MdMYB46 could enhance salt and osmotic stress tolerance in apple by directly activating stress-responsive signals

The StbHLH47 transcription factor negatively regulates drought tolerance in potato (Solanum tuberosum L.)

BACKGROUND

Drought stress is a major environmental constraint affecting crop yields. Plants in agricultural and natural environments have developed various mechanisms to cope with drought stress. Identifying genes associated with drought stress tolerance in potato and elucidating their regulatory mechanisms is crucial for the breeding of new potato germplasms. The bHLH transcription factors involved play crucial roles not only in plant development and growth but also in responsesresponse to abiotic stress.

RESULTS

In this study, the StbHLH47 gene, which is highly expressed in potato leaves, was cloned and isolated. Subcellular localization assays revealed that the gene StbHLH47 performs transcriptional functions in the nucleus, as evidenced by increased malondialdehyde (MDA) content and relative conductivity under drought stress. These findings indicate that overexpressing plants are more sensitive to drought stress. Differential gene expression analysis of wild-type plants (WT) and plants overexpressing StbHLH47 (OE-StbHLH47) under drought stress revealed that the significantly differentially expressed genes were enriched in metabolic pathways, biosynthesis of various plant secondary metabolites, biosynthesis of metabolites, plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signalling pathway-plant, phenylpropanoid biosynthesis, and plant‒pathogen interactions. Among these pathways, the phenylalanine and abscisic acid (ABA) signal transduction pathways were enriched in a greater number of differentially expressed genes, and the expression trends of these differentially expressed genes (DEGs) were significantly different between WT and OE-StbHLH47. Therefore, it is speculated that StbHLH47 may regulate drought resistance mainly through these two pathways. Additionally, RT‒qPCR was used for fluorescence quantification of the expression of StNCED1 and StERD11, which are known for their drought resistance, and the results revealed that the expression levels were much lower in OE-StbHLH47 than in WT plants.

CONCLUSION

RNA-seq, RT‒qPCR, and physiological index analyses under drought conditions revealed that overexpression of the StbHLH47 gene increased the sensitivity of potato plants to drought stress, indicating that StbHLH47 negatively regulates drought tolerance in potato plants. In summary, our results indicate that StbHLH47 is a negative regulator of drought tolerance and provide a theoretical basis for further studies on the molecular mechanism involved.

Exploring the mechanism of seed shattering in Psathyrostachys juncea through histological analysis and comparative transcriptomics

BACKGROUND

Seed shattering (SS) negatively impacts seed yield in Psathyrostachys juncea. Understanding and improving the SS trait requires elucidating the regulatory mechanisms of SS and identifying the key genes involved.

RESULTS

This study presents a comprehensive analysis of the abscission zone (AZ) structures at four developmental stages in two P. juncea genotypes. High-SS P. juncea (H) exhibited a significantly higher SS rate than low-SS P. juncea (L) at all four developmental stages. Anatomical analysis revealed that the degree of lignification in the AZ cell walls is related to the integrity of the abscission structure. The degradation of the AZ in H occurred earlier and was more severe compared to L. At different developmental stages of the AZ, H exhibited higher cellulase and polygalacturonase activities and higher abscisic acid contents compared to L. Conversely, L showed higher lignin, cytokinin, auxin, and gibberellin contents than H. Transcriptomic analysis identified key metabolic pathways related to SS in P. juncea, such as phenylpropanoid biosynthesis, fructose and mannose metabolism, galactose metabolism, and pentose and glucuronate interconversions. The integration of morphological, histological, physiochemical, and metabolic data led to the identification of critical genes, including AUX1, CKX, ABF, GH3, 4CL, CCoAOMT, BGAL, Gal, and PG. The roles of these genes were involved in the regulation of plant hormones and in the synthesis and degradation of cell walls within the AZ.

CONCLUSIONS

This study provides an in-depth understanding of the regulatory mechanisms of SS in P. juncea through comparative transcriptomic analysis. The SS in P. juncea may result from the degradation of the cell wall regulated by cell wall hydrolases genes. The genes identified in this study provide a basis for the genetic improvement of SS traits and serve as a reference for research on other grass species.

Integrated transcriptomic and metabolomic analyses uncover the key pathways of Limonium bicolor in response to salt stress

Salinity significantly inhibits plant growth and development. While the recretohalophyte Limonium bicolor can reduce its ion content by secreting salt, the metabolic pathways it employs to adapt to high salt stress remain unclear. This study aims to unravel this enigma through integrated transcriptomic and metabolomic analyses of L. bicolor under salt stress conditions. The results showed that compared to the control (S0), low salt treatment (S1) led to a significant increase in plant growth, photosynthesis efficiency and antioxidant enzyme activity but caused no significant changes in organic soluble substance and ROS contents. However, high salt treatments (S3 and S4) led to a significant decrease in plant growth, photosynthesis efficiency and antioxidant enzyme activity, accompanied by a significant increase in organic soluble substance and ROS contents. A significant increase in phenolic compounds, such as caffeoyl shikimic acid and coniferin, upon the treatments of S1, S3 and S4, and a decrease and increase in flavonoids upon the treatments of S1 and S3 were also observed, respectively. This study also demonstrated that the expression patterns of key genes responsible for the biosynthesis of these metabolites are consistent with the observed trends in their accumulation levels. These results suggest that under low salt stress conditions, the halophyte L. bicolor experiences minimal osmotic and oxidative stress. However, under high salt stress conditions, it suffers severe osmotic and oxidative stress, and the increase in organic soluble substances and flavonoids serves as a key response to these stresses and also represents a good strategy for the alleviation of them.

A glutathione S-transferase regulates lignin biosynthesis and enhances salt tolerance in tomato

Salt stress adversely affects the growth and yield of crops. Glutathione S-transferases (GSTs) are involved in plant growth and responses to biotic and abiotic stresses. In this study, 400 mm NaCl stress significantly induced the expression of Glutathione S-transferase U43 (SlGSTU43) in the roots of the wild-type tomato (Solanum lycopersicum L.) plants. Overexpressing SlGSTU43 enhanced the ability of scavenging reactive oxygen species in tomato leaves and roots under NaCl stress, while SlGSTU43 knock-out mutants showed the opposite performance. RNA sequencing analysis revealed that overexpressing SlGSTU43 affected the expression of genes related to lignin biosynthesis. We demonstrated that SlGSTU43 can regulate the lignin content in tomato through its interaction with SlCOMT2, a key enzyme involved in lignin biosynthesis, and promote the growth of tomato plants under NaCl stress. In addition, SlMYB71 and SlWRKY8 interact each other, and can directly bind to the promoter of SlGSTU43 to transcriptionally activate its expression separately or in combination. When SlMYB71 and SlWRKY8 were silenced in tomato plants individually or collectively, the plants were sensitive to NaCl stress, and their GST activities and lignin contents decreased. Our research indicates that SlGSTU43 can enhance salt stress tolerance in tomato by regulating lignin biosynthesis, which is regulated by interacting with SlCOMT2, as well as SlMYB71 and SlWRKY8. This finding broadens our understanding of GST functions.

The MdIAA29-MdARF4 complex plays an important role in balancing plant height with salt and drought stress responses

Breeding dwarf apple (Malus domestica) varieties is a recent trend in agriculture because such varieties are easy to maintain and have high yields; however, dwarf apple trees generally have poor stress tolerance. Balancing apple plant height and stress response has been an important breeding goal. In this study, aux/indole-3-acetic acid 29 gene in apple (MdIAA29) overexpression lines (#1, #2, and #3) had reduced plant height by 39%, 31%, and 35%, respectively, suitable for close planting applications. Surprisingly, the dwarf MdIAA29-overexpressing lines also showed increased plant tolerance to salt and drought stresses. Further analysis showed that MdIAA29 inhibited the regulation of auxin response factor 4 (ARF4) on Gretchen Hagen 3.9 (GH3.9) gene and 9-cis-epoxycarotenoid dioxygenase 3 (NCED3) gene in apple and changed the contents of auxin and abscisic acid in different tissues, thus achieving a balance between plant height and stress tolerance. In addition, we also found that MdIAA7 enhanced the inhibitory effect of MdIAA29 on MdARF4. In brief, the MdIAA29-MdARF4 complex significantly impacts the height of apple plants and their ability to respond to salt and drought stress.

Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa

Poplar trees are crucial for timber and greening, but high levels of salt in the soil have severely limited the yield of poplar. Ethylene response factor (ERF) transcription factors play an important role in growth, development, and stress response in eukaryotes. Our study focused on the PagERF021 gene from Populus alba × P. glandulosa, which was significantly upregulated in various tissues under salt stress [Correction added on October 4, 2024, after first online publication: "ETS2 reporter factor" is changed to "Ethylene response factor".]. Both the tissue-specific expression pattern and β-glucuronidase (GUS) staining of proPagERF021-GUS plants indicated that this gene was predominantly expressed in the roots and stems. The subcellular localization showed that the protein was only localized in the nucleus. The yeast assay demonstrated that this protein had transcriptional activation activity at its C-terminal and could specifically binding to the MYB-core cis-element. The overexpression of PagERF021 gene could scavenge the accumulation of reactive oxygen species and reduce the degree of cellular membrane damage, indicating that this gene enhanced the salt tolerance of poplars. This finding will provide a feasible insight for future research into the regulatory mechanisms of ERF genes in resisting to abiotic stress and the development of new stress-resistant varieties in plants.

Evaluation of Salt Resistance of Six Apple Rootstocks

Apples (Malus domestica Borkh) are important fruits in China; however, salt stress is severe in northern regions, and the key to plant resistance to salt stress lies in the rootstock. Therefore, it is necessary to explore rootstocks with strong salt resistance for the development of the apple industry. This study used tissue culture seedlings of six apple rootstocks, namely, '71-3-150', '54-118', 'M9T337', 'GM256', 'ML176', and 'ML2', as experimental materials. The seedlings were treated with a medium containing 150 mM NaCl, and the physiological indicators and related gene expression responses of several rootstocks were studied after salt stress. The results showed that salt stress affects the growth of both the aboveground and underground parts of plants. Through physiological indicators and the related gene expression responses of rootstocks, it was observed that salt stress significantly increased Na+ contents in different rootstocks. Simultaneously, the activity of various antioxidant enzymes and the expression levels of related genes also increased. In summary, by analyzing the parameters of various physiological indicators, it can be concluded that among the studied rootstocks, the '71-3-150' and '54-118' rootstocks have the strongest resistance to salt stress, while the 'M9T337' and 'GM256' rootstocks exhibit moderate resistance, and the 'ML176' and 'ML2' rootstocks have the weakest resistance.

Resveratrol enhances the tolerance of Malus hupehensis to potassium deficiency stress

Potassium (K) deficiency in plants can lead to metabolic disorders and growth retardation. Currently, nearly 50% of the arable land in China is experiencing a K resource deficit, significantly hindering the development of the apple industry. Resveratrol (Res), a phytoalexin, has been extensively reported to enhance plant resistance against various abiotic stresses. However, there have been no reports on the response of Res to K+ deficiency stress in apples. This study aims to investigate the effect of exogenous Res on the K+ deficiency tolerance of Malus hupehensis. The results demonstrated that applying 50 μM of exogenous Res could enhance the tolerance of M. hupehensis to K+ deficiency stress. Compared to non-Res treatments, external application of Res alleviated leaf chlorosis and improved root growth in apple seedlings. Additionally, it increased antioxidant enzyme activity, thereby reducing the production of reactive oxygen species induced by K+ deficiency stress. Res also regulated proline and soluble sugar content to maintain osmotic balance. Moreover, Res helped maintain the balance of mineral element contents in apple seedlings and the normal K+: Na+ ratio by enhancing the influx of K+. Furthermore, exogenous Res regulated the expression of related kinase genes, promoting Ca2+ signal transduction in response to K+ deficiency stress and inducing the expression of K+ transport genes to enhance K+ absorption, thus supporting normal plant growth. In conclusion, this study provides a theoretical basis for the application of exogenous Res to alleviate K+ deficiency stress in apples.

Transcriptional Profiling Analysis Providing Insights into the Harsh Environments Tolerance Mechanisms of Krascheninnikovia arborescens

Krascheninnikovia arborescens, an endemic shrub in China, thrives in desertification-prone environments due to its robust biomass, hairy leaves, and extensive root system. It is vital for ecological restoration and serves as a valuable forage plant. This study explored the molecular mechanisms underlying K. arborescens' adaptation to desert conditions, focusing on its physiological, biochemical, and transcriptomic responses to drought, salt, and alkali stresses. The results revealed that the three stresses have significant impacts on the photosynthetic, antioxidant, and ion balance systems of the plants, with the alkali stress inducing the most pronounced changes and differential gene expression. The clustering and functional enrichment analyses of differentially expressed genes (DEGs) highlighted the enrichment of the induced genes in pathways related to plant hormone signaling, phenylpropanoid biosynthesis, and transcription factors following stress treatments. In these pathways, the synthesis and signal transduction of abscisic acid (ABA) and ethylene, as well as the flavonoid and lignin synthesis pathways, and transcription factors such as MYB, AP2/ERF, bHLH, NAC, and WRKY responded actively to the stress and played pivotal roles. Through the WGCNA analysis, 10 key modules were identified, with the yellow module demonstrating a high correlation with the ABA and anthocyanin contents, while the turquoise module was enriched in the majority of genes related to hormone and phenylpropanoid pathways. The analysis of hub genes in these modules highlighted the significant roles of the bHLH and MYB transcription factors. These findings could offer new insights into the molecular mechanisms that enable the adaptation of K. arborescens to desert environments, enhancing our understanding of how other desert plants adapt to harsh conditions. These insights are crucial for exploring and utilizing high-quality forage plant germplasm resources and ecological development, with the identified candidate genes serving as valuable targets for further research on stress-resistant genes.

The function of an apple ATP-dependent Phosphofructokinase gene MdPFK5 in regulating salt stress

Salt stress severely affects the growth and yield of apples (Malus domestica Borkh). Although salt-tolerant genes have been extensively studied, documentation on the role of the ATP-dependent phosphofructokinase gene MdPFK5 in salt stress is limited. This study conducted an evolutionary tree and three-dimensional structure analysis of the PFK gene family in Arabidopsis thaliana and MdPFK (MD01G1037400), revealing a close phylogenetic relationship between MdPFK (MD01G1037400) and AtPFK5. Given the similarity in their protein tertiary structures, MdPFK was designated as MdPFK5, suggesting functional similarities with AtPFK5. Further investigation revealed elevated expression levels of MdPFK5 in apple leaves and flowers, particularly showing significant upregulation 120 days after blooming and differential expression beginning at 3 hours of salt stress. Overexpression of MdPFPK5 conferred salt tolerance in both apple calli and transgenic lines of Arabidopsis thaliana. Moreover, NaCl treatment promoted soluble sugar accumulation in apple calli and transgenic lines of Arabidopsis thaliana overexpressing MdPFK5. This study provides new insights into the salt tolerance function of MdPFK5.

Sweetpotato sucrose transporter IbSUT1 alters storage roots formation by regulating sucrose transport and lignin biosynthesis

The formation and development of storage roots is the most important physiological process in sweetpotato production. Sucrose transporters (SUTs) regulate sucrose transport from source to sink organs and play important roles in growth and development of plants. However, whether SUTs involved in sweetpotato storage roots formation is so far unknown. In this study, we show that IbSUT1, a SUT, is localized to the plasma membrane. Overexpression of IbSUT1 in sweetpotato promotes the sucrose efflux rate from leaves, leading to increased sucrose levels in roots, thus induces lignin deposition in the stele, which inhibits the storage roots formation and compromises the yield. Heterologous expression of IbSUT1 in Arabidopsis significantly increases the sucrose accumulation and promotes lignification in the inflorescence stems. RNA-seq and biochemical analysis further demonstrated that IbMYB1 negatively regulates the expression of IbSUT1. Overexpression of IbMYB1 in Arabidopsis reduces the sucrose accumulation and lignification degree in the inflorescence stems. Moreover, co-overexpression of IbMYB1 and IbSUT1 restores the phenotype of lignin over-deposition in Arabidopsis. Collectively, our results reveal that IbSUT1 regulates source-sink sucrose transport and participates in the formation of sweetpotato storage roots and highlight the potential application of IbSUT1 in improving sweetpotato yield in the future.

