Genome-Wide Characterization and Expression Analysis of Soybean TGA Transcription Factors Identified a Novel TGA Gene Involved in Drought and Salt Tolerance

Transcription factor DcbZIPs regulate secondary metabolism in Dendrobium catenatum during cold stress

Cold stress seriously affects plant development and secondary metabolism. The basic region/leucine zipper (bZIP) is one of the largest transcription factor (TFs) family and widely involved in plant cold stress response. However, the function of bZIP in Dendrobium catenatum has not been well-documented. Cold inhibited the growth of D. catenatum and increased total polysaccharide and alkaloid contents in stems. Here, 62 DcbZIP genes were identified in D. catenatum, which were divided into 13 subfamilies. Among them, 58 DcbZIPs responded to cold stress, which were selected based on the transcriptome database produced from cold-treated D. catenatum seedlings. Specifically, the expression of DcbZIP3/6/28 was highly induced by cold treatment in leaves or stems. Gene sequence analysis indicated that DcbZIP3/6/28 contains the bZIP conserved domain and is localized to the cell nucleus. Co-expression networks showed that DcbZIP6 was significantly negatively correlated with PAL2 (palmitoyl-CoA), which is involved in flavonoid metabolism. Moreover, DcbZIP28 has significant negative correlations with various metabolism-related genes in the polysaccharide metabolic pathway, including PFKA1 (6-phosphofructokinase), ALDO2 (aldose-6-phosphate reductase) and SCRK5 (fructokinase). These results implied that DcbZIP6 or DcbZIP28 are mainly involved in flavonoid or polysaccharide metabolism. Overall, these findings provide new insights into the roles of the DcbZIP gene family in secondary metabolism in D. catenatum under cold stress.

Systematic analysis of bZIP gene family in Suaeda australis reveal their roles under salt stress

BACKGROUND

Suaeda australis is one of typical halophyte owing to high levels of salt tolerance. In addition, the bZIP gene family assumes pivotal functions in response to salt stress. However, there are little reports available regarding the bZIP gene family in S. australis.

RESULTS

In this study, we successfully screened 44 bZIP genes within S. australis genome. Subsequently, we conducted an extensive analysis, encompassing investigations into chromosome location, gene structure, phylogenetic relationship, promoter region, conserved motif, and gene expression profile. The 44 bZIP genes were categorized into 12 distinct groups, exhibiting an uneven distribution among the 9 chromosomes of S. australis chromosomes, but one member (Sau23745) was mapped on unanchored scaffolds. Examination of cis-regulatory elements revealed that bZIP promoters were closely related to anaerobic induction, transcription start, and light responsiveness. Comparative transcriptome analysis between ST1 and ST2 samples identified 2,434 DEGs, which were significantly enriched in some primary biological pathways related to salt response-regulating signaling based on GO and KEGG enrichment analysis. Expression patterns analyses clearly discovered the role of several differently expressed SabZIPs, including Sau08107, Sau08911, Sau11415, Sau16575, and Sau19276, which showed higher expression levels in higher salt concentration than low concentration and a response to salt stress. These expression patterns were corroborated through RT-qPCR analysis. The six differentially expressed SabZIP genes, all localized in the nucleus, exhibited positive regulation involved in the salt stress response. SabZIP14, SabZIP26, and SabZIP36 proteins could bind to the promoter region of downstream salt stress-related genes and activate their expressions.

CONCLUSIONS

Our findings offer valuable insights into the evolutionary trajectory of the bZIP gene family in S. australis and shed light on their roles in responding to salt stress. In addition to fundamental genomic information, these results would serve as a foundational framework for future investigations into the regulation of salt stress responses in S. australis.

Genome-Wide Identification of the TGA Gene Family and Expression Analysis under Drought Stress in Brassica napus L

TGA transcription factors belong to Group D of the bZIP transcription factors family and play vital roles in the stress response of plants. Brassica napus is an oil crop with rich economic value. However, a systematic analysis of TGA gene family members in B. napus has not yet been reported. In this study, we identified 39 full-length TGA genes in B. napus, renamed TGA1~TGA39. Thirty-nine BnTGA genes were distributed on 18 chromosomes, mainly located in the nucleus, and differences were observed in their 3D structures. Phylogenetic analysis showed that 39 BnTGA genes could be divided into five groups. The BnTGA genes in the same group had similar structure and motif compositions, and all the BnTGA genes had the same conserved bZIP and DOG1 domains. Phylogenetic and synteny analysis showed that the BnTGA genes had a close genetic relationship with the TGA genes of the Brassica juncea, and BnTGA11 and BnTGA29 may play an important role in evolution. In addition, qRT-PCR revealed that three genes (BnTGA14/17/23) showed significant changes in eight experimental materials after drought treatment. Meanwhile, it can be inferred from the results of drought treatment on different varieties of rapeseed that the stress tolerance of parental rapeseed can be transmitted to the offspring through hybridization. In short, these findings have promoted the understanding of the B. napus TGA gene family and will contribute to future research aimed at B. napus resistant breeding.

Genome-wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress

In plantae, basic leucine zipper (bZIP) transcription factors (TFs) are widespread and regulate a variety of biological processes under abiotic stress. However, it has not been extensively studied in Rosaceae, and the functional effects of bZIP on Eriobotrya japonica under salt stress are still unknown. Therefore, in this study, the bZIP TF family of 12 species of Rosaceae was analyzed by bioinformatics method, and the expression profile and quantitative real-time polymerase chain reaction of E. japonica under salt stress were analyzed. The results showed that a total of 869 bZIP TFs were identified in 12 species of Rosaceae and divided into nine subfamilies. Differences in promoter cis-elements between subfamilies vary depending on their role. Species belonging to the same subfamily have a similar number of chromosomes and the number of genes contained on each chromosome. Gene duplication analysis has found segmental duplication to be a prime force in the evolution of Rosaceae species. In addition, nine EjbZIPs were significantly different, including seven up-regulated and two down-regulated in E. japonica under salt stress. Especially, EjbZIP13 was involved in the expression of SA-responsive proteins by binding to the NPR1 gene. EjbZIP27, EjbZIP30, and EjbZIP38 were highly expressed in E. japonica under salt stress, thus improving the salt tolerance capacity of the plants. These results can provide a theoretical basis for exploring the characteristics and functions of the bZIP TF family in more species and breeding salt-tolerant E. japonica varieties. It also provides a reference for resolving the response mechanism of bZIP TF in 12 Rosaceae species under salt stress.

EuTGA1, a bZIP transcription factor, positively regulates EuFPS1 expression in Eucommia ulmoides

Eucommia ulmoides (E. ulmoides) is widely cultivated and exhibits remarkable adaptability in China. It is the most promising rubber source plant in the temperate zone. E. ulmoides gum (EUG) is a trans-polyisoprene with a unique "rubber-plastic duality", and is widely used in advanced materials and biomedical fields. The transcription of Farnesyl pyrophosphate synthase (FPS), the rate-limiting enzyme of EUG biosynthesis, is controlled by regulatory mechanisms that remain poorly elucidated. In this research, 12 TGA transcription factors (TFs) in E. ulmoides were identified. Promoter prediction results revealed that the EuFPS1 promoter had binding sites for EuTGAs. Subsequently, the EuTGA1 was obtained by screening the E. ulmoides cDNA library using the EuFPS1 promoter as a bait. The individual yeast one‑hybrid and dual-luciferase assays confirmed that in the tobacco plant, EuTGA1 interacted with the EuFPS1 promoter, resulting in a more than threefold increase in the activity of the EuFPS1. Subcellular localization study further revealed that EuTGA1 is localized in the nucleus and acts as a TF to regulate EuFPS1 expression. In addition, qRT-PCR analysis demonstrated that the expression trend of EuFPS1 and EuTGA1 was the same at different time of the year. Notably, low temperature and MeJA treatments down-regulated EuTGA1 expression. Additionally, the transient transformation of EuTGA1 enhanced NtFPS1 expression in tobacco plants. Overall, this study identified a TF that interacted with EuFPS1 promoter to positively regulate EuFPS1 expression. The findings of this study provide a theoretical basis for further research on the expression regulation of EuFPS1.

