understanding the molecular mechanisms that the soybean has undergone to survive cold temperatures will have immense value in improving soybean cold tolerance. This review focuses on the molecular mechanisms involved in soybean response to cold. We summarized the recent studies on soybean cold-tolerant quantitative trait loci (QTLs), transcription factors, associated cold-regulated (COR) genes, and the regulatory pathways in response to cold stress. Cold-tolerant QTLs were found to be overlapped with the genomic region of maturity loci of E1, E3, E4, pubescence color locus of T, stem growth habit gene locus of Dt1, and leaf shape locus of Ln, indicating that pleiotropic loci may control multiple traits, including cold tolerance. The C-repeat responsive element binding factors (CBFs) are evolutionarily conserved across species. The expression of most GmDREB1s was upregulated by cold stress and overexpression of GmDREB1B;1 in soybean protoplast, and transgenic Arabidopsis plants can increase the expression of genes with the DRE core motif in their promoter regions under cold stress. Other soybean cold-responsive regulators, such as GmMYBJ1, GmNEK1, GmZF1, GmbZIP, GmTCF1a, SCOF-1 and so on, enhance cold tolerance by regulating the expression of COR genes in transgenic Arabidopsis. CBF-dependent and CBF-independent pathways are cross-talking and work together to activate cold stress gene expression. Even though it requires further dissection for precise understanding, the function of soybean cold-responsive transcription factors and associated COR genes studied in Arabidopsis shed light on the molecular mechanism of cold responses in soybeans and other crops. Furthermore, the findings may also provide practical applications for breeding cold-tolerant soybean varieties in high-latitude and high-altitude regions.

Comparative analysis of physiological variations and genetic architecture for cold stress response in soybean germplasm

Soybean (Glycine max L.) is susceptible to low temperatures. Increasing lines of evidence indicate that abiotic stress-responsive genes are involved in plant low-temperature stress response. However, the involvement of photosynthesis, antioxidants and metabolites genes in low temperature response is largely unexplored in Soybean. In the current study, a genetic panel of diverse soybean varieties was analyzed for photosynthesis, chlorophyll fluorescence and leaf injury parameters under cold stress and control conditions. This helps us to identify cold tolerant (V100) and cold sensitive (V45) varieties. The V100 variety outperformed for antioxidant enzymes activities and relative expression of photosynthesis (Glyma.08G204800.1, Glyma.12G232000.1), GmSOD (GmSOD01, GmSOD08), GmPOD (GmPOD29, GmPOD47), trehalose (GmTPS01, GmTPS13) and cold marker genes (DREB1E, DREB1D, SCOF1) than V45 under cold stress. Upon cold stress, the V100 variety showed reduced accumulation of H₂O₂ and MDA levels and subsequently showed lower leaf injury compared to V45. Together, our results uncovered new avenues for identifying cold tolerant soybean varieties from a large panel. Additionally, we identified the role of antioxidants, osmo-protectants and their posttranscriptional regulators miRNAs such as miR319, miR394, miR397, and miR398 in Soybean cold stress tolerance.

An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean

Soybean is sensitive to low temperatures during the crop growing season. An urgent demand for breeding cold-tolerant cultivars to alleviate the production loss is apparent to cope with this scenario. Cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. In this study, we proposed an advanced systems biology framework of feature engineering for the discovery of cold tolerance genes (CTgenes) from integrated omics and non-omics (OnO) data in soybean. An integrative pipeline was introduced for feature selection and feature extraction from different layers in the integrated OnO data using data ensemble methods and the non-parameter random forest prioritization to minimize uncertainties and false positives for accuracy improvement of results. In total, 44, 143, and 45 CTgenes were identified in short-, mid-, and long-term cold treatment, respectively, from the corresponding gene-pool. These CTgenes outperformed the remaining genes, the random genes, and the other candidate genes identified by other approaches in an independent RNA-seq database. Furthermore, we applied pathway enrichment and crosstalk network analyses to uncover relevant physiological pathways with the discovery of underlying cold tolerance in hormone- and defense-related modules. Our CTgenes were validated by using 55 SNP genotype data of 56 soybean samples in cold tolerance experiments. This suggests that the CTgenes identified from our proposed systematic framework can effectively distinguish cold-resistant and cold-sensitive lines. It is an important advancement in the soybean cold-stress response. The proposed pipelines provide an alternative solution to biomarker discovery, module discovery, and sample classification underlying a particular trait in plants in a robust and efficient way.