Integrated transcriptomic and proteomic analysis revealed the regulatory role of 5-azacytidine in kenaf salt stress alleviation

Salinity stress limits agricultural production. The DNA methyltransferase inhibitor, 5-azacitidine (5-azaC), plays a role in plant abiotic stress regulation, but its molecular basis in mediating salinity tolerance in kenaf remains unclear. To investigate the effects on 5-azaC on alleviating salt stress, kenaf seedlings were pre-treated with 0, 50, 100, 150, and 200 μM 5-azaC and then exposed to 150 mM NaCl in a nutrient solution. Physiological, transcriptomic, and proteomic analyses were conducted on the root system to understand the regulatory mechanism of 5-azaC (comparing 5-azaC150 and control group 5-azaC0) under salt stress. The results indicated that 5-azaC significantly mitigated salt stress in kenaf by activating the antioxidant system, reducing reactive oxygen species (ROS), and increasing starch, soluble sugars, and adenosine triphosphate (ATP) content. A total of 14,348 differentially expressed genes (DEGs) and 313 differentially abundant proteins (DAPs) were identified. Combined proteomic and transcriptomic analysis revealed 27 DEGs/DAPs, with jointly up-regulated proteins (genes) including HcTHI1, HcBGLU11, and HcCBL1, and jointly down-regulated proteins (genes) including HcGAPDH, HcSS, and HcPP2C52. Overexpression and virus-induced gene silencing (VIGS) of HcPP2C52 demonstrated its role as a negative regulator of salt tolerance. These findings provide insights into the regulatory role of 5-azaC in plant responses to abiotic stresses. SIGNIFICANCE: The specific molecular mechanism by which 5-azaC affects gene expression and protein activity of kenaf has been revealed, leading to enhanced salt tolerance.

Understanding of Plant Salt Tolerance Mechanisms and Application to Molecular Breeding

Soil salinization is a widespread hindrance that endangers agricultural production and ecological security. High salt concentrations in saline soils are primarily caused by osmotic stress, ionic toxicity and oxidative stress, which have a negative impact on plant growth and development. In order to withstand salt stress, plants have developed a series of complicated physiological and molecular mechanisms, encompassing adaptive changes in the structure and function of various plant organs, as well as the intricate signal transduction networks enabling plants to survive in high-salinity environments. This review summarizes the recent advances in salt perception under different tissues, physiological responses and signaling regulations of plant tolerance to salt stress. We also examine the current knowledge of strategies for breeding salt-tolerant plants, including the applications of omics technologies and transgenic approaches, aiming to provide the basis for the cultivation of salt-tolerant crops through molecular breeding. Finally, future research on the application of wild germplasm resources and muti-omics technologies to discover new tolerant genes as well as investigation of crosstalk among plant hormone signaling pathways to uncover plant salt tolerance mechanisms are also discussed in this review.

The miR7125-MdARF1 module enhances the resistance of apple to Colletotrichum gloeosporioides by promoting lignin synthesis in response to salicylic acid signalling

Apple is an important cash crop in China, and it is susceptible to fungal infections that have deleterious effects on its yield. Apple bitter rot caused by Colletorichum gloeosporioides is one of the most severe fungal diseases of apple. Salicylic acid (SA) is a key signalling molecule in the plant disease resistance signalling pathways. Lignin synthesis also plays a key role in conferring disease resistance. However, few studies have clarified the relationship between the SA disease resistance signalling pathway and the lignin disease resistance pathway in apple. MdMYB46 has previously been shown to promote lignin accumulation in apple and enhance salt and osmotic stress tolerance. Here, we investigated the relationship between MdMYB46 and biological stress; we found that MdMYB46 overexpression enhances the resistance of apple to C. gloeosporioides. We also identified MdARF1, a transcription factor upstream of MdMYB46, via yeast library screening and determined that MdARF1 was regulated by miR7125 through psRNATarget prediction. This regulatory relationship was confirmed through LUC and qRT-PCR experiments, demonstrating that miR7125 negatively regulates MdARF1. Analysis of the miR7125 promoter revealed that miR7125 responds to SA signals. The accumulation of SA level will result in the decrease of miR7125 expression level. In sum, the results of our study provide novel insights into the molecular mechanisms underlying the resistance of apple to C. gloeosporioides and reveal a new pathway that enhances lignin accumulation in apple in response to SA signals. These findings provide valuable information for future studies aimed at breeding apple for disease resistance.

Genome-Wide Identification and Characterization of MYB Transcription Factors in Sudan Grass under Drought Stress

Sudan grass (Sorghum sudanense S.) is a warm-season annual grass with high yield, rich nutritional value, good regeneration, and tolerance to biotic and abiotic stresses. However, prolonged drought affects the yield and quality of Sudan grass. As one of the largest families of multifunctional transcription factors in plants, MYB is widely involved in regulating plant growth and development, hormonal signaling, and stress responses at the gene transcription level. However, the regulatory role of MYB genes has not been well characterized in Sudan grass under abiotic stress. In this study, 113 MYB genes were identified in the Sudan grass genome and categorized into three groups by phylogenetic analysis. The promoter regions of SsMYB genes contain different cis-regulatory elements, which are involved in developmental, hormonal, and stress responses, and may be closely related to their diverse regulatory functions. In addition, collinearity analysis showed that the expansion of the SsMYB gene family occurred mainly through segmental duplications. Under drought conditions, SsMYB genes showed diverse expression patterns, which varied at different time points. Interaction networks of 74 SsMYB genes were predicted based on motif binding sites, expression correlations, and protein interactions. Heterologous expression showed that SsMYB8, SsMYB15, and SsMYB64 all significantly enhanced the drought tolerance of yeast cells. Meanwhile, the subcellular localization of all three genes is in the nucleus. Overall, this study provides new insights into the evolution and function of MYB genes and provides valuable candidate genes for breeding efforts in Sudan grass.

Genome-Wide Identification and Expression Pattern Analysis of the WNK Gene Family in Apple under Abiotic Stress and Colletotrichum siamense Infection

With-no-lysine kinase (WNK) is a unique serine/threonine kinase family member. WNK differs from other protein kinases by not having a standard lysine in subdomain II of the universally preserved kinase catalytic region. Conversely, the amino acid lysine located in subdomain I plays a crucial role in its phosphorylation. The WNK family has been reported to regulate Arabidopsis flowering, circadian rhythm, and abiotic stress. Eighteen members of the WNK gene family were discovered in apples in this research, and they were primarily grouped into five categories on the phylogenetic tree. Conserved domains and motifs also confirmed their identity as members of the WNK family. Promoter cis-acting element analysis indicated their potential role in responses to both abiotic stress and phytohormones. Furthermore, qRT-PCR analysis showed that the expression of MdWNK family genes was stimulated to different extents by Colletotrichum siamense, NaCl, mannitol, ABA, JA, and SA, with Colletotrichum siamense being the most prominent stimulant. MdWNK family genes were expressed across all apple tissues, with young fruits showing the greatest expression and roots showing the least expression. The research offered detailed insights into the MdWNK gene family, serving as a crucial basis for investigating the biological roles of MdWNK genes.

Overexpression of a Grape WRKY Transcription Factor VhWRKY44 Improves the Resistance to Cold and Salt of Arabidopsis thaliana

Plants are often exposed to biotic or abiotic stress, which can seriously impede their growth and development. In recent years, researchers have focused especially on the study of plant responses to biotic and abiotic stress. As one of the most widely planted grapevine rootstocks, 'Beta' has been extensively proven to be highly resistant to stress. However, further research is needed to understand the mechanisms of abiotic stress in 'Beta' rootstocks. In this study, we isolated and cloned a novel WRKY transcription factor, VhWRKY44, from the 'Beta' rootstock. Subcellular localization analysis revealed that VhWRKY44 was a nuclear-localized protein. Tissue-specific expression analysis indicated that VhWRKY44 had higher expression levels in grape roots and mature leaves. Further research demonstrated that the expression level of VhWRKY44 in grape roots and mature leaves was highly induced by salt and cold treatment. Compared with the control, Arabidopsis plants overexpressing VhWRKY44 showed stronger resistance to salt and cold stress. The activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were significantly increased, and the contents of proline, malondialdehyde (MDA) and chlorophyll were changed considerably. In addition, significantly higher levels of stress-related genes were detected in the transgenic lines. The results indicated that VhWRKY44 was an important transcription factor in 'Beta' with excellent salt and cold tolerance, providing a new foundation for abiotic stress research.

