Plant Hormone Signaling Pathways Research Articles

Zero-valent iron (nZVI) nanoparticles mediate SlERF1 expression to enhance cadmium stress tolerance in tomato

Cadmium (Cd) pollution threatens plant physiological and biochemical activities and crop production. Significant progress has been made in characterizing how nanoparticles affect Cd stress tolerance; however, the molecular mechanism of nZVI nanoparticles in Cd stress remains largely uncharacterized. Plants treated with nZVI and exposed to Cd had increased antioxidant capacity and reduced Cd accumulation in plant tissues. The nZVI treatment differentially affected the expression of genes involved in plant environmental responses, including those associated with the ERF transcription factor. SlEFR1 was upregulated by Cd stress in nZVI-treated plants when compared with the control and the predicted protein-protein interactions suggested SlERF1 interacts with proteins associated with plant hormone signaling pathway and related to stress. Yeast overexpressing SlEFR1 grew faster after Cd exposure and significantly had higher Cd stress tolerance when compared with empty vector controls. These results suggest that nZVI induces Cd stress tolerance by activating SlERF1 expression to improve plant growth and nutrient accumulation. Our study reveals the molecular mechanism of Cd stress tolerance for improved plant growth and will support new research on overcoming Cd stress and improving vegetable crop production.

Exogenous Abscisic Acid Regulates Anthocyanin Biosynthesis and Gene Expression in Blueberry Leaves

Blueberry (Vaccinium corymbosum) leaves have a positive influence on health because of their phenolic contents, including anthocyanins. Phytohormone abscisic acid (ABA) promotes anthocyanin accumulation, but the underlying mechanisms are unclear in blueberry leaves. In this study, we found that exogenous ABA promotes anthocyanin accumulation in blueberry leaves and we explored the global molecular events involved in these physiological changes by treating in vitro-grown blueberry seedlings with ABA and performing transcriptome deep sequencing (RNA-seq). We identified 6390 differentially expressed genes (DEGs), with 2893 DEGs at 6 h and 4789 at 12 h of ABA treatment compared to the control. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to plant hormone signal transduction and phenylpropanoid and flavonoid biosynthesis were significantly enriched at both stages of the ABA treatment. Analysis of DEGs in plant hormone signal transduction pathways revealed that exogenous ABA affected the expression of genes from other plant hormone signaling pathways, especially brassinosteroid, auxin, and gibberellin signaling. To elucidate the mechanism driving anthocyanin biosynthesis in blueberry in response to ABA treatment, we screened anthocyanin biosynthesis structural genes (ASG) from the phenylpropanoid and flavonoid biosynthetic pathways, MYB transcription factor genes from R2R3-MYB subgroups 5, 6, and 7 and ABRE-binding factor (ABF) genes from the ABA signal transduction pathway. Pearson’s correlation coefficient (r) analysis indicated that the ABFs, MYBs, and structural genes form a network to regulate ABA-induced anthocyanin biosynthesis and MYBA1 is likely to play an important role in this regulatory network. These findings lay the foundation for improving anthocyanin biosynthesis in blueberry leaves.

Comparative Transcriptomics Analysis Reveals the Differences in Transcription between Resistant and Susceptible Pepper (Capsicum annuum L.) Varieties in Response to Anthracnose.