Genome-Wide Identification and Expression Analysis of TGA Family Genes Associated with Abiotic Stress in Sunflowers (Helianthus annuus L.)

Sunflower (Helianthus annuus L.) is an important, substantial global oil crop with robust resilience to drought and salt stresses. The TGA (TGACG motif-binding factor) transcription factors, belonging to the basic region leucine zipper (bZIP) family, have been implicated in orchestrating multiple biological processes. Despite their functional significance, a comprehensive investigation of the TGA family's abiotic stress tolerance in sunflowers remains elusive. In the present study, we identified 14 TGA proteins in the sunflower genome, which were unequally distributed across 17 chromosomes. Employing phylogenetic analysis encompassing 149 TGA members among 13 distinct species, we revealed the evolutionary conservation of TGA proteins across the plant kingdom. Collinearity analysis suggested that both HaTGA01 and HaTGA03 were generated due to HaTGA08 gene duplication. Notably, qRT-PCR analysis demonstrated that HaTGA04, HaTGA05, and HaTGA14 genes were remarkably upregulated under ABA, MeJA, and salt treatments, whereas HaTGA03, HaTGA06, and HaTGA07 were significantly repressed. This study contributes valuable perspectives on the potential roles of the HaTGA gene family under various stress conditions in sunflowers, thereby enhancing our understanding of TGA gene family dynamics and function within this agriculturally significant species.

A comprehensive review of TGA transcription factors in plant growth, stress responses, and beyond

TGA transcription factors (TFs), belonging to the D clade of the basic region leucine zipper (bZIP) family, exhibit a specific ability to recognize and bind to regulatory elements with TGACG as the core recognition sequence, enabling the regulation of target gene expression and participation in various biological regulatory processes. In plant growth and development, TGA TFs influence organ traits and phenotypes, including initial root length and flowering time. They also play a vital role in responding to abiotic stresses like salt, drought, and cadmium exposure. Additionally, TGA TFs are involved in defending against potential biological stresses, such as fungal bacterial diseases and nematodes. Notably, TGA TFs are sensitive to the oxidative-reductive state within plants and participate in pathways that aid in the elimination of reactive oxygen species (ROS) generated during stressful conditions. TGA TFs also participate in multiple phytohormonal signaling pathways (ABA, SA, etc.). This review thoroughly examines the roles of TGA TFs in plant growth, development, and stress response. It also provides detailed insights into the mechanisms underlying their involvement in physiological and pathological processes, and their participation in plant hormone signaling. This multifaceted exploration distinguishes this review from others, offering a comprehensive understanding of TGA TFs.

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Abstract Germin-like proteins (GLPs) play an important role against various stresses. Vitis vinifera L. genome contains 7 GLPs; many of them are functionally unexplored. However, the computational analysis may provide important new insight into their function. Currently, physicochemical properties, subcellular localization, domain architectures, 3D structures, N-glycosylation & phosphorylation sites, and phylogeney of the VvGLPs were investigated using the latest computational tools. Their functions were predicted using the Search tool for the retrieval of interacting genes/proteins (STRING) and Blast2Go servers. Most of the VvGLPs were extracellular (43%) in nature but also showed periplasmic (29%), plasma membrane (14%), and mitochondrial- or chloroplast-specific (14%) expression. The functional analysis predicted unique enzymatic activities for these proteins including terpene synthase, isoprenoid synthase, lipoxygenase, phosphate permease, receptor kinase, and hydrolases generally mediated by Mn+ cation. VvGLPs showed similarity in the overall structure, shape, and position of the cupin domain. Functionally, VvGLPs control and regulate the production of secondary metabolites to cope with various stresses. Phylogenetically VvGLP1, -3, -4, -5, and VvGLP7 showed greater similarity due to duplication while VvGLP2 and VvGLP6 revealed a distant relationship. Promoter analysis revealed the presence of diverse cis-regulatory elements among which CAAT box, MYB, MYC, unnamed-4 were common to all of them. The analysis will help to utilize VvGLPs and their promoters in future food programs by developing resistant cultivars against various biotic (Erysiphe necator and in Powdery Mildew etc.) and abiotic (Salt, drought, heat, dehydration, etc.) stresses.

Caffeine Produced in Rice Plants Provides Tolerance to Water-Deficit Stress

Exogenous or endogenous caffeine application confers resistance to diverse biotic stresses in plants. In this study, we demonstrate that endogenous caffeine in caffeine-producing rice (CPR) increases tolerance even to abiotic stresses such as water deficit. Caffeine produced by CPR plants influences the cytosolic Ca2+ ion concentration gradient. We focused on examining the expression of Ca2+-dependent protein kinase genes, a subset of the numerous proteins engaged in abiotic stress signaling. Under normal conditions, CPR plants exhibited increased expressions of seven OsCPKs (OsCPK10, OsCPK12, OsCPK21, OsCPK25, OsCPK26, OsCPK30, and OsCPK31) and biochemical modifications, including antioxidant enzyme (superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase) activity and non-enzymatic antioxidant (ascorbic acid) content. CPR plants exhibited more pronounced gene expression changes and biochemical alterations in response to water-deficit stress. CPR plants revealed increased expressions of 16 OsCPKs (OsCPK1, OsCPK2, OsCPK3, OsCPK4, OsCPK5, OsCPK6, OsCPK9, OsCPK10, OsCPK11, OsCPK12, OsCPK14, OsCPK16, OsCPK18, OsCPK22, OsCPK24, and OsCPK25) and 8 genes (OsbZIP72, OsLEA25, OsNHX1, OsRab16d, OsDREB2B, OsNAC45, OsP5CS, and OsRSUS1) encoding factors related to abiotic stress tolerance. The activity of antioxidant enzymes increased, and non-enzymatic antioxidants accumulated. In addition, a decrease in reactive oxygen species, an accumulation of malondialdehyde, and physiological alterations such as the inhibition of chlorophyll degradation and the protection of photosynthetic machinery were observed. Our results suggest that caffeine is a natural chemical that increases the potential ability of rice to cope with water-deficit stress and provides robust resistance by activating a rapid and comprehensive resistance mechanism in the case of water-deficit stress. The discovery, furthermore, presents a new approach for enhancing crop tolerance to abiotic stress, including water deficit, via the utilization of a specific natural agent.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

Dissecting the features of TGA gene family in Saccharum and the functions of ScTGA1 under biotic stresses

Sugarcane is an important sugar and energy crop and smut disease caused by Sporisorium scitamineum is a major fungal disease which can seriously reduce the yield and quality of sugarcane. In plants, TGACG motif binding (TGA) transcription factors are involved in the regulation of salicylic acid (SA) and methyl jasmonate (MeJA) signaling pathways, as well as in response to various biotic and abiotic stresses. However, no TGA-related transcription factor has been reported in Saccharum. In the present study, 44 SsTGA genes were identified from Saccharum spontaneum, and were assorted into three clades (I, II, III). Cis-regulatory elements (CREs) analysis revealed that SsTGA genes may be involved in hormone and stress response. RNA-seq data and RT-qPCR analysis indicated that SsTGAs were constitutively expressed in different tissues and induced by S. scitamineum stress. In addition, a ScTGA1 gene (GenBank accession number ON416997) was cloned from the sugarcane cultivar ROC22, which was homologous to SsTGA1e in S. spontaneum and encoded a nucleus protein. It was constitutively expressed in sugarcane tissues and up-regulated by SA, MeJA and S. scitamineum stresses. Furthermore, transient overexpression of ScTGA1 in Nicotiana benthamiana could enhance its resistance to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum, by regulating the expression of immune genes related to hypersensitive response (HR), ethylene (ET), SA and jasmonic acid (JA) pathways. This study should contribute to our understanding on the evolution and function of the SsTGA gene family in Saccharum, and provide a basis for the functional identification of ScTGA1 under biotic stresses.