The transcription factor MdERF023 negatively regulates salt tolerance by modulating ABA signaling and Na+/H+ transport in apple

KEY MESSAGE

MdERF023 is a transcription factor that can reduce salt tolerance by inhibiting ABA signaling and Na+/H+ homeostasis. Salt stress is one of the principal environmental stresses limiting the growth and productivity of apple (Malus × domestica). The APETALA2/ethylene response factor (AP2/ERF) family plays key roles in plant growth and various stress responses; however, the regulatory mechanism involved has not been fully elucidated. In the present study, we identified an AP2/ERF transcription factor (TF), MdERF023, which plays a negative role in apple salt tolerance. Stable overexpression of MdERF023 in apple plants and calli significantly decreased salt tolerance. Biochemical and molecular analyses revealed that MdERF023 directly binds to the promoter of MdMYB44-like, a positive modulator of ABA signaling-mediated salt tolerance, and suppresses its transcription. In addition, MdERF023 downregulated the transcription of MdSOS2 and MdAKT1, thereby reducing the Na+ expulsion, K+ absorption, and salt tolerance of apple plants. Taken together, these results suggest that MdERF023 reduces apple salt tolerance by inhibiting ABA signaling and ion transport, and that it could be used as a potential target for breeding new varieties of salt-tolerant apple plants via genetic engineering.

PagbHLH35 Enhances Salt Tolerance through Improving ROS Scavenging in Transgenic Poplar

The bHLH transcription factor family plays crucial roles in plant growth and development and their responses to adversity. In this study, a highly salt-induced bHLH gene, PagbHLH35 (Potri.018G141600), was identified from Populus alba × P. glandullosa (84K poplar). PagbHLH35 contains a highly conserved bHLH domain within the region of 52-114 amino acids. A subcellular localization result confirmed its nuclear localization. A yeast two-hybrid assay indicated PagbHLH35 lacks transcriptional activation activity, while a yeast one-hybrid assay indicated it could specifically bind to G-box and E-box elements. The expression of PagbHLH35 reached its peak at 12 h and 36 h time points under salt stress in the leaves and roots, respectively. A total of three positive transgenic poplar lines overexpressing PagbHLH35 were generated via Agrobacterium-mediated leaf disk transformation. Under NaCl stress, the transgenic poplars exhibited significantly enhanced morphological and physiological advantages such as higher POD activity, SOD activity, chlorophyll content, and proline content, and lower dehydration rate, MDA content and hydrogen peroxide (H2O2) content, compared to wild-type (WT) plants. In addition, histological staining showed that there was lower ROS accumulation in the transgenic poplars under salt stress. Moreover, the relative expression levels of several antioxidant genes in the transgenic poplars were significantly higher than those in the WT. All the results indicate that PagbHLH35 can improve salt tolerance by enhancing ROS scavenging in transgenic poplars.

The BTB-BACK-TAZ domain protein MdBT2 reduces drought resistance by weakening the positive regulatory effect of MdHDZ27 on apple drought tolerance via ubiquitination

Drought stress is one of the dominating challenges to the growth and productivity in crop plants. Elucidating the molecular mechanisms of plants responses to drought stress is fundamental to improve fruit quality. However, such molecular mechanisms are poorly understood in apple (Malus domestica Borkh.). In this study, we explored that the BTB-BACK-TAZ protein, MdBT2, negatively modulates the drought tolerance of apple plantlets. Moreover, we identified a novel Homeodomain-leucine zipper (HD-Zip) transcription factor, MdHDZ27, using a yeast two-hybrid (Y2H) screen with MdBT2 as the bait. Overexpression of MdHDZ27 in apple plantlets, calli, and tomato plantlets enhanced their drought tolerance by promoting the expression of drought tolerance-related genes [responsive to dehydration 29A (MdRD29A) and MdRD29B]. Biochemical analyses demonstrated that MdHDZ27 directly binds to and activates the promoters of MdRD29A and MdRD29B. Furthermore, in vitro and in vivo assays indicate that MdBT2 interacts with and ubiquitinates MdHDZ27, via the ubiquitin/26S proteasome pathway. This ubiquitination results in the degradation of MdHDZ27 and weakens the transcriptional activation of MdHDZ27 on MdRD29A and MdRD29B. Finally, a series of transgenic analyses in apple plantlets further clarified the role of the relationship between MdBT2 and MdHDZ27, as well as the effect of their interaction on drought resistance in apple plantlets. Collectively, our findings reveal a novel mechanism by which the MdBT2-MdHDZ27 regulatory module controls drought tolerance, which is of great significance for enhancing the drought resistance of apple and other plants.

Brassinosteroids biosynthetic gene MdBR6OX2 regulates salt stress tolerance in both apple and Arabidopsis

Salt stress is a critical limiting factor for fruit yield and quality of apples. Brassinosteroids (BRs) play an important role in response to abiotic stresses. In the present study, application of 2,4- Epicastasterone on seedlings of Malus 'M9T337' and Malus domestica 'Gala3' alleviated the physiological effects, such as growth inhibition and leaf yellowing, induced by salt stress. Further analysis revealed that treatment with NaCl induced expression of genes involved in BR biosynthesis in 'M9T337' and 'Gala3'. Among which, the expression of BR biosynthetic gene MdBR6OX2 showed a three-fold upregulation upon salt treatment, suggesting its potential role in response to salt stress in apple. MdBR6OX2, belonging to the CYP450 family, contains a signal peptide region and a P450 domain. Expression patterns analysis showed that the expression of MdBR6OX2 can be significantly induced by different abiotic stresses. Overexpressing MdBR6OX2 enhanced the tolerance of apple callis to salt stress, and the contents of endogenous BR-related compounds, such as Typhastero (TY), Castasterone (CS) and Brassinolide (BL) were significantly increased in transgenic calli compared with that of wild-type. Extopic expression of MdBR6OX2 enhanced tolerance to salt stress in Arabidopsis. Genes associated with salt stress were significantly up-regulated, and the contents of BR-related compounds were significantly elevated under salt stress. Our data revealed that BR-biosynthetic gene MdBR6OX2 positively regulates salt stress tolerance in both apple calli and Arabidopsis.

MaMYBR30, a Novel 1R-MYB, Plays Important Roles in Plant Development and Abiotic Stress Resistance

The V-myb myeloblastosis viral oncogene homolog (MYB) family participate in various bioprocesses including development and abiotic stress responses. In the present study, we first report a 1R SHAQKYF-class MYB, MaMYBR30, in mulberry. Subcellular localization and sequence analysis indicated MaMYBR30 is located in the nucleus and belongs to a CCA-like subgroup with a conserved SHAQKYF motif. Expression profile analysis showed that MaMYBR30 is expressed in leaves and can be induced by drought and salt stress. The down-regulation of MaMYBR30 using virus-induced gene silence (VIGS) in mulberry and the overexpression of MaMYBR30 in Arabidopsis were induced to explore the function of MaMYBR30. The functional characterization of MaMYBR30 in vivo indicated that MaMYBR30 can positively regulate the resistance of mulberry to drought while negatively regulating the resistance of mulberry to salt stress. In addition, MaMYBR30 also affects flower development and reproductive growth, especially after exposure to salt stress. Weighted gene co-expression network analysis (WGCNA) primarily revealed the possible genes and signal pathways that are regulated by MaMYBR30. Our results also imply that complex molecular mechanisms mediated by MaMYBR30, including crosstalk of ion toxicity, phytohormone signal transduction, flowering development, and epigenetic modification, need to be further explored in the future.

Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar

The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.

Regulation of SmEXPA13 expression by SmMYB1R1-L enhances salt tolerance in Salix matsudana Koidz

Expansins, cell wall proteins, play a significant role in plant stress resistance. Our previous study confirmed the expression of the expansin gene SmEXPA13 from Salix matsudana Koidz. enhanced salt tolerance of plants. This report presented an assay that the expression of SmEXPA13 was higher in the salt-resistant willow variety 9901 than in the salt-sensitive variety Yanjiang. In order to understand the possible reasons, a study of the regulation process was conducted. Despite being cloned from both varieties, SmEXPA13 and its promotor showed no significant differences in the structure and sequence. A transcription factor (TF), SmMYB1R1-L, identified through screening the yeast library of willow cDNA, was found to regulate SmEXPA13. Yeast one-hybrid (Y1H) assay confirmed that SmMYB1R1-L could bind to the MYB element at the -520 bp site on the SmEXPA13 promotor. A dual-luciferase reporter assay also demonstrated that SmMYB1R1-L could greatly activate SmEXPA13 expression. The willow calli with over-expression of SmMYB1R1-L exhibited better physiological performance than the wild type under salt stress. Further testing the expression of SmMYB1R1-L displayed it significantly higher in 9901 willow than that in Yanjiang under salt stress. In conclusion, the high accumulation of SmMYB1R1-L in 9901 willow under salt stress led to the high expression of SmEXPA13, resulting in variations in salt stress resistance among willow varieties. The SmMYB1R1-L/SmEXPA13 cascade module in willow offers a new perspective on plant resistance mechanisms.