Pepper (Capsicum annuum L.) is a herbaceous plant species in the family Solanaceae. Capsicum anthracnose is caused by the genus Colletotrichum. spp., which decreases pepper production by about 50% each year due to anthracnose. In this study, we evaluated the resistance of red ripe fruits from 17 pepper varieties against anthracnose fungus Colletotrichum capsici. We assessed the size of the lesion diameter and conducted significance analysis to identify the resistant variety of B158 and susceptible variety of B161. We selected a resistant cultivar B158 and a susceptible cultivar B161 of pepper and used a transcription to investigate the molecular mechanisms underlying the plant's resistance to C. capsici, of which little is known. The inoculated fruit from these two varieties were used for the comparative transcription analysis, which revealed the anthracnose-induced differential transcription in the resistant and susceptible pepper samples. In the environment of an anthrax infection, we found that there were more differentially expressed genes in resistant varieties compared to susceptible varieties. Moreover, the response to stimulus and stress ability was stronger in the KANG. The transcription analysis revealed the activation of plant hormone signaling pathways, phenylpropanoid synthesis, and metabolic processes in the defense response of peppers against anthracnose. In addition, ARR-B, AP2-EREBP, bHLH, WRKY, and NAC are associated with disease resistance to anthracnose. Notably, WRKY and NAC were found to have a potentially positive regulatory role in the defense response against anthracnose. These findings contribute to a more comprehensive understanding of the resistance mechanisms of red pepper fruit to anthracnose infection, providing valuable molecular insights for further research on the resistance mechanisms and genetic regulations during this developmental stage of pepper.

Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.)

BackgroundThe U-box gene family encodes E3 ubiquitin ligases involved in plant hormone signaling pathways and abiotic stress responses. However, there has yet to be a comprehensive analysis of the U-box gene family in maize (Zea mays L.) and its responses to abiotic stress.ResultsIn this study, 85 U-box family proteins were identified in maize and were classified into four subfamilies based on phylogenetic analysis. In addition to the conserved U-box domain, we identified additional functional domains, including Pkinase, ARM, KAP and Tyr domains, by analyzing the conserved motifs and gene structures. Chromosomal localization and collinearity analysis revealed that gene duplications may have contributed to the expansion and evolution of the U-box gene family. GO annotation and KEGG pathway enrichment analysis identified a total of 105 GO terms and 21 KEGG pathways that were notably enriched, including ubiquitin-protein transferase activity, ubiquitin conjugating enzyme activity and ubiquitin-mediated proteolysis pathway. Tissue expression analysis showed that some ZmPUB genes were specifically expressed in certain tissues and that this could be due to their functions. In addition, RNA-seq data for maize seedlings under salt stress revealed 16 stress-inducible plant U-box genes, of which 10 genes were upregulated and 6 genes were downregulated. The qRT-PCR results for genes responding to abiotic stress were consistent with the transcriptome analysis. Among them, ZmPUB13, ZmPUB18, ZmPUB19 and ZmPUB68 were upregulated under all three abiotic stress conditions. Subcellular localization analysis showed that ZmPUB19 and ZmPUB59 were located in the nucleus.ConclusionsOverall, our study provides a comprehensive analysis of the U-box gene family in maize and its responses to abiotic stress, suggesting that U-box genes play an important role in the stress response and providing insights into the regulatory mechanisms underlying the response to abiotic stress in maize.

Full-length transcriptome reveals the pivotal role of ABA and ethylene in the cold stress response of Tetrastigma hemsleyanum.

Tetrastigma hemsleyanum is a valuable herb widely used in Chinese traditional and modern medicine. Winter cold severely limits the artificial cultivation of this plant, but the physiological and molecular mechanisms upon exposure to cold stress in T. hemsleyanum are unclear. T. hemsleyanum plants with different geographical origins exhibit large differences in response to cold stress. In this research study, using T. hemsleyanum ecotypes that exhibit frost tolerance (FR) and frost sensitivity (FS), we analyzed the response of cottage seedlings to a simulated frost treatment; plant hormones were induced with both short (2 h) and long (9 h) frost treatments, which were used to construct the full-length transcriptome and obtained 76,750 transcripts with all transcripts mapped to 28,805 genes, and 27,215 genes, respectively, annotated to databases. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in plant hormone signaling pathways. Further analysis shows that differently expressed genes (DEGs) concentrated on calcium signaling, ABA biosynthesis and signal transduction, and ethylene in response to cold stress. We also found that endogenous ABA and ethylene content were increased after cold treatment, and exogenous ABA and ethylene significantly improved cold tolerance in both ecotypes. Our results elucidated the pivotal role of ABA and ethylene in response to cold stress in T. hemsleyanum and identified key genes.