Exogenous melatonin stimulated isoflavone biosynthesis in NaCl-stressed germinating soybean (Glycine max L.)

Melatonin (MT) has gained increasing attention due to its pleiotropic effects. In this study, the function of exogenous MT on the response to NaCl stress and isoflavone biosynthesis in germinating soybeans was investigated. Results showed the exogenous MT (100 μM) application neutralised the negative effects of NaCl stress (60 mM), induced sprout growth, biomass and fluorescence intensity of intracellular free calcium, decreased malondialdehyde, H2O2 content and fluorescence intensity of O2•-, and enhanced superoxide dismutase, catalase and peroxidas activities of germinating soybeans. Meanwhile, total flavonoids and different forms of isoflavone content were enhanced by MT application, not only companied by the up-regulated relative gene expression of cinnamic acid 4-hydroxylase chalcone reductase, chalcone isomerase 1A, isoflavone reductase and isoflavone synthase 1 that involved in isoflavone biosynthesis, but also increased activities of phenylalanine ammonia lyase and 4-coumarate coenzyme A ligase. Given the evidence from the present study, it's proposed that the exogenous MT could relieve NaCl stress and stimulate isoflavone biosynthesis in germinating soybeans.

Time-series transcriptome comparison reveals the gene regulation network under salt stress in soybean (Glycine max) roots

BACKGROUND

Soil salinity is a primary factor limiting soybean (Glycine max) productivity. Breeding soybean for tolerance to high salt conditions is therefore critical for increasing yield. To explore the molecular mechanism of soybean responses to salt stress, we performed a comparative transcriptome time-series analysis of root samples collected from two soybean cultivars with contrasting salt sensitivity.

RESULTS

The salt-tolerant cultivar 'Qi Huang No.34' (QH34) showed more differential expression of genes than the salt-sensitive cultivar 'Dong Nong No.50' (DN50). We identified 17,477 genes responsive to salt stress, of which 6644 exhibited distinct expression differences between the two soybean cultivars. We constructed the corresponding co-expression network and performed Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The results suggested that phytohormone signaling, oxidoreduction, phenylpropanoid biosynthesis, the mitogen-activated protein kinase pathway and ribosome metabolism may play crucial roles in response to salt stress.

CONCLUSIONS

Our comparative analysis offers a comprehensive understanding of the genes involved in responding to salt stress and maintaining cell homeostasis in soybean. The regulatory gene networks constructed here also provide valuable molecular resources for future functional studies and breeding of soybean with improved tolerance to salinity.

The response mechanism to salt stress in Arabidopsis transgenic lines over-expressing of GmG6PD

Glucose-6-phosphate dehydrogenase (G6PD or G6PDH) plays an important role in response to salt stress in plants. However, much less is known about G6PD proteins in soybean (Glycine max L.). Here, we found that a soybean cytosolic G6PD gene, GmG6PD7, was induced by NaCl. We generated Arabidopsis transgenic lines overexpressing GmG6PD7. The seed germination rate and primary root length of Arabidopsis thaliana over-expressing GmG6PD7 under NaCl treatment were enhanced. Salt stress induced an obvious increase of the total and cytosolic G6PD activity and the marked decrease of ROS levels in the transgenic plants. At the same time, over-expressing GmG6PD7 in Arabidopsis affected the glutathione and NADPH level and activated ROS scavengers, suggesting that GmG6PD7 contributes to increase salinity tolerance by decreasing ROS accumulation. What's more, we found GmG6PD7 overexpression led to the up-regulation of abscisic acid (ABA) degradation gene and the down-regulation of ABA synthesis and ABA-responsive genes, which finally reduced ABA content to improve seed germination rate under salinity stress. It was noteworthy that GmG6PD7 can rescue the seed and root phenotype of Arabidopsis cytosolic G6PD mutant (Atg6pd5 and Atg6pd6) under salt stress, suggesting cytosolic G6PD may have a conserved function in soybean and Arabidopsis.