Physiological and Transcriptomic Analyses of the Effects of Exogenous Lauric Acid on Drought Resistance in Peach (Prunus persica (L.) Batsch)

Peach (Prunus persica (L.) Batsch) is a fruit tree of economic and nutritional importance, but it is very sensitive to drought stress, which affects its growth to a great extent. Lauric acid (LA) is a fatty acid produced in plants and associated with the response to abiotic stress, but the underlying mechanism remains unclear. In this study, physiological analysis showed that 50 ppm LA pretreatment under drought stress could alleviate the growth of peach seedlings. LA inhibits the degradation of photosynthetic pigments and the closing of pores under drought stress, increasing the photosynthetic rate. LA also reduces the content of O₂^-, H₂O₂, and MDA under drought stress; our results were confirmed by Evans Blue, nitroblue tetrazolium (NBT), and DAB(3,3-diaminobenzidine) staining experiments. It may be that, by directly removing reactive oxygen species (ROS) and improving enzyme activity, i.e., catalase (CAT) activity, peroxidase (POD) activity, superoxide dismutase (SOD) activity, and ascorbate peroxidase (APX) activity, the damage caused by reactive oxygen species to peach seedlings is reduced. Peach seedlings treated with LA showed a significant increase in osmoregulatory substances compared with those subjected to drought stress, thereby regulating osmoregulatory balance and reducing damage. RNA-Seq analysis identified 1876 DEGs (differentially expressed genes) in untreated and LA-pretreated plants under drought stress. In-depth analysis of these DEGs showed that, under drought stress, LA regulates the expression of genes related to plant-pathogen interaction, phenylpropanoid biosynthesis, the MAPK signaling pathway, cyanoamino acid metabolism, and sesquiterpenoid and triterpenoid biosynthesis. In addition, LA may activate the Ca²⁺ signaling pathway by increasing the expressions of CNGC, CAM/CML, and CPDK family genes, thereby improving the drought resistance of peaches. In summary, via physiological and transcriptome analyses, the mechanism of action of LA in drought resistance has been revealed. Our research results provide new insights into the molecular regulatory mechanism of the LA-mediated drought resistance of peach trees.

GmDof41 regulated by the DREB1-type protein improves drought and salt tolerance by regulating the DREB2-type protein in soybean

Despite their essential and multiple roles in biological processes, the molecular mechanism of Dof transcription factors (TFs) for responding to abiotic stresses is rarely reported in plants. We identified a soybean Dof gene GmDof41 which was involved in the responses to drought, salt, and exogenous ABA stresses. Overexpression of GmDof41 in soybean transgenic hairy roots attenuated H₂O₂ accumulation and regulated proline homeostasis, resulting in the drought and salt tolerance. Yeast one-hybrid and electrophoretic mobility shift assay (EMSA) illustrated that GmDof41 was regulated by the DREB1-type protein GmDREB1B;1 that could improve drought and salt tolerance in plants. Further studies illustrated GmDof41 can directly bind to the promoter of GmDREB2A which encodes a DREB2-type protein and affects abiotic stress tolerance in plants. Collectively, our results suggested that GmDof41 positively regulated drought and salt tolerance by correlating with GmDREB1B;1 and GmDREB2A. This study provides an important basis for further exploring the abiotic stress-tolerance mechanism of Dof TFs in soybean.

Emerging Roles of Salicylic Acid in Plant Saline Stress Tolerance

One of the most important phytohormones is salicylic acid (SA), which is essential for the regulation of plant growth, development, ripening, and defense responses. The role of SA in plant-pathogen interactions has attracted a lot of attention. Aside from defense responses, SA is also important in responding to abiotic stimuli. It has been proposed to have great potential for improving the stress resistance of major agricultural crops. On the other hand, SA utilization is dependent on the dosage of the applied SA, the technique of application, and the status of the plants (e.g., developmental stage and acclimation). Here, we reviewed the impact of SA on saline stress responses and the associated molecular pathways, as well as recent studies toward understanding the hubs and crosstalk between SA-induced tolerances to biotic and saline stress. We propose that elucidating the mechanism of the SA-specific response to various stresses, as well as SA-induced rhizosphere-specific microbiome modeling, may provide more insights and support in coping with plant saline stress.

Genome-wide identification of the TGA genes in common bean (Phaseolus vulgaris) and revealing their functions in response to Fusarium oxysporum f. sp. phaseoli infection

Fusarium wilt, which affects common bean all across the world, is caused by Fusarium oxysporum f. sp. Phaseoli (Fop). It is necessary to have functional genes in response to Fop infection because they might be used to manage disease. As a crucial regulator, TGA-binding transcription factor (TGA) is engaged in the defense mechanism of plants against pathogens. The role of TGA regulators in common bean in response to Fop infection, however, has not been documented. Hence, we performed genome-wide identified and characterized eight TGA genes in common bean. In this study, eight PvTGA genes were distributed on six chromosomes and classified into four subgroups. The PvTGA genes have the same conserved bZIP and DOG1 domains, but there are specific sequence structures in different PvTGAs. Phylogenetic and synteny analysis explained that PvTGA gene has a close genetic relationship with legume TGAs and that PvTGA03 and PvTGA05 may play an important role in evolution. Transcriptome data explained that expression levels of PvTGA genes showed diversity in different tissues. After Fop inoculation, the expression levels of PvTGA03 and PvTGA07 were significantly different between resistant and susceptible genotypes. Under SA treatment, the expression levels of PvTGA03, PvTGA04, PvTGA06, PvTGA07 and PvTGA08 were significantly different. These results imply that PvTGA03 and PvTGA07 play key roles in SA-mediated resistance to Fusarium wilt. Together, these findings advance knowledge of the PvTGA gene family in common bean and will help future studies aimed at reducing Fusarium wilt.

Divergence of functions and expression patterns of soybean bZIP transcription factors

Soybean (Glycine max) is a major protein and oil crop. Soybean basic region/leucine zipper (bZIP) transcription factors are involved in many regulatory pathways, including yield, stress responses, environmental signaling, and carbon-nitrogen balance. Here, we discuss the members of the soybean bZIP family and their classification: 161 members have been identified and clustered into 13 groups. Our review of the transcriptional regulation and functions of soybean bZIP members provides important information for future study of bZIP transcription factors and genetic resources for soybean breeding.