GhMYB52 Like: A Key Factor That Enhances Lint Yield by Negatively Regulating the Lignin Biosynthesis Pathway in Fibers of Upland Cotton (Gossypium hirsutum L.)

In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization.

Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon because of high temperatures, resulting in a significant yield reduction. However, the molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat-response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata that differed between heat-stress and room-temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, and catalytic and binding activities. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed between the two test conditions. According to the analysis, genes and miRNAs associated with the regulation of transcription, DNA template, transcription factor activity, and sequence-specific DNA binding pathways may play a major role in the resistance to heat stress in P. ternata. Integrated analysis of the transcriptome and miRNAome expression data revealed 41 high-confidence miRNA-mRNA pairs, forming 25 modules. MYB-like proteins and calcium-responsive transcription coactivators may play an integral role in heat-stress resistance in P. ternata. Additionally, the candidate genes and miRNAs were subjected to quantitative real-time polymerase chain reaction to validate their expression patterns. These results offer a foundation for future studies exploring the mechanisms and critical genes involved in heat-stress resistance in P. ternata.

Cloning and functional identification of apple LATERAL ORGAN BOUNDARY DOMAIN 3 (LBD3) transcription factor in the regulation of drought and salt stress

MAIN CONCLUSION

Overexpression of MdLBD3 in Arabidopsis reduced sensitivity to salt and drought stresses and was instrumental in promoting early flowering. Salt and drought stresses have serious effects on plant growth. LATERAL ORGAN BOUNDARY DOMAIN (LBD) proteins are a plant-specific transcription factors (TFs) family and play important roles in plants in resisting to abiotic stress. However, about the function of LBDs in apple and other woody plants is little known. In this study, protein sequences of the LBD family TFs in apples were identified which contained conserved LOB domains. The qRT-PCR analysis showed that the MdLBD3 gene was widely expressed in various tissues and organs. The subcellular localization assay showed that the MdLBD3 protein was localized in the nucleus. Ectopic expression of MdLBD3 in Arabidopsis positively regulated its salt and drought resistance, and promoted early flowering. Collectively, these results showed that MdLBD3 improved the abiotic stress resistance, plant growth and development. Overall, this study provided a new gene for breeding that can increase the abiotic stress tolerance in apple.

MdMYB44-like positively regulates salt and drought tolerance via the MdPYL8-MdPP2CA module in apple

Abscisic acid (ABA) is involved in salt and drought stress responses, but the underlying molecular mechanism remains unclear. Here, we demonstrated that the overexpression of MdMYB44-like, an R2R3-MYB transcription factor, significantly increases the salt and drought tolerance of transgenic apples and Arabidopsis. MdMYB44-like inhibits the transcription of MdPP2CA, which encodes a type 2C protein phosphatase that acts as a negative regulator in the ABA response, thereby enhancing ABA signaling-mediated salt and drought tolerance. Furthermore, we found that MdMYB44-like and MdPYL8, an ABA receptor, form a protein complex that further enhances the transcriptional inhibition of the MdPP2CA promoter by MdMYB44-like. Significantly, we discovered that MdPP2CA can interfere with the physical association between MdMYB44-like and MdPYL8 in the presence of ABA, partially blocking the inhibitory effect of the MdMYB44-like-MdPYL8 complex on the MdPP2CA promoter. Thus, MdMYB44-like, MdPYL8, and MdPP2CA form a regulatory loop that tightly modulates ABA signaling homeostasis under salt and drought stress. Our data reveal that MdMYB44-like precisely modulates ABA-mediated salt and drought tolerance in apples through the MdPYL8-MdPP2CA module.

The GARP family transcription factor MtHHO3 negatively regulates salt tolerance in Medicago truncatula

High salinity is one of the detrimental environmental factors restricting plant growth and crop production throughout the world. This study demonstrated that the GARP family transcription factor MtHHO3 is involved in response to salt stress and abscisic acid (ABA) signaling in Medicago truncatula. The transcription of MtHHO3 was repressed by salt, osmotic stress, and ABA treatment. The seed germination assay showed that, overexpression of MtHHO3 in Arabidopsis thaliana caused hypersensitivity to salt and osmotic stress, but increased resistance to ABA inhibition. Overexpression of MtHHO3 in M. truncatula resulted in decreased tolerance of salinity, while loss-of-function mutants mthho3-1 and mthho3-2 were more resistant to salt stress compared with wild-type plants. qRT-PCR analyses showed that MtHHO3 downregulated the expression of genes in stress and ABA responsive pathways. We further demonstrated that MtHHO3 repressed the transcription of the pathogenesis-related gene MtPR2 by binding to its promoter. Overall, these results indicate that MtHHO3 negatively regulates salt stress response in plants and deepen our understanding of the role of the GARP subfamily transcription factors in modulating salt stress and ABA signaling.

Overexpression of transcription factor FaMYB63 enhances salt tolerance by directly binding to the SOS1 promoter in Arabidopsis thaliana

Salinity is a pivotal abiotic stress factor with far-reaching consequences on global crop growth, yield, and quality and which includes strawberries. R2R3-MYB transcription factors encompass a range of roles in plant development and responses to abiotic stress. In this study, we identified that strawberry transcription factor FaMYB63 exhibited a significant upregulation in its expression under salt stress conditions. An analysis using yeast assay demonstrated that FaMYB63 exhibited the ability to activate transcriptional activity. Compared with those in the wild-type (WT) plants, the seed germination rate, root length, contents of chlorophyll and proline, and antioxidant activities (SOD, CAT, and POD) were significantly higher in FaMYB63-overexpressing Arabidopsis plants exposed to salt stress. Conversely, the levels of malondialdehyde (MDA) were considerably lower. Additionally, the FaMYB63-overexpressed Arabidopsis plants displayed a substantially improved capacity to scavenge active oxygen. Furthermore, the activation of stress-related genes by FaMYB63 bolstered the tolerance of transgenic Arabidopsis to salt stress. It was also established that FaMYB63 binds directly to the promoter of the salt overly sensitive gene SOS1, thereby activating its expression. These findings identified FaMYB63 as a possible and important regulator of salt stress tolerance in strawberries.

Caffeic Acid O-Methyltransferase Gene Family in Mango (Mangifera indica L.) with Transcriptional Analysis under Biotic and Abiotic Stresses and the Role of MiCOMT1 in Salt Tolerance

Caffeic acid O-methyltransferase (COMT) participates in various physiological activities in plants, such as positive responses to abiotic stresses and the signal transduction of phytohormones. In this study, 18 COMT genes were identified in the chromosome-level reference genome of mango, named MiCOMTs. A phylogenetic tree containing nine groups (I-IX) was constructed based on the amino acid sequences of the 71 COMT proteins from seven species. The phylogenetic tree indicated that the members of the MiCOMTs could be divided into four groups. Quantitative real-time PCR showed that all MiCOMT genes have particularly high expression levels during flowering. The expression levels of MiCOMTs were different under abiotic and biotic stresses, including salt and stimulated drought stresses, ABA and SA treatment, as well as Xanthomonas campestris pv. mangiferaeindicae and Colletotrichum gloeosporioides infection, respectively. Among them, the expression level of MiCOMT1 was significantly up-regulated at 6-72 h after salt and stimulated drought stresses. The results of gene function analysis via the transient overexpression of the MiCOMT1 gene in Nicotiana benthamiana showed that the MiCOMT1 gene can promote the accumulation of ABA and MeJA, and improve the salt tolerance of mango. These results are beneficial to future researchers aiming to understand the biological functions and molecular mechanisms of MiCOMT genes.

Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control

Bananas (Musa spp.) are one of the world's most important fruit crops and play a vital role in food security for many developing countries. Most banana cultivars are triploids derived from inter- and intraspecific hybridizations between the wild diploid ancestor species Musa acuminate (AA) and M. balbisiana (BB). We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types, Plantain and Silk, and precisely characterize ancestral contributions by examining ancestry mosaics across the genome. Widespread asymmetric evolution is observed in their subgenomes, which can be linked to frequent homologous exchange events. We reveal the genetic makeup of triploid banana cultivars and verify that subgenome B is a rich source of disease resistance genes. Only 58.5% and 59.4% of Plantain and Silk genes, respectively, are present in all three haplotypes, with >50% of genes being differentially expressed alleles in different subgenomes. We observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4 (Foc TR4), which confirms that Plantain can initiate defense responses faster than Silk. Additionally, we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and Silk. Our study provides resources for better understanding the genomic architecture of cultivated bananas and has important implications for Musa genetics and breeding.

