Phytohormone Signaling Pathways Research Articles

Transcriptome analysis suggested that lncRNAs regulate rapeseed seedlings in responding to drought stress by coordinating the phytohormone signal transduction pathways

The growth, yield, and seed quality of rapeseed are negatively affected by drought stress. Therefore, it is of great value to understand the molecular mechanism behind this phenomenon. In a previous study, long non-coding RNAs (lncRNAs) were found to play a key role in the response of rapeseed seedlings to drought stress. However, many questions remained unanswered. This study was the first to investigate the expression profile of lncRNAs not only under control and drought treatment, but also under the rehydration treatment. A total of 381 differentially expressed lncRNA and 10,253 differentially expressed mRNAs were identified in the comparison between drought stress and control condition. In the transition from drought stress to rehydration, 477 differentially expressed lncRNAs and 12,543 differentially expressed mRNAs were detected. After identifying the differentially expressed (DE) lncRNAs, the comprehensive lncRNAs-engaged network with the co-expressed mRNAs in leaves under control, drought and rehydration was investigated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of co-expressed mRNAs identified the most significant pathways related with plant hormones (expecially abscisic acid, auxin, cytokinins, and gibberellins) in the signal transduction. The genes, co-expressed with the most-enriched DE-lncRNAs, were considered as the most effective candidates in the water-loss and water-recovery processes, including protein phosphatase 2 C (PP2C), ABRE-binding factors (ABFs), and SMALL AUXIN UP-REGULATED RNAs (SAURs). In summary, these analyses clearly demonstrated that DE-lncRNAs can act as a regulatory hub in plant-water interaction by controlling phytohormone signaling pathways and provided an alternative way to explore the complex mechanisms of drought tolerance in rapeseed.

Comprehensive genomic screening and expression profiling of trihelix family in pearl millet under abiotic stresses with emphasis on functional insights of PgTHX24

The trihelix transcription factors (THX TFs) play a crucial role in light responses and are involved in plant growth, development, and stress responses. In this study, we have identified 35 trihelix TFs in pearl millet (Pennisetum glaucum), which is one of the most widely grown C4 cereal crops in tropical semi-arid regions. Identified PgTHXs (Trihelix members of P. glaucum) were classified into 5 subgroups (GT1, GT2, GTγ, SH4, and SIP1) based on phylogenetic analysis, and these subgroup members shared similar gene structure and motif distribution pattern. Collinearity analysis exhibited gene duplication events of trihelix family members in pearl millet across the genome. Gene ontology (GO) annotation and cis-regulatory elements (CREs) analysis of PgTHXs suggested their involvement in diverse biological and molecular functions associated with plant growth, development, and stress responses. RNA sequencing data and expression profile displayed differential expression patterns of PgTHXs under abiotic stress and phytohormone treatments. The induced expression pattern of the PgTHX4, PgTHX5, PgTHX24, and PgTHX30 suggested their potential involvement in abiotic stress responses through phytohormonal signalling pathways. Among these, PgTHX24, a GT-3b member, was localized in the nucleus with self-transactivation ability. Overexpression of PgTHX24 positively regulated expression of stress-related markers in transformed pearl millet calli under drought stress conditions. Promoter activity analysis also highlighted the stress-inducible nature of PgTHX24’s promoter. Overall, our findings provide a comprehensive understanding of PgTHXs with a framework for further functional characterization to understand their regulatory role in pearl millet’s growth, development, and stress responses. Key messageThirty-five trihelix TFs were identified in pearl millet, and a comprehensive expression profile highlighted their functional diversity. Overexpression of PgTHX24 exhibited its potential involvement in abiotic stress responses.