Unfolding molecular switches for salt stress resilience in soybean: recent advances and prospects for salt-tolerant smart plant production

The increasing sodium salts (NaCl, NaHCO3, NaSO4 etc.) in agricultural soil is a serious global concern for sustainable agricultural production and food security. Soybean is an important food crop, and their cultivation is severely challenged by high salt concentration in soils. Classical transgenic and innovative breeding technologies are immediately needed to engineer salt tolerant soybean plants. Additionally, unfolding the molecular switches and the key components of the soybean salt tolerance network are crucial for soybean salt tolerance improvement. Here we review our understandings of the core salt stress response mechanism in soybean. Recent findings described that salt stress sensing, signalling, ionic homeostasis (Na⁺/K⁺) and osmotic stress adjustment might be important in regulating the soybean salinity stress response. We also evaluated the importance of antiporters and transporters such as Arabidopsis K⁺ Transporter 1 (AKT1) potassium channel and the impact of epigenetic modification on soybean salt tolerance. We also review key phytohormones, and osmo-protectants and their role in salt tolerance in soybean. In addition, we discuss the progress of omics technologies for identifying salt stress responsive molecular switches and their targeted engineering for salt tolerance in soybean. This review summarizes recent progress in soybean salt stress functional genomics and way forward for molecular breeding for developing salt-tolerant soybean plant.

Leaf-transcriptome profiles of phoebe bournei provide insights into temporal drought stress responses

Phoebe bournei (Hemsl.) Yang is used as a commercial wood in China and is enlisted as a near-threatened species. Prolonged droughts pose a serious threat to young seedlings (1-2 years old). A transcriptome sequencing approach, together with the measurement of growth parameters and biochemical analyses were used to understand P. bournei's drought responses on 15d, 30d, and 45d of drought stress treatment. The stem and root dry weights decreased significantly with drought stress duration. Activities of antioxidative enzymes i.e., peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) increased significantly with the increase in drought stress duration. A total of 13,274, 15,648, and 9,949 genes were differentially expressed in CKvs15d, CKvs30d, and CKvs45d, respectively. The differential expression analyses showed that photosystem I and II underwent structural changes, chlorophyll biosynthesis, and photosynthesis were reduced. The genes annotated as POD, SOD, and CAT were upregulated in drought-treated leaves as compared to control. Additionally, plant-hormone signal transduction, MAPK signaling-plant, phenylpropanoid biosynthesis, flavonoid biosynthesis, and starch and sucrose metabolism pathways showed large-scale expression changes in major genes. We also found that members of 25 transcription factor families were differentially expressed. Our study presents and discusses these transcriptome signatures. Overall, our findings represent key data for breeding towards drought stress tolerance in P. bournei.

Molecular Tools and Their Applications in Developing Salt-Tolerant Soybean (Glycine max L.) Cultivars

Abiotic stresses are one of the significant threats to soybean (Glycine max L.) growth and yields worldwide. Soybean has a crucial role in the global food supply chain and food security and contributes the main protein share compared to other crops. Hence, there is a vast scientific saddle on soybean researchers to develop tolerant genotypes to meet the growing need of food for the huge population. A large portion of cultivated land is damaged by salinity stress, and the situation worsens yearly. In past years, many attempts have increased soybean resilience to salinity stress. Different molecular techniques such as quantitative trait loci mapping (QTL), genetic engineering, transcriptome, transcription factor analysis (TFs), CRISPR/Cas9, as well as other conventional methods are used for the breeding of salt-tolerant cultivars of soybean to safeguard its yield under changing environments. These powerful genetic tools ensure sustainable soybean yields, preserving genetic variability for future use. Only a few reports about a detailed overview of soybean salinity tolerance have been published. Therefore, this review focuses on a detailed overview of several molecular techniques for soybean salinity tolerance and draws a future research direction. Thus, the updated review will provide complete guidelines for researchers working on the genetic mechanism of salinity tolerance in soybean.

Genome-wide identification of the TGA gene family in kiwifruit (Actinidia chinensis spp.) and revealing its roles in response to Pseudomonas syringae pv. actinidiae (Psa) infection

Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is a destructive disease of kiwifruit worldwide. Functional genes in response to Psa infection are needed, as they could be utilized to control disease. TGACG-binding transcription factor (TGA), as an essential regulator, involved in the process of plant against pathogens. However, the function of TGA regulators has not been reported in kiwifruit. It is unclear that whether TGA genes play a role in response to Psa infection. Here, we performed genome-wide screening and identified 13 TGA genes in kiwifruit. Phylogenetic analysis showed that 13 members of the AcTGA gene family could be divided into five groups. AcTGA proteins were mainly located in the nucleus, and significant differences were identified in their 3D structures. Segmental duplications promoted the expansion of the AcTGA family. Additionally, RNA-Seq and qRT-PCR revealed that four genes (AcTGA01/06/07/09) were tissue-specific and responsive to hormones at different levels. Subcellular localization showed that four proteins located in the nucleus, and among them, three (AcTGA01/06/07) had transcriptional activation activity. Lastly, transient overexpression proved that these three genes (AcTGA01/06/07) potentially played a role in the resistance to kiwifruit canker. These results provided a theoretical basis for revealing TGA involved in kiwifruit regulation against Psa.

Modulation of GmFAD3 expression alters abiotic stress responses in soybean

KEY MESSAGE

This study focused on enhancing resilience of soybean crops to drought and salinity stresses by overexpression of GmFAD3A gene, which plays an important role in modulating membrane fluidity and ultimately influence plants response to various abiotic stresses. Fatty acid desaturases (FADs) are a class of enzymes that mediate desaturation of fatty acids by introducing double bonds. They play an important role in modulating membrane fluidity in response to various abiotic stresses. However, a comprehensive analysis of GmFAD3 in drought and salinity stress tolerance in soybean is lacking. We used bean pod mottle virus (BPMV)-based vector for achieving rapid and efficient overexpression as well as silencing of Omega-3 Fatty Acid Desaturase gene from Glycine max (GmFAD3) to assess the functional role of GmFAD3 in abiotic stress responses in soybean. Higher levels of recombinant BPMV-GmFAD3A transcripts were detected in overexpressing soybean plants. Overexpression of GmFAD3A in soybean resulted in increased levels of jasmonic acid and higher expression of GmWRKY54 as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants under drought and salinity stress conditions. The GmFAD3A-overexpressing plants showed higher levels of chlorophyll content, efficient photosystem-II, relative water content, transpiration rate, stomatal conductance, proline content and also cooler canopy under drought and salinity stress conditions as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants. Results from the current study revealed that GmFAD3A-overexpressing soybean plants exhibited tolerance to drought and salinity stresses. However, soybean plants silenced for GmFAD3 were vulnerable to drought and salinity stresses.

A Genome-Wide Analysis of StTGA Genes Reveals the Critical Role in Enhanced Bacterial Wilt Tolerance in Potato During Ralstonia solanacearum Infection

TGA is one of the members of TGACG sequence-specific binding protein family, which plays a crucial role in the regulated course of hormone synthesis as a stress-responsive transcription factor (TF). Little is known, however, about its implication in response to bacterial wilt disease in potato (Solanum tuberosum) caused by Ralstonia solanacearum. Here, we performed an in silico identification and analysis of the members of the TGA family based on the whole genome data of potato. In total, 42 StTGAs were predicted to be distributed on four chromosomes in potato genome. Phylogenetic analysis showed that the proteins of StTGAs could be divided into six sub-families. We found that many of these genes have more than one exon according to the conserved motif and gene structure analysis. The heat map inferred that StTGAs are generally expressed in different tissues which are at different stages of development. Genomic collinear analysis showed that there are homologous relationships among potato, tomato, pepper, Arabidopsis, and tobacco TGA genes. Cis-element in silico analysis predicted that there may be many cis-acting elements related to abiotic and biotic stress upstream of StTGA promoter including plant hormone response elements. A representative member StTGA39 was selected to investigate the potential function of the StTGA genes for further analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) assays indicated that the expression of the StTGAs was significantly induced by R. solanacearum infection and upregulated by exogenous salicylic acid (SA), abscisic acid (ABA), gibberellin 3 (GA₃), and methyl jasmonate (MeJA). The results of yeast one-hybrid (Y1H) assay showed that StTGA39 regulates S. tuberosum BRI1-associated receptor kinase 1 (StBAK1) expression. Thus, our study provides a theoretical basis for further research of the molecular mechanism of the StTGA gene of potato tolerance to bacterial wilt.