Molecular mechanism of salinity and waterlogging tolerance in mangrove Kandelia obovata

Mangrove forests are colloquially referred to as "Earth's kidneys" and serve many important ecological and commercial functions. Salinity and waterlogging stress are the most important abiotic stressors restricting the growth and development of mangroves. Kandelia obovata (K. obovata) is the greatest latitudinally-distributed salt mangrove species in China.Here, morphology and transcriptomics were used to study the response of K. obovata to salt and waterlogging stress. In addition, weighted gene co-expression network analysis of the combined gene expression and phenotypic datasets was used to identify core salinity- and waterlogging-responsive modules. In this study, we observed that both high salinity and waterlogging significantly inhibited growth and development in K. obovata. Notably, growth was negatively correlated with salt concentration and positively correlated with waterlogging duration, and high salinity was significantly more inhibitive than waterlogging. A total of 7, 591 salt-responsive and 228 waterlogging-responsive differentially expressed genes were identified by RNA sequencing. Long-term salt stress was highly correlated with the measured physiological parameters while long-term waterlogging was poorly correlated with these traits. At the same time, 45 salinity-responsive and 16 waterlogging-responsive core genes were identified. All 61 core genes were mainly involved in metabolic and biosynthesis of secondary metabolites pathways. This study provides valuable insight into the molecular mechanisms of salinity and waterlogging tolerance in K. obovata, as well as a useful genetic resource for the improvement of mangrove stress tolerance using molecular breeding techniques.

Bp-miR408a participates in osmotic and salt stress responses by regulating BpBCP1 in Betula platyphylla

The microRNAs, which are small RNAs of 18-25 nt in length, act as key regulatory factors in posttranscriptional gene expression during plant growth and development. However, little is known about their regulatory roles in response to stressful environments in birch (Betula platyphylla). Here, we characterized and further explored miRNAs from osmotic- and salt-stressed birch. Our analysis revealed a total of 190 microRNA (miRNA) sequences, which were classified into 180 conserved miRNAs and 10 predicted novel miRNAs based on sequence homology. Furthermore, we identified Bp-miR408a under osmotic and salt stress and elucidated its role in osmotic and salt stress responses in birch. Notably, under osmotic and salt stress, Bp-miR408a contributed to osmotic and salt tolerance sensitivity by mediating various physiological changes, such as increases in reactive oxygen species accumulation, osmoregulatory substance contents and Na+ accumulation. Additionally, molecular analysis provided evidence of the in vivo targeting of BpBCP1 (blue copper protein) transcripts by Bp-miR408a. The overexpression of BpBCP1 in birch enhanced osmotic and salt tolerance by increasing the antioxidant enzyme activity, maintaining cellular ion homeostasis and decreasing lipid peroxidation and cell death. Thus, we reveal a Bp-miR408a-BpBCP1 regulatory module that mediates osmotic and salt stress responses in birch.

Jasmonate activates secondary cell wall biosynthesis through MYC2-MYB46 module

Formation of secondary cell wall (SCW) is tightly regulated spatiotemporally by various developmental and environmental signals. Successful fine-tuning of the trade-off between SCW biosynthesis and stress responses requires a better understanding of how plant growth is regulated under environmental stress conditions. However, the current understanding of the interplay between environmental signaling and SCW formation is limited. The lipid-derived plant hormone jasmonate (JA) and its derivatives are important signaling components involved in various physiological processes including plant growth, development, and abiotic/biotic stress responses. Recent studies suggest that JA is involved in SCW formation but the signaling pathway has not been studied for how JA regulates SCW formation. We tested this hypothesis using the transcription factor MYB46, a master switch for SCW biosynthesis, and JA treatments. Both the transcript and protein levels of MYB46, a master switch for SCW formation, were significantly increased by JA treatment, resulting in the upregulation of SCW biosynthesis. We then show that this JA-induced upregulation of MYB46 is mediated by MYC2, a central regulator of JA signaling, which binds to the promoter of MYB46. We conclude that this MYC2-MYB46 module is a key component of the plant response to JA in SCW formation.

FvemiR160-FveARF18A-FveAP1/FveFUL module regulates flowering time in woodland strawberry

Flowering is an indicator of plant transformation from vegetative to reproductive growth. miR160 has been shown to have a significant effect on the growth and development of fruits, leaves, and roots of plants or their stress response to environment, but the participation of miR160 in regulating flowering time in plants is unclear. In this study, we found that two FvemiR160s (FvemiR160a/FvemiR160b) mature sequences in strawberry (Fragaria vesca) were consistent. It was displayed that the miR160 mature sequence is highly conserved in various species, and the miR160 mature sequence formed by the 5' arm of the MIR160 precursor was more conserved. Three FveARFs in woodland strawberry were negatively regulated by FvemiR160a, among which FveARF18A was the most significant. Phylogenetic analysis indicated that FvemiR160 is closely related to apple (Malus domestica), grape (Vitis vinifera), and Arabidopsis thaliana, while FveARF18A is closely related to RcARF18. Subsequently, we demonstrated that FvemiR160a can target cutting FveARF18A to negatively regulate its expression by RLM-5' RACE, cleavage site mutation, and GFP fluorescence assay. Moreover, we observed that FveMIR160a overexpressed plants have advanced flowering, while mFveARF18A overexpressed plants have delayed flowering. We also verified that FveARF18A negatively regulates the expression of FveAP1 and FveFUL by binding their promoters by yeast one-hybrid, LUC, and GUS assay, and FveAP1 and FveFUL transgenic Arabidopsis showed early flowering phenotype. In addition, the expression level of FvemiR160a was decreased obviously while that of FveARF18A was increased obviously by MeJA, GA and IAA. In conclusion, our study reveals the important role of the FvemiR160-FveARF18A-FveAP1/FveFUL module in the flowering process of woodland strawberry and provides a new pathway for studying flowering.

RtNAC055 promotes drought tolerance via a stomatal closure pathway linked to methyl jasmonate/hydrogen peroxide signaling in Reaumuria trigyna

The stomata regulate CO2 uptake and efficient water usage, thereby promoting drought stress tolerance. NAC proteins (NAM, ATAF1/2, and CUC2) participate in plant reactions following drought stress, but the molecular mechanisms underlying NAC-mediated regulation of stomatal movement are unclear. In this study, a novel NAC gene from Reaumuria trigyna, RtNAC055, was found to enhance drought tolerance via a stomatal closure pathway. It was regulated by RtMYC2 and integrated with jasmonic acid signaling and was predominantly expressed in stomata and root. The suppression of RtNAC055 could improve jasmonic acid and H2O2 production and increase the drought tolerance of transgenic R. trigyna callus. Ectopic expression of RtNAC055 in the Arabidopsis atnac055 mutant rescued its drought-sensitive phenotype by decreasing stomatal aperture. Under drought stress, overexpression of RtNAC055 in poplar promoted ROS (H2O2) accumulation in stomata, which accelerated stomatal closure and maintained a high photosynthetic rate. Drought upregulated the expression of PtRbohD/F, PtP5CS2, and PtDREB1.1, as well as antioxidant enzyme activities in heterologous expression poplars. RtNAC055 promoted H2O2 production in guard cells by directly binding to the promoter of RtRbohE, thus regulating stomatal closure. The stress-related genes RtDREB1.1/P5CS1 were directly regulated by RtNAC055. These results indicate that RtNAC055 regulates stomatal closure by maintaining the balance between the antioxidant system and H2O2 level, reducing the transpiration rate and water loss, and improving photosynthetic efficiency and drought resistance.

The chromosome-level genome assembly of Fraxinus americana provides insights into the evolution of Oleaceae plants

White ash (Fraxinus americana linn.) originates from the southeastern United States. It is a tall and fast-growing tree species with strong salt-alkali resistance and cold tolerance, making it an important reforestation species and widely planted worldwide. Here, we completed the chromosome-level reference genome assembly of F. americana based on Illumina, PacBio, and Hi-C reads, with a genome size of 878.98 Mb, an N50 of 3.27 Mb, and a heterozygosity rate of 0.3 %. Based on de novo prediction, transcriptome prediction, and homology-based protein prediction, we obtained 39,538 genes. Approximately 843.21 Mb of the assembly genome was composed of 37,928 annotated protein-coding genes, with a gene function annotation rate of 95.93 %. 99.94 % of the overlap clusters (877.44 Mb) were anchored to 23 chromosomes. Synteny analysis of F. americana and other Oleaceae plants showed that F. americana underwent frequent chromosome rearrangements. The amplification of the Ale transposons effectively promoted the genome size of F. americana. Compared with other Oleaceae plants, the Glutathione S-transferase (GST) gene family in the F. americana genome has undergone significant expansion, which may help F. americana cope with adverse natural environments. Furthermore, we found that key enzyme-coding gene families related to lignin biosynthesis were expanded and highly expressed in F. americana leaves. These key genes drive lignin synthesis and benefit F. americana in fast-growing, as well as resisting biotic and abiotic stress. Overall, the F. americana genome assembly provides insights into the evolution of Oleaceae plants and provides abundant resources for breeding and germplasm conservation of white ash.