Molecular warfare between pathogenic Fusarium oxysporum R1 and host Crocus sativus L. unraveled by dual transcriptomics.

Phenylpropanoid biosynthesis and plant-pathogen interaction pathways in saffron and cell wall degrading enzymes in Fusarium oxysporum R1 are key players involved in the interaction. Fusarium oxysporum causes corm rot in saffron (Crocus sativus L.), which is one of the most devastating fungal diseases impacting saffron yield globally. Though the corm rot agent and its symptoms are known widely, little is known about the defense mechanism of saffron in response to Fusarium oxysporum infection at molecular level. Therefore, the current study reports saffron-Fusarium oxysporum R1 (Fox R1) interaction at the molecular level using dual a transcriptomics approach. The results indicated the activation of various defense related pathways such as the mitogen activated protein kinase pathway (MAPK), plant-hormone signaling pathways, plant-pathogen interaction pathway, phenylpropanoid biosynthesis pathway and PR protein synthesis in the host during the interaction. The activation of pathways is involved in the hypersensitive response, production of various secondary metabolites, strengthening of the host cell wall, systemic acquired resistance etc. Concurrently, in the pathogen, 60 genes reported to be linked to pathogenicity and virulence has been identified during the invasion. The expression of genes encoding plant cell wall degrading enzymes, various transcription factors and effector proteins indicated the strong pathogenicity of Fusarium oxysporum R1. Based on the results obtained, the putative molecular mechanism of the saffron-Fox R1 interaction was identified. As saffron is a male sterile plant, and can only be improved by genetic manipulation, this work will serve as a foundation for identifying genes that can be used to create saffron varieties, resistant to Fusarium oxysporum infection.

Analysis on morphological characteristics and identification of candidate genes during the flowering development of alfalfa.

Flower development is a crucial and complex process in the reproductive stage of plants, which involves the interaction of multiple endogenous signals and environmental factors. However, regulatory mechanism of flower development was unknown in alfalfa (Medicago sativa). In this study, the three stages of flower development of 'M. sativa cv. Gannong No. 5' (G5) and its early flowering and multi flowering mutant (MG5) were comparatively analyzed by transcriptomics. The results showed that compared with late bud stage (S1), 14287 and 8351 differentially expressed genes (DEGs) were identified at early flower stage (S2) in G5 and MG5, and 19941 and 19469 DEGs were identified at late flower stage (S3). Compared with S2, 9574 and 10870 DEGs were identified at S3 in G5 and MG5, respectively. Venn analysis revealed that 547 DEGs were identified among the three comparison groups. KEGG pathway enrichment analysis showed that these genes were involved in the development of alfalfa flowers through redox pathways and plant hormone signaling pathways. Key candidate genes including SnRK2, BSK, GID1, DELLA and CRE1, for regulating the development from buds to mature flowers in alfalfa were screened. In addition, differential expression of transcription factors such as MYB, AP2, bHLH, C2C2, MADS-box, NAC, bZIP, B3 and AUX/IAA also played an important role in this process. The results laid a theoretical foundation for studying the molecular mechanisms of the development process from buds to mature flowers in alfalfa.

Functional identification of Medicago truncatulaMtRAV1 in regulating growth and development1

Related to ABI3 and VP1 (RAV) transcription factors belong to the AP2 and B3 superfamily. RAVs genes have been reported to be involved in plant growth and development regulation. This study screened three RAV genes from Medicago truncatula and named one of them MtRAV1. The MtRAV1 overexpressing plants exhibits traits such as plant dwarfing, delayed flowering, reduced leaf and floral organs, increased branching, and reduced pods and seeds. Gene expression analysis results showed that overexpression of MtRAV1 inhibited the expression of Flowering Locus T (MtFTa1), Suppressor of Overexpression of CO 1 (MtSOC1), GA3-oxidase1 (MtGA3OX1), DWARF14 (MtD14) and Carotenoid Cleavage Dioxygenase 7 (MtCCD7). To further investigate the regulation pathway involved by MtRAV1, RNA-sequencing (RNA-seq) and DNA affinity purification sequencing (DAP-seq) analysis were conducted. RNA-seq results indicated that MtRAV1 might affect plant growth and development by regulating some genes in photosynthesis, circadian rhythm and plant hormone signaling pathways, especially the auxin signaling pathway. Conjoint analysis of DAP-seq and RNA-seq revealed that MtRAV1 might inhibit the expression of Ferredoxin (MtFd-l3), Light-harvesting Chlorophyll a/b Binding Protein 1 (MtLhcb-l2) and Small Auxin Up-regulated RNA (MtSAUR-l), which related to photosystem II and auxin signaling pathway. Summarily, MtRAV1 was preliminarily proven to be a key growth inhibitory factor in M. truncatula.