Comparative Physiological and Transcriptome Analysis Reveal the Molecular Mechanism of Melatonin in Regulating Salt Tolerance in Alfalfa (Medicago sativa L.)

As a high-quality legume forage, alfalfa is restricted by various abiotic stresses during its growth and development. Melatonin is a multifunctional signaling molecule that involves in plant defense against multiple stresses. However, little is known about its downstream signaling pathway and regulatory mechanisms in salt stress of alfalfa. In this study, we investigated the protective effects and key regulatory pathways of melatonin on alfalfa under salt tolerance. The results showed that melatonin promoted the growth of alfalfa seedlings under salt stress, as demonstrated by higher plant height, leaf area, and fresh weight. Melatonin treatment resulted in an increase in the photosynthetic capacity and starch content of alfalfa. Moreover, melatonin decreased cell membrane damage and reactive oxygen species (ROS) accumulation by enhancing antioxidant defense activity under salt stress conditions. Transcriptome sequencing (RNA-seq) analysis revealed that melatonin mainly induced the transcription of genes involved in Ca²⁺ signaling (cyclic nucleotide gated channel, CNGCs; cam modulin/calmodulin-like protein, CAM/CMLs and calcium-dependent protein kinase, CDPKs), starch and sucrose metabolism (α-amylase, AMYs; β-amylase, BAMs; starch synthase, SSs and sucrose synthase, SUSs), plant hormone signal transduction (auxin/indole acetic acid protein, AUX/IAAs; ABA receptor, PYL4; protein phosphatase 2C, PP2Cs; scarecrow-like protein, SCLs and ethylene-responsive transcription factor 1B, ERF1B), and key transcription factors (C3Hs, MYBs, ERFs, and WRKYs). Specifically, we focused on starch and sucrose metabolism and plant hormone signal transduction pathways. The interactions between melatonin and other phytohormones occurred via regulation of the expression of genes involved in hormone signaling pathways. In addition, melatonin increased the contents of endogenous melatonin, auxin, gibberellic acid (GA₃), salicylic acid, brassinosteroids, and ethylene, while decreasing the abscisic acid content under salt stress. In summary, this study established a regulatory network for melatonin-induced key signaling pathways and functional genes under salt stress and provided a theoretical basis for salt tolerance breeding in alfalfa.

HbTGA1, a TGA Transcription Factor From Hevea brasiliensis, Regulates the Expression of Multiple Natural Rubber Biosynthesis Genes

The TGA transcription factors are known to modulate the biosynthesis of secondary metabolites in plants. However, their regulatory function in natural rubber (NR) biosynthesis was not revealed in the rubber tree (Hevea brasiliensis). Here, 14 genes encoding TGA transcription factors (name HbTGA1-HbTGA14) were identified in the rubber tree. HbTGAs were differentially expressed in different tissues. HbTGA1 was expressed at its highest level in latex. We found specific in vitro and in vivo binding of the HbTGA1 protein with promoters of multiple NR biosynthesis genes (HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2). The activation of the promoters of HbHMGS2 and HbCPT6 was significantly suppressed by HbTGA1, while the activities of promoters of HbHMGR2, HbCPT8, and HbSRPP2 were increased by HbTGA1. The promoter activities of HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2 were significantly increased by HbTGA1 under jasmonate stress, while the promoter activities of HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2 were also significantly increased by HbTGA1 under salicylic acid stress. The present study provides insights into the role of TGA transcription factors in regulating the expression of NR biosynthesis genes from H. brasiliensis.

Constitutive expression of a pea apyrase, psNTP9, increases seed yield in field-grown soybean

To address the demand for food by a rapidly growing human population, agricultural scientists have carried out both plant breeding and genetic engineering research. Previously, we reported that the constitutive expression of a pea apyrase (Nucleoside triphosphate, diphosphohydrolase) gene, psNTP9, under the control of the CaMV35S promoter, resulted in soybean plants with an expanded root system architecture, enhanced drought resistance and increased seed yield when they are grown in greenhouses under controlled conditions. Here, we report that psNTP9-expressing soybean lines also show significantly enhanced seed yields when grown in multiple different field conditions at multiple field sites, including when the gene is introgressed into elite germplasm. The transgenic lines have higher leaf chlorophyll and soluble protein contents and decreased stomatal density and cuticle permeability, traits that increase water use efficiency and likely contribute to the increased seed yields of field-grown plants. These altered properties are explained, in part, by genome-wide gene expression changes induced by the transgene.

Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean

Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.

OsTGAL1 suppresses the resistance of rice to bacterial blight disease by regulating the expression of salicylic acid glucosyltransferase OsSGT1

Many TGA transcription factors participate in immune responses in the SA-mediated signaling pathway in Arabidopsis. This study identified a transcription factor OsTGAL1, which is induced upon infection by Xoo. Overexpression of OsTGAL1 increased the susceptibility of rice to Xoo. Plants overexpressing OsTGAL1 could affect the expression of many SA signaling-related genes. OsTGAL1 was able to interact with the promoter of OsSGT1, which encodes a key enzyme for SA metabolism. The transcript of OsSGT1 was induced by Xoo and this responsive expression was further increased in plants overexpressing OsTGAL1. OsSGT1 knockout lines had enhanced resistance to Xoo, and knocking out OsSGT1 in plants overexpressing OsTGAL1 blocked the susceptibility caused by OsTGAL1. Altered expression levels of several OsPRs in all the transgenic plants demonstrated that SA-mediated signaling had been affected. Furthermore, we identified an oxidoreductase of CC-type glutaredoxin, OsGRX17, which interacted with OsTGAL1. OsGRX17 reduced the regulation of OsTGAL1 on OsSGT1, and this may be due to its redox modulation. Thus, our results demonstrate that OsTGAL1 negatively regulates resistance to Xoo by its effects on SA metabolism via the activation of OsSGT1, which provides valuable targets for plant breeders in developing new cultivars that are resistant to Xoo.

The soybean TGA transcription factor GmTGA13 plays important roles in the response to salinity stress

Soybean (Glycine max L.) is an important oil, food and economic crop in the world. High salinity severely affects the growth and yield of soybean. Overexpressing a specific anti-retroviral transcription factor by biotechnology is an effective way to cultivate new stress-tolerant varieties of soybean. TGA transcription factor is a subfamily of bZIP and plays an important role in abiotic stress responses. A TGA subfamily gene GmTGA13 was cloned and the gene expression, subcellular localization and transcriptional activity were measured. Through the Ag. tumefaciens mediated flower dip method and the Ag. rhizogenes mediated transformation of soybean hairy roots, the transgenic Arabidopsis and the 'combination' soybean plants of overexpressing GmTGA13 were obtained. The two types of transgenic plants were treated with salt stress respectively, and the related physiological indexes were determined. Furthermore, the expression levels of five abiotic stress responsive genes were analyzed in GmTGA13 overexpression hairy roots. GmTGA13 gene was highly expressed in roots and significantly induced by saline stress in soybean. GmTGA13 encoded a nuclear localization protein and had transcriptional activation activity. Overexpression of GmTGA13 enhanced the saline stress tolerance of transgenic Arabidopsis and the 'combination' soybean plants. Furthermore, overexpression of GmTGA13 enhanced the expression of the stress responsive genes in transgenic soybean hairy roots. In conclusion, overexpression of GmTGA13 is beneficial to the absorption of K+ and Ca2+ by the cell, thereby regulating the ion homeostasis in the cell balance. GmTGA13 enhanced salt resistance of plants by regulating the expression of many stress-responsive genes.