Mechanisms of the response of apple fruit to postharvest compression damage analyzed by integrated transcriptome and metabolome

Apple fruit is susceptible to compression damage within the postharvest supply chain given its thin peels and brittle texture, which can result in decay and deterioration and have a substantial impact on its marketability and competitiveness. Thorough bioinformatics investigations are lacking on postharvest compression damage stress-induced alterations in genes and metabolic regulatory networks in fruits. In the present study, a comprehensive analysis of both the transcriptome and metabolome was conducted on 'Red Fuji' apples experiencing compression-induced damage. During the storage after damage has occurred, the gene expression of MdOFUT19, MdWRKY48, MdCBP60E, MdCYP450 and MdSM-like of the damaged apples was consistently higher than that of the control group. The damaged apples also had higher contents of some metabolites such as procyanidin A1, Dl-2-Aminooctanoic acid, 5-O-p-Coumaroyl shikimic acid and 5,7-Dihydroxy-3',4',5'-trimethoxyflavone. Analysis of genes and metabolites with distinct expressions on the common annotation pathway suggested that the fruit may respond to compression stress by promoting volatile ester and lignin synthesis. The above results can deepen the comprehension of the response mechanisms in apple fruits undergoing compression-induced damage.

Silicon inhibits cadmium uptake by regulating the genes associated with the lignin biosynthetic pathway and plant hormone signal transduction in maize plants

Cadmium (Cd) contamination in soil poses a severe threat to plant growth and development. In contrast, silicon (Si) has shown promise in enhancing plant resilience under Cd-induced stress. In this study, we conducted an integrated investigation employing morphological studies, gene expression analysis, and metabolomics to unravel the molecular mechanisms underlying Cd tolerance in maize plants. Our results demonstrate that Si biofortification significantly mitigated Cd stress by reducing Cd accumulation in plant tissues, increasing Si content, and enhancing maize biomass in Cd-stressed plants resulted in a substantial enhancement in shoot dry weight (+ 75%) and root dry weight (+ 30%). Notably, Si treatment upregulated key lignin-related genes (TaPAL, TaCAD, Ta4CL, and TaCOMT) and promoted the accumulation of metabolites (sinapyl alcohol, phenylalanine, p-coumaryl alcohol, cafeyl alcohol, and coniferaldehyde) essential for cell wall strength, particularly under Cd stress conditions. Si application enriched the signal transduction by hormones and increased resistance by induction of biosynthesis genes (TaBZR1, TaLOX3, and TaNCDE1) and metabolites (brassinolide, abscisic acid, and jasmonate) in the roots and leaves under Cd stress. Furthermore, our study provides a comprehensive view of the intricate molecular crosstalk between Si, Cd stress, and plant hormonal responses. We unveil a network of genetic and metabolic interactions that culminate in a multifaceted defense system, enabling maize plants to thrive even in the presence of Cd-contaminated soil. This knowledge not only advances our understanding of the protective role of Si but also highlights the broader implications for sustainable agricultural practices. By harnessing the insights gained from this research, we may pave the way for innovative strategies to fortify crops against environmental stressors, ultimately contributing to the goal of food security in an ever-changing world. In summary, our research offers valuable insights into the protective mechanisms facilitated by Si, which enhance plants' ability to withstand environmental stress, and holds promise for future applications in sustainable agriculture.

Comparative transcriptome analysis of major lodging resistant factors in hulless barley

Hulless barley (Hordeum vulgare L. var. nudum Hook. f.), belonging to the genus Gramineae, has high and steady output and thus considered as a principal food crop by Tibetan people. Hulless barley grain can be used for food, brewing, and functional health product development, while its straw serves as an essential supplementary forage and is a crucial cereal crop. Lodging can reduce the yield and quality of barley grain and straw, and it hinders mechanical harvesting. It is a significant factor affecting high and stable yields of barley. Unlike other Poaceae plants (such as rice, wheat), hulless barley is mainly grown in high-altitude regions, where it is susceptible to low temperatures, strong winds, and heavy rainfall. As a result, its stem lodging resistance is relatively weak, making it prone to lodging during the growth period. In this study, we observed that the lignin concentration and the contents of lignin monomers (H, S, and G), and neutral detergent fibre of the lodging-resistant variety Kunlun14 were substantially greater than those of the lodging-sensitive variety Menyuanlianglan. We performed the weighted gene co-expression network analysis (WGCNA) and Short Time-series Expression Miner (STEM) analysis of both the lodging-resistant and lodging-sensitive varieties. Through transcriptome sequencing analysis at different developmental stages, combined with the previously annotated genes related to lodging resistance, a total of 72 DEGs were identified. Among these DEGs, 17 genes were related to lignin, cellulose, and hemicellulose synthesis or regulation, including five transcription factors about NAC, MYB and WRKY. Our results provide a basis for further exploring the molecular mechanism of stem lodging resistance in hulless barley and provide valuable gene resources for stem lodging resistance molecular breeding.

MdGRF11-MdARF19-2 module acts as a positive regulator of drought resistance in apple rootstock

14-3-3 proteins play an important role in the response of plants to drought resistance. In this study, 14-3-3 protein MdGRF11 was cloned from Malus xiaojinensis, and its positive regulation of drought resistance was verified using Orin calli and M. xiaojinensis plants. The transcription factor MdARF19-2 was further screened for interaction with this protein in vitro and in vivo. We also conducted experiments using Orin calli and found that the overexpression of MdARF19-2 decreased the level of reactive oxygen species (ROS) and increased the activity of enzymes that scavenge ROS in plant materials. This indicates that MdARF19-2 is a positive regulator in the drought resistance of plants. The drought tolerance was further improved by the overexpression of both MdGRF11 and MdARF19-2 in the calli. In addition, we examined several genes related to ROS scavenging with auxin response factor binding elements in their promoters and found that their level of expression was regulated by the MdGRF11-MdARF19-2 module. In conclusion, the enhancement of plant drought resistance by MdGRF11 could be owing to its accumulation at the protein level in response to drought, which then combined with MdARF19-2, affecting the expression of MdARF19-2 downstream genes. Thus, it scavenges ROS, which ultimately improves the resistance of plant to drought stress.

Drought Stress Tolerance in Vegetables: The Functional Role of Structural Features, Key Gene Pathways, and Exogenous Hormones

The deleterious effects of drought stress have led to a significant decline in vegetable production, ultimately affecting food security. After sensing drought stress signals, vegetables prompt multifaceted response measures, eventually leading to changes in internal cell structure and external morphology. Among them, it is important to highlight that the changes, including changes in physiological metabolism, signal transduction, key genes, and hormone regulation, significantly influence drought stress tolerance in vegetables. This article elaborates on vegetable stress tolerance, focusing on structural adaptations, key genes, drought stress signaling transduction pathways, osmotic adjustments, and antioxidants. At the same time, the mechanisms of exogenous hormones such as abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) toward improving the adaptive drought tolerance of vegetables were also reviewed. These insights can enhance the understanding of vegetable drought tolerance, supporting vegetable tolerance enhancement by cultivation technology improvements under changing climatic conditions, which provides theoretical support and technical reference for innovative vegetable stress tolerance breeding and food security.

Transcriptional repression of MdMa1 by MdMYB21 in Ma locus decreases malic acid content in apple fruit

Malic acid is a major organic acid component of apples and a crucial determinant of fruit organoleptic quality. A candidate gene for malic acid content, designated MdMa1, was previously identified in the Ma locus, which is a major quantitative trait locus (QTL) for apple fruit acidity located on the linkage group 16. Region-based association mapping to detect candidate genes in the Ma locus identified MdMa1 and an additional MdMYB21 gene putatively associated with malic acid. MdMYB21 was significantly associated with fruit malic acid content, accounting for ~7.48% of the observed phenotypic variation in the apple germplasm collection. Analyses of transgenic apple calli, fruits and tomatoes demonstrated that MdMYB21 negatively regulated malic acid accumulation. The apple fruit acidity-related MdMa1 and its tomato ortholog, SlALMT9, exhibited lower expression profiles in apple calli, mature fruits and tomatoes in which MdMYB21 was overexpressed, compared with their corresponding wild-type variety. MdMYB21 directly binds to the MdMa1 promoter and represses its expression. Interestingly, a 2-bp variation in the MdMYB21 promoter region altered its expression and regulation of its target gene, MdMa1, expression. Our findings not only demonstrate the efficiency of integrating QTL and association mapping in the identification of candidate genes controlling complex traits in apples, but also provide insights into the complex regulatory mechanism of fruit malic acid accumulation.