Plant microRNAs regulate the defense response against pathogens.

MicroRNAs (miRNAs) are a class of small non-coding RNAs, typically 20-25 nucleotides in length, that play a crucial role in regulating gene expression post-transcriptionally. They are involved in various biological processes such as plant growth, development, stress response, and hormone signaling pathways. Plants interact with microbes through multiple mechanisms, including mutually beneficial symbiotic relationships and complex defense strategies against pathogen invasions. These defense strategies encompass physical barriers, biochemical defenses, signal recognition and transduction, as well as systemic acquired resistance. MiRNAs play a central role in regulating the plant's innate immune response, activating or suppressing the transcription of specific genes that are directly involved in the plant's defense mechanisms against pathogens. Notably, miRNAs respond to pathogen attacks by modulating the balance of plant hormones such as salicylic acid, jasmonic acid, and ethylene, which are key in activating plant defense mechanisms. Moreover, miRNAs can cross boundaries into fungal and bacterial cells, performing cross-kingdom RNA silencing that enhances the plant's disease resistance. Despite the complex and diverse roles of miRNAs in plant defense, further research into their function in plant-pathogen interactions is essential. This review summarizes the critical role of miRNAs in plant defense against pathogens, which is crucial for elucidating how miRNAs control plant defense mechanisms.

Transcriptome Analysis Reveals the Response of Cryptomeria japonica to Feeding Stress of Dendrolimus houi Lajonquière Larvae

The Japanese fir, Cryptomeria japonica, is ecologically and commercially vital in China. However, infestations by Dendrolimus houi Lajonquière larvae cause widespread dieback, mimicking mechanical damage effects, with unclear differential impacts and mechanisms. To address this, 6th instar larvae of D. houi were introduced to three-year-old C. japonica seedlings to induce pest infestation, while mechanical damage and non-infested pests were controlled. Then, next-generation sequencing techniques were employed, and transcriptome sequencing was conducted to analyze the distinct damage mechanisms responding to C. japonica. This study revealed 10,412 DEGs between pest infestation and controls and 5535 DEGs comparing pest infestation to mechanical damage. Functional enrichment analysis highlighted the involvement of these DEGs in crucial processes such as photosynthesis, amino acid and nucleotide metabolism, flavonoid biosynthesis, and plant hormone signaling pathways. In particular, 786 unique DEGs were discerned in pest-infested samples. Key enriched pathways, such as pyruvate and propionate metabolism, were pinpointed, with flavonoid biosynthesis potentially closely linked to pest-feeding inductions. These findings provided valuable insights into the molecular responses of C. japonica to D. houi infestation, laying the foundation for future research aimed at developing pest-resistant varieties of Japanese fir.

Transcriptome profiling of Bergenia purpurascens under cold stress

Bergenia purpurascens is an important medicinal, edible and ornamental plant. It generally grows in high-altitude areas with complex climates. There have been no reports about how B. purpurascens survives under cold stress. Here, the B. purpurascens under low temperature were subjected to transcriptomics analysis to explore the candidate genes and pathways that involved in the cold tolerance of B. purpurascens. Compared with the control treatment, we found 9,600 up-regulated differentially expressed genes (DEGs) and 7,055 down-regulated DEGs. A significant number of DEGs were involved in the Ca2+ signaling pathway, mitogen-activated protein kinase (MAPK) cascade, plant hormone signaling pathway, and lipid metabolism. A total of 400 transcription factors were found to respond to cold stress, most of which belonged to the MYB and AP2/ERF families. Five novel genes were found to be potential candidate genes involved in the cold tolerance of B. purpurascens. The study provide insights into further investigation of the molecular mechanism of how B. purpurascens survives under cold stress.