Selenite improves growth by modulating phytohormone pathways and reprogramming primary and secondary metabolism in tomato plants

Selenium (Se) is an essential micronutrient in organisms that has a significant impact on physiological activity and gene expression in plants, thereby affecting growth and development. Humans and animals acquire Se from plants. Tomato (Solanum lycopersicum L.) is an important vegetable crop worldwide. Improving the Se nutrient level not only is beneficial for growth, development and stress resistance in tomato plants but also contributes to improving human health. However, the molecular basis of Se-mediated tomato plant growth has not been fully elucidated. In this study, using physiological and transcriptomic analyses, we investigated the effects of a low dosage of selenite [Se(Ⅳ)] on tomato seedling growth. Se(IV) enhanced the photosynthetic efficiency and increased the accumulation of soluble sugars, dry matter and organic matter, thereby promoting tomato plant growth. Transcriptome analysis revealed that Se(IV) reprogrammed primary and secondary metabolic pathways, thus modulating plant growth. Se(IV) also increased the concentrations of auxin, jasmonic acid and salicylic acid in leaves and the concentration of cytokinin in roots, thus altering phytohormone signaling pathways and affecting plant growth and stress resistance in tomato plants. Furthermore, exogenous Se(IV) alters the expression of genes involved in flavonoid biosynthesis, thereby modulating plant growth and development in tomato plants. Taken together, these findings provide important insights into the regulatory mechanisms of low-dose Se(IV) on tomato growth and contribute to the breeding of Se-accumulating tomato cultivars.

WRKY Transcription Factor Responses and Tolerance to Abiotic Stresses in Plants.

Plants are subjected to abiotic stresses throughout their developmental period. Abiotic stresses include drought, salt, heat, cold, heavy metals, nutritional elements, and oxidative stresses. Improving plant responses to various environmental stresses is critical for plant survival and perpetuation. WRKY transcription factors have special structures (WRKY structural domains), which enable the WRKY transcription factors to have different transcriptional regulatory functions. WRKY transcription factors can not only regulate abiotic stress responses and plant growth and development by regulating phytohormone signalling pathways but also promote or suppress the expression of downstream genes by binding to the W-box [TGACCA/TGACCT] in the promoters of their target genes. In addition, WRKY transcription factors not only interact with other families of transcription factors to regulate plant defence responses to abiotic stresses but also self-regulate by recognising and binding to W-boxes in their own target genes to regulate their defence responses to abiotic stresses. However, in recent years, research reviews on the regulatory roles of WRKY transcription factors in higher plants have been scarce and shallow. In this review, we focus on the structure and classification of WRKY transcription factors, as well as the identification of their downstream target genes and molecular mechanisms involved in the response to abiotic stresses, which can improve the tolerance ability of plants under abiotic stress, and we also look forward to their future research directions, with a view of providing theoretical support for the genetic improvement of crop abiotic stress tolerance.

Transcriptome Analysis of Seed in Dormancy and Dormancy Release State of Epimedium koreanum Nakai

Epimedium koreanum is a perennial herb of the Berberidaceae family, which is a traditional tonic in Chinese medicine. Seed germination of E. koreanum is difficult. Dormancy is an intrinsic factor that affects seed germination. Elucidating the molecular mechanism of seed dormancy and the lifting process of E. koreanum is of great significance for the breeding, conservation, and utilization of E. koreanum. Previous studies have concluded that E. koreanum seed dormancy breakage requires warm-temperature stratification followed by low-temperature stratification treatments. Therefore, we performed transcriptome sequencing using freshly harvested, untreated seeds (NS), seeds that developed a cotyledonary embryo after 90 d of constant-temperature stratification at 15 °C (CS), and seeds that broke dormancy by 90 d of stratification at 15 °C and 60 d of stratification at 5 °C (ND) in order to find the responsive genes and regulatory genes that regulate dormancy. A total of 92,867 genes with differential expression were identified. GO enrichment analysis highlighted redox processes, as well as structural components of the nucleus and ribosomes. KEGG enrichment analysis revealed a significant enrichment of phytohormone signaling pathways, which play a crucial role in seed dormancy release. Additionally, protein–protein interactions (PPIs) were predicted with starch and sucrose metabolic pathways. This study introduces a novel concept for a more profound comprehension of the molecular regulatory mechanism of E. koreanum and lays a theoretical foundation for the screening of E. koreanum candidate genes.