AP2/ERF transcription factor GmDREB1 confers drought tolerance in transgenic soybean by interacting with GmERFs

Soybean is the main economic crop, and also the main source of oil and protein for human consumption. Drought stress has a great influence on the growth and yield of soybean crops. Therefore, improving the drought resistance of soybean, especially drought resistance in the field, is important to increase soybean yield. AP2/ERF (APETALA2/ethylene responsive factor) transcription factors are one of the largest families of transcription factors in plants. However, there has been little research on the value of applying DREB (dehydration-responsive element-binding)-like genes in improving the drought resistance of soybean. Here, we further study the value of the application of GmDREB1 in soybean. The results of drought resistance identification in the field and greenhouse showed that the overexpression of GmDREB1 could significantly enhance the drought resistance of transgenic soybean, and the yield was clearly higher than that of the wild type. GmDREB1 has transcriptional activity and is located in the nucleus. For mechanism analysis of GmDREB1 in soybean, two ERF-like transcription factors, GmERF008 and GmERF106, were shown to interact with GmDREB1 using yeast two-hybrid (Y2H) and bimolecular fluorescence complementary (BiFC) experiments. qRT-PCR (quantitative real-time PCR) results showed that the expression of many stress-related genes in GmDREB1 transgenic soybean were significantly up-regulated compared with the WT under a drought environment. In conclusion, GmDREB1 can regulate the expression of downstream stress-related genes by forming a heterodimer with ERF-like transcription factors, which can improve the drought resistance of transgenic soybean.

Two TGA Transcription Factor Members from Hyper-Susceptible Soybean Exhibiting Significant Basal Resistance to Soybean mosaic virus

TGA transcription factors (TFs) exhibit basal resistance in Arabidopsis, but susceptibility to a pathogen attack in tomatoes; however, their roles in soybean (Glycine max) to Soybean mosaic virus (SMV) are unknown. In this study, 27 TGA genes were isolated from a SMV hyper-susceptible soybean NN1138-2, designated GmTGA1~GmTGA27, which were clustered into seven phylogenetic groups. The expression profiles of GmTGAs showed that the highly expressed genes were mainly in Groups I, II, and VII under non-induction conditions, while out of the 27 GmTGAs, 19 responded to SMV-induction. Interestingly, in further transient N. benthamiana-SMV pathosystem assay, all the 19 GmTGAs overexpressed did not promote SMV infection in inoculated leaves, but they exhibited basal resistance except one without function. Among the 18 functional ones, GmTGA8 and GmTGA19, with similar motif distribution, nuclear localization sequence and interaction proteins, showed a rapid response to SMV infection and performed better than the others in inhibiting SMV multiplication. This finding suggested that GmTGA TFs may support basal resistance to SMV even from a hyper-susceptible source. What the mechanism of the genes (GmTGA8, GmTGA19, etc.) with basal resistance to SMV is and what their potential for the future improvement of resistance to SMV in soybeans is, are to be explored.

Expression Analysis of MaTGA8 Transcription Factor in Banana and Its Defence Functional Analysis by Overexpression in Arabidopsis

TGA transcription factor is a member of the D subfamily of the basic region-leucine zippers (bZIP) family. It is a type of transcription factor that was first identified in plants and is the main regulator in plant development and physiological processes, including morphogenesis and seed formation in response to abiotic and biotic stress and maintaining plant growth. The present study examined the sequence of the MaTGA8 transcription factor, the sequence of which belonged to subfamily D of the bZIP and had multiple cis-acting elements such as the G-box, TCA-element, TGACG-element, and P-box. Quantitative real time polymerase chain reaction (qRT-PCR) analyses showed that MaTGA8 was significantly down-regulated by the soil-borne fungus Fusarium oxysporum f. sp. cubense race 4 (Foc TR4). Under the induction of salicylic acid (SA), MaTGA8 was down-regulated, while different members of the MaNPR1 family responded significantly differently. Among them, MaNPR11 and MaNPR3 showed an overall upward trend, and the expression level of MaNPR4, MaNPR8, and MaNPR13 was higher than other members. MaTGA8 is a nuclear-localized transcription factor through strong interaction with MaNPR11 or weaker interaction with MaNPR4, and it is implied that the MaPR gene can be activated. In addition, the MaTGA8 transgenic Arabidopsis has obvious disease resistance and higher chlorophyll content than the wild-type Arabidopsis with the infection of Foc TR4. These results indicate that MaTGA8 may enhance the resistance of bananas to Foc TR4 by interacting with MaNPR11 or MaNPR4. This study provides a basis for further research on the application of banana TGA transcription factors in Foc TR4 stress and disease resistance and molecular breeding programs.

Nuclear transport factor GmNTF2B-1 enhances soybean drought tolerance by interacting with oxidoreductase GmOXR17 to reduce reactive oxygen species content

Drought is a critical abiotic stressor that modulates soybean yield. Drought stress drastically enhances reactive oxygen species (ROS) formation, and maintaining ROS content above a cytostatic level but below a cytotoxic level is essential for normal biology processes in plants. At present, most of the known ROS-scavenging systems are in the cytoplasm, and the mechanism of ROS regulation in the nucleus remains unclear. GmNTF2B-1 is a member of the IV subgroup in the nucleus transporter family. Its expression is localized to the roots and is stimulated by drought stress. In this study, the overexpression of GmNTF2B-1 was found to improve the drought tolerance of transgenic soybean by influencing the ROS content in plants. An oxidoreductase, GmOXR17, was identified to interact with GmNTF2B-1 in the nucleus through the yeast two-hybrid, coimmunoprecipitation and bimolecular fluorescence complementation assays. The drought tolerance of GmOXR17 transgenic soybean was similar to that of GmNTF2B-1. GmNTF2B-1 was expressed in both cytoplasm and nucleus, and GmOXR17 transferred from the cytoplasm to the nucleus under drought stress. The overexpression of GmNTF2B-1 enhanced the nuclear entry of GmOXR17, and the overexpression of GmNTF2B-1 or GmOXR17 could decrease the H2 O2 content and oxidation level in the nucleus. In conclusion, the interaction between GmNTF2B-1 and GmOXR17 may enhance the nuclear entry of GmOXR17, thereby enhancing nuclear ROS scavenging to improve the drought resistance of soybean.