Transcriptomic analysis reveals the role of abscisic acid and ethylene in regulating starch-source biosynthesis associated with soft nose disorder in ‘Keitt’ mango fruit during postharvest

Soft nose is a physiological disorder in the distal flesh of mango fruit during ripening, which results in the decline in its consumer acceptance and salability. In this study, transcriptomic methods were used to compare mesocarp tissue from soft nose and healthy ‘Keitt’ mango fruit at different ripeness stages to identify the genes that are affected by soft nose disorder. The analysis revealed that the occurrence of soft nose affected plant hormone signaling pathways, particularly for abscisic acid (ABA) and ethylene. Also, accelerated starch decomposition and sucrose accumulation were found to be involved in development of soft nose disorder in mango fruit. Thus, soft nose fruit had lower contents of ABA and starch, and higher contents of sucrose, fructose, glucose and β-carotene compared to the healthy fruit. Also, we constructed a network of potential transcription factors and genes related to ABA and starch-sucrose metabolism that might be associated with soft nose disorder, and suggested that ABA might interact with ethylene to collectively regulate changes in downstream metabolic networks, thereby promoting development of soft nose disorder in ‘Keitt’ mango fruit during postharvest.

Red and Blue Light Induce Soybean Resistance to Soybean Mosaic Virus Infection through the Coordination of Salicylic Acid and Jasmonic Acid Defense Pathways.

Soybean mosaic virus (SMV) seriously harms soybean quality and yield. In order to understand the effect of a heterogeneous light environment on the disease resistance of intercropped soybeans, we simulated three kinds of light environments to learn the effects of white light, blue light, and far-red light on the SMV resistance of soybeans. The results showed that compared with the control, SMV-infected soybeans showed dwarfing and enhanced defense. The symptoms of leaves under red and blue light were less severe than those under white light, the virus content of infected plants was about 90% lower than under white light, the activity of antioxidant enzymes increased, and the accumulation of reactive oxygen species decreased. The oxidation damage in SMV-infected soybeans was serious under far-red light. Transcriptome data showed that the biostimulatory response, plant-pathogen interaction, and plant hormone signaling pathway gene expression of SMV-infected soybeans were significantly up-regulated under red light compared with the control. Compared with the control, the genes in the biostimulatory response, calcium ion binding, carbohydrate-binding, mitogen-activated protein kinase (MAPK) signaling, and plant-pathogen interaction pathways, were significantly up-regulated in SMV-infected soybeans under blue light. In far-red light, only 39 genes were differentially expressed in SMV-infected soybeans compared with the control, and most of the genes were down-regulated. Compared with the control, the up-regulation of the salicylic acid (SA) pathway defense gene in SMV-infected soybeans under red light was higher than under other light treatments. Compared with the control, the up-regulation of the jasmonic acid (JA) and ethylene (ET) pathway defense genes in SMV-infected soybeans under blue light was higher than under other light treatments. Compared with the control, most defense-related genes in the SA and JA pathways were inhibited in SMV-infected soybeans under far-red light, while genes in the ET pathway were significantly up-regulated. These results will advance our understanding of the disease resistance mechanism of intercropping soybeans in a heterogeneous light environment and provide new ideas for the prevention and control of viral diseases.

Biocontrol fungi induced stem-base rot disease resistance of Morinda officinalis How revealed by transcriptome analysis.