LcFIN2, a novel chloroplast protein gene from sheepgrass, enhances tolerance to low temperature in Arabidopsis and rice

Adverse environmental stresses affect plant growth and crop yields. Sheepgrass (Leymus chinensis (Trin.) Tzvel), an important forage grass that is widely distributed in the east of Eurasia steppe, has high tolerance to extreme low temperature. Many genes that respond to cold stress were identified in sheepgrass by RNA-sequencing, but more detailed studies are needed to dissect the function of those genes. Here, we found that LcFIN2, a sheepgrass freezing-induced protein 2, encoded a chloroplast-targeted protein. Expression of LcFIN2 was upregulated by freezing, chilling, NaCl and abscisic acid (ABA) treatments. Overexpression of LcFIN2 enhanced the survival rate of transgenic Arabidopsis after freezing stress. Importantly, heterologous expression of LcFIN2 in rice exhibited not only higher survival rate but also accumulated various soluble substances and reduced membrane damage in rice under chilling stress. Furthermore, the chlorophyll content, the quantum photochemistry efficiency of photosystem II (ΦPSII), the non-photochemical quenching (NPQ), the net photosynthesis rate (Pn) and the expression of some chloroplast ribosomal-related and photosynthesis-related genes were higher in the transgenic rice under chilling stress. These findings suggested that the LcFIN2 gene could potentially be used to improve low-temperature tolerance in crops.

A late embryogenesis abundant protein GsPM30 interacts with a receptor like cytoplasmic kinase GsCBRLK and regulates environmental stress responses

A Glycine soja receptor like cytoplasmic kinase GsCBRLK was previously characterized as a positive regulator of salt tolerance. However, how GsCBRLK regulates stress responses remains obscure. Here, we report the interaction between GsCBRLK and a group 3 late embryogenesis abundant protein GsPM30, and suggest its role in stress responses. GsPM30 was found to physically associate with GsCBRLK through yeast two hybrid assays, which was verified by bimolecular fluorescence complementation analysis. Deletion analyses showed that the N-terminal variable domain of GsCBRLK was sufficient for GsPM30 interaction. Besides GsPM30, GsCBRLK could associate with several group 3 LEAs, of which the N-terminus sequences show high identity with GsPM30. Lower binding affinity or even no interaction was observed between GsCBRLK and other group 3 LEAs, which are less closely related to GsPM30. Furthermore, we observed that GsPM30 could localize surrounding the internal circumference of plant cells, as well as in cytoplasm and nucleus. In addition, GUS staining and quantitative real-time PCR results suggested the ubiquitous expression in different tissues and induced expression by NaCl and mannitol treatments for GsPM30. Consistently, GsPM30 overexpression in Arabidopsis caused increased tolerance to high salinity and dehydration/water deficit at both the young and adult seedling stages. Our results demonstrated the interaction between GsCBRLK and LEAs, and revealed the positive role of GsPM30 in stress responses.

Large-Scale Investigation of Soybean Gene Functions by Overexpressing a Full-Length Soybean cDNA Library in Arabidopsis

Molecular breeding has become an important approach for crop improvement, and a prerequisite for molecular breeding is elucidation of the functions of genetic loci or genes. Soybean is one of the most important food and oil crops worldwide. However, due to the difficulty of genetic transformation in soybean, studies of its functional genomics lag far behind those of other crops such as rice, which severely impairs the progress of molecular improvement in soybean. Here, we describe an effective large-scale strategy to investigate the functions of soybean genes via overexpression of a full-length soybean cDNA library in Arabidopsis. The overexpression vector pJL12 was modified for use in the construction of a normalized full-length cDNA library. The constructed cDNA library showed good quality; repetitive clones represented approximately 4%, insertion fragments were approximately 2.2 kb, and the full-length rate was approximately 98%. This cDNA library was then overexpressed in Arabidopsis, and approximately 2000 transgenic lines were preliminarily obtained. Phenotypic analyses of the positive T₁ transgenic plants showed that more than 5% of the T₁ transgenic lines displayed abnormal developmental phenotypes, and approximately 1% of the transgenic lines exhibited potentially favorable traits. We randomly amplified 4 genes with obvious phenotypes (enlarged seeds, yellowish leaves, more branches, and dense siliques) and repeated the transgenic analyses in Arabidopsis. Subsequent phenotypic observation demonstrated that these phenotypes were indeed due to the overexpression of soybean genes. We believe our strategy represents an effective large-scale approach to investigate the functions of soybean genes and further reveal genes favorable for molecular improvement in soybean.

Dissecting the Genetic Basis of Local Adaptation in Soybean

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep gradients in allele frequency across geographical distance and between landrace and modern cultivars. Our combined application of methods in environmental association mapping and detection of selection targets provide a better understanding of how geography and selection may have shaped genetic variation among soybean landraces. Moreover, we identified several important candidate genes related to drought and heat stress, and revealed important genomic regions possibly involved in the geographic divergence of soybean.