Osmotic stress-induced lignin synthesis is regulated at multiple levels in alfalfa (Medicago sativa L.)

Alfalfa is an important forage crop. Yield and quality are frequently threatened by extreme environments such as drought and salt stress. As a component of the cell wall, lignin plays an important role in the abiotic stress response, the mechanisms of which have not been well clarified. In this study, we combined physiological, transcriptional, and metabolic analyses to reveal the changes in lignin content in alfalfa under mannitol-induced osmotic stress. Osmotic stress enhanced lignin accumulation by increasing G and S units, which was associated with increases in enzyme activities and decreases in 8 intermediate metabolites. Upon combined analysis of the transcriptome and metabolome, we identified five key structural genes and several coexpressed transcription factors, such as MYB and WRKY, which may play a core role in regulating lignin content and composition under osmotic stress. In addition, lignin synthesis was positively regulated by ABA but negatively regulated by ethylene under osmotic stress. These results provide new insight into the regulatory mechanism of lignin synthesis under abiotic stress.

Insights into the molecular mechanisms underlying responses of apple trees to abiotic stresses

Apple (Malus[Formula: see text]domestica) is a popular temperate fruit crop worldwide. However, its growth, productivity, and quality are often adversely affected by abiotic stresses such as drought, extreme temperature, and high salinity. Due to the long juvenile phase and highly heterozygous genome, the conventional breeding approaches for stress-tolerant cultivars are time-consuming and resource-intensive. These issues may be resolved by feasible molecular breeding techniques for apples, such as gene editing and marker-assisted selection. Therefore, it is necessary to acquire a more comprehensive comprehension of the molecular mechanisms underpinning apples' response to abiotic stress. In this review, we summarize the latest research progress in the molecular response of apples to abiotic stressors, including the gene expression regulation, protein modifications, and epigenetic modifications. We also provide updates on new approaches for improving apple abiotic stress tolerance, while discussing current challenges and future perspectives for apple molecular breeding.

The NAC transcription factor MdNAC29 negatively regulates drought tolerance in apple

Drought stress is an adverse stimulus that affects agricultural production worldwide. NAC transcription factors are involved in plant development and growth but also play different roles in the abiotic stress response. Here, we isolated the apple MdNAC29 gene and investigated its role in regulating drought tolerance. Subcellular localization experiments showed that MdNAC29 was localized to the nucleus and transcription was induced by the PEG treatment. Over-expression of MdNAC29 reduced drought tolerance in apple plants, calli, and tobacco, and exhibited higher relative conductivity, malondialdehyde (MDA) content, and lower chlorophyll content under drought stress. The transcriptomic analyses revealed that MdNAC29 reduced drought resistance by modulating the expression of photosynthesis and leaf senescence-related genes. The qRT-PCR results showed that overexpression of MdNAC29 repressed the expression of drought-resistance genes. Yeast one-hybrid and dual-luciferase assays demonstrated that MdNAC29 directly repressed MdDREB2A expression. Moreover, the yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that MdNAC29 interacted with the MdPP2-B10 (F-box protein), which responded to drought stress, and MdPP2-B10 enhanced the repressive effect of MdNAC29 on the transcriptional activity of the MdDREB2A. Taken together, our results indicate that MdNAC29 is a negative regulator of drought resistance, and provide a theoretical basis for further molecular mechanism research.

Characterization of wheat Wrab18 gene promoter and expression analysis under abiotic stress

BACKGROUND

Promoters play key roles in plant gene expression in complex and varied natural environments. The type and amount of cis-acting elements in the promoter sequence tend to indicate the response of genes to induction factors. WRAB18 is a group III member of the late embryogenesis abundant (LEA) protein family that performs multiple functions in plant stress physiology. To elucidate the particularly biological effects of WRAB18 on stress, exploration of its promoter sequence is necessary.

METHODS AND RESULTS

In this study, the full-length and promoter sequences of Wrab18 were isolated from the Zhengyin 1 cultivar of Triticum aestivum. The gene sequences and cis-acting elements in the promoter were analyzed using the Plant Promoter Database and bioinformatics methods. The results showed that Wrab18 possessed one intron with 100 bp, the promoter sequence contained various stress-related cis-acting elements, and the functionality of the promoter was checked using green fluorescent protein (GFP) marker protein expression by transient assay in Nicotiana benthamiana. Furthermore, based on promoter prediction analysis, quantitative real-time fluorescent PCR results confirmed the response of gene expression levels to stress factors.

CONCLUSIONS

In summary, the promoter sequence of Wrab18 plays a role in plant stress responses, contains multiple cis-acting elements, and provides insights into the role of WRAB18 in plant resilience to stress. This study has guiding significance for further studies of gene function and mechanism of action, and lays a theoretical foundation for improving wheat quality.

Genome-Wide Analysis of Strictosidine Synthase-like Gene Family Revealed Their Response to Biotic/Abiotic Stress in Poplar

The strictosidine synthase-like (SSL) gene family is a small plant immune-regulated gene family that plays a critical role in plant resistance to biotic/abiotic stresses. To date, very little has been reported on the SSL gene in plants. In this study, a total of thirteen SSLs genes were identified from poplar, and these were classified into four subgroups based on multiple sequence alignment and phylogenetic tree analysis, and members of the same subgroup were found to have similar gene structures and motifs. The results of the collinearity analysis showed that poplar SSLs had more collinear genes in the woody plants Salix purpurea and Eucalyptus grandis. The promoter analysis revealed that the promoter region of PtrSSLs contains a large number of biotic/abiotic stress response elements. Subsequently, we examined the expression patterns of PtrSSLs following drought, salt, and leaf blight stress, using RT-qPCR to validate the response of PtrSSLs to biotic/abiotic stresses. In addition, the prediction of transcription factor (TF) regulatory networks identified several TFs, such as ATMYB46, ATMYB15, AGL20, STOP1, ATWRKY65, and so on, that may be induced in the expression of PtrSSLs in response to adversity stress. In conclusion, this study provides a solid basis for a functional analysis of the SSL gene family in response to biotic/abiotic stresses in poplar.

BcMYB111 Responds to BcCBF2 and Induces Flavonol Biosynthesis to Enhance Tolerance under Cold Stress in Non-Heading Chinese Cabbage

Flavonols have been shown to respond to a variety of abiotic stresses in plants, including cold stress. Higher total flavonoid content was found in non-heading Chinese cabbage (NHCC, Brassica campestris (syn. Brassica rapa) ssp. chinensis) after cold stress. A non-targeted metabolome analysis showed a significant increase in flavonol content, including that of quercetin and kaempferol. Here, we found that an R2R3-MYB transcription factor, BcMYB111, may play a role in this process. BcMYB111 was up-regulated in response to cold treatment, with an accompanying accumulation of flavonols. Then, it was found that BcMYB111 could regulate the synthesis of flavonols by directly binding to the promoters of BcF3H and BcFLS1. In the transgenic hairy roots of NHCC or stable transgenic Arabidopsis, overexpression of BcMYB111 increased flavonol synthesis and accumulation, while these were reduced in virus-induced gene silencing lines in NHCC. After cold stress, the higher proline content and lower malondialdehyde (MDA) content showed that there was less damage in transgenic Arabidopsis than in the wild-type (WT). The BcMYB111 transgenic lines performed better in terms of antioxidant capacity because of their lower H₂O₂ content and higher superoxide dismutase (SOD) and peroxidase (POD) enzyme activities. In addition, a key cold signaling gene, BcCBF2, could specifically bind to the DRE element and activate the expression of BcMYB111 in vitro and in vivo. The results suggested that BcMYB111 played a positive role in enhancing the flavonol synthesis and cold tolerance of NHCC. Taken together, these findings reveal that cold stress induces the accumulation of flavonols to increase tolerance via the pathway of BcCBF2-BcMYB111-BcF3H/BcFLS1 in NHCC.