Morinda officinalis How (MO) is a Rubiaceae plant, and its medicinal part is dried root, which is one of the "Four Southern Medicines" in China. At present, the plant MO breed seedlings mainly by cutting methods. Long-term asexual propagation makes pathogenic fungi accumulate in MO, leading to stem-base rot, which is caused by Fusarium oxysporum (Fon). In this study, we used Trichoderma harzianum and Pestalotiopsis sp. as biocontrol fungi to investigate their antagonistic ability to Fon through in vitro antagonism and pot experiments, and combined with transcriptome sequencing to explore the mechanism of biocontrol. The results showed that both Trichoderma harzianum and Pestalotiopsis sp. could inhibit the growth of Fon. In addition, Trichoderma harzianum and Pestalotiopsis sp. could also enhance the basic immunity to Fon by increasing the activities of defensive enzymes such as POD and SOD, chlorophyll content, soluble sugar content, and oligosaccharide content of MO. The mechanism of biological control of stem-base rot of MO was discussed by transcriptome technology. MO was treated with two treatments, root irrigation with biocontrol fungi or inoculation with Fon after root irrigation with biocontrol fungi. Transcriptome sequencing revealed that nearly 11,188 differentially expressed genes (DEGs) were involved in the process of inducing MO systemic resistance to Fon by biocontrol fungi. Meanwhile, Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, as well as transcription factor (TFs) prediction showed that there were significant differences in the expression levels of MO roots under different treatments. Also, the genes of the "MAPK signaling pathway" and "plant hormone signaling pathway" were analyzed, in which the ERFs gene of the ethylene signal transduction pathway participated in the metabolism of glycosyl compounds. It is speculated that the ethylene signal may participate in the immune response of the sugar signal to the infection of Fon. After qRT-PCR verification of 10 DEGs related to the ethylene signal transduction pathway, the expression trend is consistent with the results of transcriptome sequencing, which proves the reliability of transcriptome sequencing. In conclusion, this study preliminarily identified the molecular mechanism of the biological control of MO stem-base rot and provided a scientific basis for further research on the prevention and control mechanism of MO stem-base rot.

Transcriptome Analysis of Native Kentucky Bluegrass (Poa pratensis L.) in Response to Osmotic Stress

Kentucky bluegrass (Poa pratensis L.) is an important cool season turfgrass species with a high cold tolerance, but it is sensitive to drought. It is valuable for the applications of Kentucky bluegrass to improve its drought tolerance. However, little is known about the underlying drought mechanism. In the present study, transcriptomic profiling in the roots and leaves of the Kentucky bluegrass cultivar ‘Qinghai’, in response to osmotic stress in the form of treatment with 2 h and 50 h of 25% (v/v) PEG-6000, was analyzed. The results showed that a large number of genes were significantly up-regulated or down-regulated under osmotic stress. The majority of genes were up-regulated in leaves but down-regulated in roots after 2 h and 50 h of osmotic stress, among them were 350 up-regulated DEGs and 20 down-regulated DEGs shared in both leaves and roots. GO and KEGG analysis showed that carbohydrate metabolism, polyamine and amino acid metabolism and the plant hormone signaling pathway were enriched in the leaves and roots of ‘Qinghai’ after osmotic stress. The genes involving in carbohydrate metabolism were up-regulated, and sucrose, trehalose and raffinose levels were consistently increased. The genes involved in polyamine and amino acid metabolism were up-regulated in leaves in response to osmotic stress and several amino acids, such as Glu, Met and Val levels were increased, while the genes involved in photosynthesis, carbon fixation and citrate cycle in leaves were down-regulated. In addition, the genes involved in plant hormone biosynthesis and signal transduction were altered in leaves after osmotic stress. This study provided promising candidate genes for studying drought mechanisms in ‘Qinghai’ and improving the drought tolerance of Kentucky bluegrass and drought-sensitive crops.