Transcriptome Characterization and Expression Profiles of Disease Defense-Related Genes of Table Grapes in Response to Pichia anomala Induced with Chitosan

Transcriptome analysis (TA) was conducted to characterize the transcriptome changes in postharvest disease-related genes of table grapes following treatment with Pichia anomala induced with chitosan (1% w/v). In the current study, the difference in the gene expression of table grapes after treatment with P. anomala induced with chitosan and that of a control group was compared 72 h post-inoculation. The study revealed that postharvest treatment of table grapes with P. anomala induced with chitosan could up-regulate genes that have a pivotal role in the fruit’s disease defense. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results also confirmed that GO terms and the KEGG pathways, which have pivotal roles in plant disease resistance, were significantly enriched. The up-regulated genes of the treatment group have a unique function in the fruit’s disease resistance compared to the control group. Generally, most genes in the plant–pathogen interaction pathway; the plant Mitogen-activated protein kinase (MAPK) signaling pathway; the plant hormone signal transduction pathway; the pathway of glutathione metabolism; the pathway of phenylalanine, tyrosine, and tryptophan biosynthesis; and the pathway of flavonoid biosynthesis were all up-regulated. These up-regulations help the fruit to synthesize disease-resistant substances, regulate the reactive oxygen species (ROS), enhance the fruit cell wall, and enrich hormone signal transduction during the pathogen’s attack. This study is useful to overcome the lags in applying transcriptomics technology in postharvest pathology, and will provide insight towards developing other alternative methods to using bio-pesticides to control postharvest diseases of perishables.

Seed 'primeomics': plants memorize their germination under stress

Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl₂ and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.

Isolation and Functional Characterization of the Promoters of Miltiradiene Synthase Genes, TwTPS27a and TwTPS27b, and Interaction Analysis with the Transcription Factor TwTGA1 from Tripterygium wilfordii

Miltiradiene synthase (MS) genes, TwTPS27a and TwTPS27b, are the key diterpene synthase genes in the biosynthesis of triptolide, which is an important medicinally active diterpenoid in Tripterygium wilfordii. However, the mechanism underlying the regulation of key genes TwTPS27a/b in triptolide biosynthesis remains unclear. In this study, the promoters of TwTPS27a (1496 bp) and TwTPS27b (1862 bp) were isolated and analyzed. Some hormone-/stress-responsive elements and transcription factor (TF) binding sites were predicted in both promoters, which might be responsible for the regulation mechanism of TwTPS27a/b. The β-glucuronidase (GUS) activity analysis in promoter deletion assays under normal and methyl jasmonate (MeJA) conditions showed that the sequence of −921 to −391 bp is the potential core region of the TwTPS27b promoter. And the TGACG-motif, a MeJA-responsive element found in this core region, might be responsible for MeJA-mediated stress induction of GUS activity. Moreover, the TGACG-motif is also known as the TGA TF-binding site. Yeast one-hybrid and GUS transactivation assays confirmed the interaction between the TwTPS27a/b promoters and the TwTGA1 TF (a MeJA-inducible TGA TF upregulating triptolide biosynthesis in T. wilfordii), indicating that TwTPS27a/b are two target genes regulated by TwTGA1. In conclusion, our results provide important information for elucidating the regulatory mechanism of MS genes, TwTPS27a and TwTPS27b, as two target genes of TwTGA1, in jasmonic acid (JA)-inducible triptolide biosynthesis.

Overexpression of Transcription Factor GmTGA15 Enhances Drought Tolerance in Transgenic Soybean Hairy Roots and Arabidopsis Plants

Soybean (Glycine max) is one of the important oil crops worldwide. In recent years, environmental stresses such as drought and soil salinization have severely deteriorated soybean yield and quality. We investigated the overexpression of the transcription factor GmTGA15 in response to drought stress in transgenic soybean hairy roots and Arabidopsis plants. The results of quantitative real time polymerase chain reaction (qRT-PCR) analyses showed that GmTGA15 was greatly induced by salt, PEG6000, salicylic acid (SA), gibberellic acid (GA), abscisic acid (ABA), and methyl jasmonate (MeJA) in soybean. In response to drought stress, the contents of both chlorophyll and proline were significantly increased, while the content of malondialdehyde (MDA) was significantly decreased in the soybean hairy roots with the overexpression of GmTGA15 in comparison to wild type (WT). Under the simulated drought conditions, the transgenic Arabidopsis plants showed significantly longer roots and lower mortality than that of the wild type. These results suggest that GmTGA15 promotes tolerance to drought stress in both soybean and Arabidopsis plants. This study provides the scientific evidence for further functional analysis of soybean TGA transcription factors in drought stress and the breeding of drought-resistance crops.

The Ankyrin-Repeat Gene GmANK114 Confers Drought and Salt Tolerance in Arabidopsis and Soybean

Ankyrin repeat (ANK) proteins are essential in cell growth, development, and response to hormones and environmental stresses. In the present study, 226 ANK genes were identified and classified into nine subfamilies according to conserved domains in the soybean genome (Glycine max L.). Among them, the GmANK114 was highly induced by drought, salt, and abscisic acid. The GmANK114 encodes a protein that belongs to the ANK-RF subfamily containing a RING finger (RF) domain in addition to the ankyrin repeats. Heterologous overexpression of GmANK114 in transgenic Arabidopsis improved the germination rate under drought and salt treatments compared to wild-type. Homologous overexpression of GmANK114 improved the survival rate under drought and salt stresses in transgenic soybean hairy roots. In response to drought or salt stress, GmANK114 overexpression in soybean hairy root showed higher proline and lower malondialdehyde contents, and lower H2O2 and O2- contents compared control plants. Besides, GmANK114 activated transcription of several abiotic stress-related genes, including WRKY13, NAC11, DREB2, MYB84, and bZIP44 under drought and salt stresses in soybean. These results provide new insights for functional analysis of soybean ANK proteins and will be helpful for further understanding how ANK proteins in plants adapt to abiotic stress.

GmNFYA13 Improves Salt and Drought Tolerance in Transgenic Soybean Plants

NF-YA transcription factors function in modulating tolerance to abiotic stresses that are serious threats to crop yields. In this study, GmNFYA13, an NF-YA gene in soybean, was strongly induced by salt, drought, ABA, and H₂O₂, and suppressed by tungstate, an ABA synthesis inhibitor. The GmNFYA13 transcripts were detected in different tissues in seedling and flowering stages, and the expression levels in roots were highest. GmNFYA13 is a nuclear localization protein with self-activating activity. Transgenic Arabidopsis plants overexpressing GmNFYA13 with higher transcript levels of stress-related genes showed ABA hypersensitivity and enhanced tolerance to salt and drought stresses compared with WT plants. Moreover, overexpression of GmNFYA13 resulted in higher salt and drought tolerance in OE soybean plants, while suppressing it produced the opposite results. In addition, GmNFYA13 could bind to the promoters of GmSALT3, GmMYB84, GmNCED3, and GmRbohB to regulate their expression abundance in vivo. The data in this study suggested that GmNFYA13 enhanced salt and drought tolerance in soybean plants.

Overexpression of GmUBC9 Gene Enhances Plant Drought Resistance and Affects Flowering Time via Histone H2B Monoubiquitination

Ubiquitylation is a form of post-translational modification of proteins that can alter localization, functionality, degradation, or transcriptional activity within a cell. E2 ubiquitin-conjugating enzyme (UBC) and E3 ubiquitin ligases are the primary determinants of substrate specificity in the context of ubiquitin conjugation. Multiubiquitination modifies target proteins for 26S proteasome degradation, while monoubiquitination controls protein activation and localization. At present, research on the monoubiquitination, especially histone monoubiquitination, has mostly focused on model plants with relatively few on crop species. In this study, we identified 91 UBC-like genes in soybean. The chromosomal localization, phylogenetic relationships, gene structures, and putative cis-acting elements were evaluated. Furthermore, the tissue-specific expression patterns of UBC Class I genes under drought stress were also investigated. Among Class I genes, GmUBC9 induction in response to drought stress was evident, and so this gene was selected for further analysis. GmUBC9 localized to the nucleus and endoplasmic reticulum. The overexpression of GmUBC9 in Arabidopsis led to enhanced tolerance for drought conditions across a range of stages of development, while overexpression in soybean hairy roots similarly led to improvements in tolerance for drought conditions, increased proline content, and reduced MDA content in soybean seedlings compared to wild type plants. HISTONE MONOUBIQUITINATION 2 (HUB2), an E3-like protein involved in histone H2B ubiquitylation (H2Bub1), was found to interact with GmUBC9 through Y2H analysis and BiFC assays in Arabidopsis and soybean. Under drought conditions, the level of H2Bub1 increased, and transcription of drought response genes was activated in GmUBC9 transgenic Arabidopsis and soybean. In addition, GmUBC9 transgenic Arabidopsis and soybean showed a late-flowering phenotype and had increased expression levels of the flowering related genes FLC and MAF4. These findings indicate that GmUBC9 is important for drought stress response and regulation of flowering time in soybean.