Transcription Factor and Zeatin Co-Regulate Mixed Catkin Differentiation of Chinese Chestnut (Castanea mollissima)

Castanea mollissima is an important monoecious fruit crop with high economic and ecological value in China. However, its yield is restricted by an imbalanced ratio of male and female flowers for chestnut production. To address this issue, we examined the morphology of bisexual flower organs, measured the levels of endogenous hormones in the flowers, profiled gene expression related to plant hormone biosynthesis and signaling pathways and transcription factors, and investigated the effects of exogenous jasmonic acid (JA) and zeatin (ZT) hormone application on flower development in C. mollissima ‘Tanqiao’. Morphological studies indicated that the development of male and female flowers can be divided into nine and eight stages, respectively. Male flowers contained higher levels of gibberellic acid (GA3) and abscisic acid (ABA) than female flowers, whereas female flowers had higher levels of JA and ZT. The analysis of the Kyoto encyclopedia of genes and genomes (KEGG) pathways revealed that the major significant enrichment pathways of differentially expressed genes (DEGs) consisted of plant hormone signal transduction and zeatin biosynthesis. Through time-series analyses, we screened 3 genes related to jasmonic acid biosynthesis and signal transduction and 21 genes related to zeatin biosynthesis and transduction. Among these genes, only the gene family LOG, related to zeatin biosynthesis, was highly expressed in female flowers. This result indicated that LOG may be the core gene hormone family involved in regulating female flower development. However, a weighted gene co-expression network analysis (WGCNA) suggested that IDD7 was the core gene involved in regulating female flower development. The results of exogenous hormone application indicated that zeatin could greatly increase the quantity of fertile female flowers, but JA was not significant. These findings demonstrated that zeatin and transcription factors were crucial regulators in the formation of female flowers in C. mollissima.

Physiological and transcriptomic analysis of the mangrove species Kandelia obovata in response to flooding stress

Flooding stress on mangroves is growing continually with rising sea level. In this study, the physiology and transcriptome of the mangrove species Kandelia obovata under flooding stress were analyzed. With increasing inundation time, malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), soluble sugar (SS), soluble protein (SP), and proline (Pro) content declined, while peroxidase (POD) and ascorbate peroxidase (APX) activity rose significantly. According to the KEGG pathway enrichment analysis, upregulated differentially expressed genes (DEGs) were enriched in the plant hormone signaling pathway. Furthermore, MYB44 and MYB108 genes from the MYB transcription factor family and RAP2.12, DREB2B, and ERF4 genes from the AP2/ERF family were up-regulated under flooding conditions. A strong correlation was established between the expression levels of 12 DEGs under flooding stress and RNA sequencing data and was verified by qRT-PCR. These results provide new insights into the molecular mechanism of K. obovata in response to flooding stress.

Transcriptomics combined with physiological analysis reveals the mechanism of cadmium uptake and tolerance in Ligusticum chuanxiong Hort. under cadmium treatment.

Ligusticum chuanxiong Hort. is a widely used medicinal plant, but its growth and quality can be negatively affected by contamination with the heavy metal cadmium (Cd). Despite the importance of understanding how L. chuanxiong responds to Cd stress, but little is currently known about the underlying mechanisms. To address this gap, we conducted physiological and transcriptomic analyses on L. chuanxiong plants treated with different concentrations of Cd2+ (0 mg·L-1, 5 mg·L-1, 10 mg·L-1, 20 mg·L-1, and 40 mg·L-1). Our findings revealed that Cd stress inhibited biomass accumulation and root development while activating the antioxidant system in L. chuanxiong. Root tissues were the primary accumulation site for Cd in this plant species, with Cd being predominantly distributed in the soluble fraction and cell wall. Transcriptomic analysis demonstrated the downregulation of differential genes involved in photosynthetic pathways under Cd stress. Conversely, the plant hormone signaling pathway and the antioxidant system exhibited positive responses to Cd regulation. Additionally, the expression of differential genes related to cell wall modification was upregulated, indicating potential enhancements in the root cell wall's ability to sequester Cd. Several differential genes associated with metal transport proteins were also affected by Cd stress, with ATPases, MSR2, and HAM3 playing significant roles in Cd passage from the apoplast to the cell membrane. Furthermore, ABC transport proteins were found to be key players in the intravesicular compartmentalization and efflux of Cd. In conclusion, our study provides preliminary insights into the mechanisms underlying Cd accumulation and tolerance in L. chuanxiong, leveraging both physiological and transcriptomic approaches. The decrease in photosynthetic capacity and the regulation of plant hormone levels appear to be major factors contributing to growth inhibition in response to Cd stress. Moreover, the upregulation of differential genes involved in cell wall modification suggests a potential mechanism for enhancing root cell wall capabilities in isolating and sequestering Cd. The involvement of specific metal transport proteins further highlights their importance in Cd movement within the plant.

Transcriptomic and Metabolomic Analyses Reveal the Key Genes Related to Shade Tolerance in Soybean.

Soybean (Glycine max) is an important crop, rich in proteins, vegetable oils and several other phytochemicals, which is often affected by light during growth. However, the specific regulatory mechanisms of leaf development under shade conditions have yet to be understood. In this study, the transcriptome and metabolome sequencing of leaves from the shade-tolerant soybean 'Nanxiadou 25' under natural light (ND1) and 50% shade rate (SHND1) were carried out, respectively. A total of 265 differentially expressed genes (DEGs) were identified, including 144 down-regulated and 121 up-regulated genes. Meanwhile, KEGG enrichment analysis of DEGs was performed and 22 DEGs were significantly enriched in the top five pathways, including histidine metabolism, riboflavin metabolism, vitamin B6 metabolism, glycerolipid metabolism and cutin, suberine and wax biosynthesis. Among all the enrichment pathways, the most DEGs were enriched in plant hormone signaling pathways with 19 DEGs being enriched. Transcription factors were screened out and 34 differentially expressed TFs (DETFs) were identified. Weighted gene co-expression network analysis (WGCNA) was performed and identified 10 core hub genes. Combined analysis of transcriptome and metabolome screened out 36 DEGs, and 12 potential candidate genes were screened out and validated by quantitative real-time polymerase chain reaction (qRT-PCR) assay, which may be related to the mechanism of shade tolerance in soybean, such as ATP phosphoribosyl transferase (ATP-PRT2), phosphocholine phosphatase (PEPC), AUXIN-RESPONSIVE PROTEIN (IAA17), PURPLE ACID PHOSPHATASE (PAP), etc. Our results provide new knowledge for the identification and function of candidate genes regulating soybean shade tolerance and provide valuable resources for the genetic dissection of soybean shade tolerance molecular breeding.

Analysis of the response mechanisms of Pinellia ternata to terahertz wave stresses using transcriptome and metabolic data.

Pinellia ternata (Thunb.) Breit. (Araceae), a significant medicinal plant, has been used to treat various diseases for centuries. Terahertz radiation (THZ) is located between microwaves and infrared rays on the electromagnetic spectrum. THZ possesses low single-photon energy and a spectral fingerprint, but its effects on plant growth have not yet been investigated. The study's primary objective was to examine the transcriptome and metabolome databases of the SY line to provide a new perspective for identifying genes associated with resistance and growth promotion and comprehending the underlying molecular mechanism. Variations in the biological characteristics of P. ternata grown under control and experimental conditions were analyzed to determine the effect of THZ. Compared with the control group, phenotypic variables such as leaf length, petiole length, number of leaves, leaf petiole diameter, and proliferation coefficient exhibited significant differences. P. ternata response to THZ was analyzed regarding the effects of various coercions on root exudation. The experimental group contained considerably more sugar alcohol than the control group. The transcriptome analysis revealed 1,695 differentially expressed genes (DEGs), including 509 upregulated and 1,186 downregulated genes. In the KEGG-enriched plant hormone signaling pathway, there were 19 differentially expressed genes, 13 of which were downregulated and six of which were upregulated. In the metabolomic analysis, approximately 416 metabolites were uncovered. There were 112 DEMs that were downregulated, whereas 148 were upregulated. The P. ternata leaves displayed significant differences in phytohormone metabolites, specifically in brassinolide (BR) and abscisic acid (ABA). The rise in BR triggers alterations in internal plant hormones, resulting in faster growth and development of P. ternata. Our findings demonstrated a link between THZ and several metabolic pathway processes, which will enhance our understanding of P. ternata mechanisms.