Overexpression of GmNFYA5 confers drought tolerance to transgenic Arabidopsis and soybean plants

BACKGROUND

Crop productivity is challenged by abiotic stresses, among which drought stress is the most common. NF-Y genes, especially NF-YA genes, regulate tolerance to abiotic stress.

RESULTS

Soybean NF-Y gene GmNFYA5 was identified to have the highest transcript level among all 21 NF-YA genes in soybean (Glycine max L.) under drought stress. Drought-induced transcript of GmNFYA5 was suppressed by the ABA synthesis inhibitor naproxen (NAP). GmNFYA5 transcript was detected in various tissues at vegetative and reproductive growth stages with higher levels in roots and leaves than in other tissues, which was consist with the GmNFYA5 promoter: GUS fusion assay. Overexpression of GmNFYA5 in transgenic Arabidopsis plants caused enhanced drought tolerance in seedlings by decreasing stomatal aperture and water loss from leaves. Overexpression and suppression of GmNFYA5 in soybean resulted in increased and decreased drought tolerance, respectively, relative to plants with an empty vector (EV). Transcript levels of ABA-dependent genes (ABI2, ABI3, NCED3, LEA3, RD29A, P5CS1, GmWRKY46, GmNCED2 and GmbZIP1) and ABA-independent genes (DREB1A, DREB2A, DREB2B, GmDREB1, GmDREB2 and GmDREB3) in transgenic plants overexpressing GmNFYA5 were higher than those of wild-type plants under drought stress; suppression of GmNFYA5 transcript produced opposite results. GmNFYA5 probably regulated the transcript abundance of GmDREB2 and GmbZIP1 by binding to the promoters in vivo.

CONCLUSIONS

Our results suggested that overexpression of GmNFYA5 improved drought tolerance in soybean via both ABA-dependent and ABA-independent pathways.

Genome-Wide Identification, Evolution, and Expression of GDSL-Type Esterase/Lipase Gene Family in Soybean

GDSL-type esterase/lipase proteins (GELPs) belong to the SGNH hydrolase superfamily and contain a conserved GDSL motif at their N-terminus. GELPs are widely distributed in nature, from microbes to plants, and play crucial roles in growth and development, stress responses and pathogen defense. However, the identification and functional analysis of GELP genes are hardly explored in soybean. This study describes the identification of 194 GELP genes in the soybean genome and their phylogenetic classification into 11 subfamilies (A-K). GmGELP genes are disproportionally distributed on 20 soybean chromosomes. Large-scale WGD/segmental duplication events contribute greatly to the expansion of the soybean GDSL gene family. The Ka/Ks ratios of more than 70% of duplicated gene pairs ranged from 0.1-0.3, indicating that most GmGELP genes were under purifying selection pressure. Gene structure analysis indicate that more than 74% of GmGELP genes are interrupted by 4 introns and composed of 5 exons in their coding regions, and closer homologous genes in the phylogenetic tree often have similar exon-intron organization. Further statistics revealed that approximately 56% of subfamily K members contain more than 4 introns, and about 28% of subfamily I members consist of less than 4 introns. For this reason, the two subfamilies were used to simulate intron gain and loss events, respectively. Furthermore, a new model of intron position distribution was established in current study to explore whether the evolution of multi-gene families resulted from the diversity of gene structure. Finally, RNA-seq data were used to investigate the expression profiles of GmGELP gene under different tissues and multiple abiotic stress treatments. Subsequently, 7 stress-responsive GmGELP genes were selected to verify their expression levels by RT-qPCR, the results were consistent with RNA-seq data. Among 7 GmGELP genes, GmGELP28 was selected for further study owing to clear responses to drought, salt and ABA treatments. Transgenic Arabidopsis thaliana and soybean plants showed drought and salt tolerant phenotype. Overexpression of GmGELP28 resulted in the changes of several physiological indicators, which allowed plants to adapt adverse conditions. In all, GmGELP28 is a potential candidate gene for improving the salinity and drought tolerance of soybean.

The ABA-induced soybean ERF transcription factor gene GmERF75 plays a role in enhancing osmotic stress tolerance in Arabidopsis and soybean

BACKGROUND

Ethylene-responsive factors (ERFs) play important roles in plant growth and development and the response to adverse environmental factors, including abiotic and biotic stresses.

RESULTS

In the present study, we identified 160 soybean ERF genes distributed across 20 chromosomes that could be clustered into eight groups based on phylogenetic relationships. A highly ABA-responsive ERF gene, GmERF75, belonging to Group VII was further characterized. Subcellular localization analysis showed that the GmERF75 protein is localized in the nucleus, and qRT-PCR results showed that GmERF75 is responsive to multiple abiotic stresses and exogenous hormones. GmERF75-overexpressing Arabidopsis lines showed higher chlorophyll content compared to WT and mutants under osmotic stress. Two independent Arabidopsis mutations of AtERF71, a gene homologous to GmERF75, displayed shorter hypocotyls, and overexpression of GmERF75 in these mutants could rescue the short hypocotyl phenotypes. Overexpressing GmERF75 in soybean hairy roots improved root growth under exogenous ABA and salt stress.

CONCLUSIONS

These results suggested that GmERF75 is an important plant transcription factor that plays a critical role in enhancing osmotic tolerance in both Arabidopsis and soybean.

Hairy Root Transformation: A Useful Tool to Explore Gene Function and Expression in Salix spp. Recalcitrant to Transformation

Willow (Salix spp. L.) species are fast-growing trees and shrubs that have attracted emergent attention for their potential as feedstocks for bioenergy and biofuel production, as well as for pharmaceutical and phytoremediation applications. This economic and environmental potential has propelled the creation of several genetic and genomic resources for Salix spp. Furthermore, the recent availability of an annotated genome for Salix purpurea has pinpointed novel candidate genes underlying economically relevant traits. However, functional studies have been stalled by the lack of rapid and efficient coupled regeneration-transformation systems for Salix purpurea and Salix spp. in general. In this report, we describe a fast and highly efficient hairy root transformation protocol for S. purpurea. It was effective for different explant sources and S. purpurea genotypes, with efficiencies between 63.4% and 98.7%, and the screening of the transformed hairy roots was easily carried out using the fluorescent marker DsRed. To test the applicability of this hairy root transformation system for gene functional analysis, we transformed hairy roots with the vector pGWAY-SpDRM2, where the gene SpDRM2 encoding a putative Domain Rearranged Methyltransferase (DRM) was placed under the control of the CaMV 35S constitutive promoter. Indeed, the transgenic hairy roots obtained exhibited significantly increased expression of SpDRM2 as compared to controls, demonstrating that this protocol is suitable for the medium/high-throughput functional characterization of candidate genes in S. purpurea and other recalcitrant Salix spp.