Physiological response and molecular mechanism of Quercus variabilis under cadmium stress

Heavy metal pollution is a global environmental problem, and Quercus variabilis has a stronger tolerance to Cd stress than do other species. We aimed to explore the physiological response and molecular mechanisms of Q. variabilis to Cd stress. In this study, the antioxidant enzyme activities of leaves were determined, while the photosynthetic parameters of leaves were measured using Handy PEA, and ion fluxes and DEGs in the roots were investigated using noninvasive microtest technology (NMT) and RNA sequencing techniques, respectively. Cd stress at different concentrations and for different durations affected the uptake patterns of Cd2+ and H+ by Q. variabilis and affected the photosynthetic efficiency of leaves. Moreover, there was a positive relationship between antioxidant enzyme (CAT and POD) activity and Cd concentration. Transcriptome analysis revealed that many genes, including genes related to the cell wall, glutathione metabolism, ion uptake and transport, were significantly upregulated in response to cadmium stress in Q. variabilis roots. WGCNA showed that these DEGs could be divided into eight modules. The turquoise and blue modules exhibited the strongest correlations, and the most significantly enriched pathways were the phytohormone signaling pathway and the phenylpropanoid biosynthesis pathway, respectively. These findings suggest that Q. variabilis can bolster plant tolerance by modulating signal transduction and increasing the synthesis of compounds, such as lignin, under Cd stress. In summary, Q. variabilis can adapt to Cd stress by increasing the activity of antioxidant enzymes, and regulating the fluxes of Cd2+ and H+ ions and the expression of Cd stress-related genes.

Phytohormone profiling in an evolutionary framework

The genomes of charophyte green algae, close relatives of land plants, typically do not show signs of developmental regulation by phytohormones. However, scattered reports of endogenous phytohormone production in these organisms exist. We performed a comprehensive analysis of multiple phytohormones in Viridiplantae, focusing mainly on charophytes. We show that auxin, salicylic acid, ethylene and tRNA-derived cytokinins including cis-zeatin are found ubiquitously in Viridiplantae. By contrast, land plants but not green algae contain the trans-zeatin type cytokinins as well as auxin and cytokinin conjugates. Charophytes occasionally produce jasmonates and abscisic acid, whereas the latter is detected consistently in land plants. Several phytohormones are excreted into the culture medium, including auxin by charophytes and cytokinins and salicylic acid by Viridiplantae in general. We note that the conservation of phytohormone biosynthesis and signaling pathways known from angiosperms does not match the capacity for phytohormone biosynthesis in Viridiplantae. Our phylogenetically guided analysis of established algal cultures provides an important insight into phytohormone biosynthesis and metabolism across Streptophyta.

Cytological, Phytohormone, and Transcriptome Analyses Provide Insights into Persimmon Fruit Shape Formation (Diospyros kaki Thunb.).

Fruit shape is an important external feature when consumers choose their preferred fruit varieties. Studying persimmon (Diospyros kaki Thunb.) fruit shape is beneficial to increasing its commodity value. However, research on persimmon fruit shape is still in the initial stage. In this study, the mechanism of fruit shape formation was studied by cytological observations, phytohormone assays, and transcriptome analysis using the long fruit and flat fruit produced by 'Yaoxianwuhua' hermaphroditic flowers. The results showed that stage 2-3 (June 11-June 25) was the critical period for persimmon fruit shape formation. Persimmon fruit shape is determined by cell number in the transverse direction and cell length in the longitudinal direction. High IAA, GA4, ZT, and BR levels may promote long fruit formation by promoting cell elongation in the longitudinal direction, and high GA3 and ABA levels may be more conducive to flat fruit formation by increasing the cell number in the transverse direction and inhibiting cell elongation in the longitudinal direction, respectively. Thirty-two DEGs related to phytohormone biosynthesis and signaling pathways and nine DEGs related to cell division and cell expansion may be involved in the persimmon fruit shape formation process. These results provide valuable information for regulatory mechanism research on persimmon fruit formation.

Recent advances in research on phosphate starvation signaling in plants

Phosphorus is indispensable for plant growth and development, with its status crucial for determining crop productivity. Plants have evolved various biochemical, morphological, and developmental responses to thrive under conditions of low P availability, as inorganic phosphate (Pi), the primary form of P uptake, is often insoluble in soils. Over the past 25 years, extensive research has focused on understanding these responses, collectively forming the Pi starvation response system. This effort has not only expanded our knowledge of strategies to cope with Pi starvation (PS) but also confirmed their adaptive significance. Moreover, it has identified and characterized numerous components of the intricate regulatory network governing P homeostasis. This review emphasizes recent advances in PS signaling, particularly highlighting the physiological importance of local PS signaling in inhibiting primary root growth and uncovering the role of TORC1 signaling in this process. Additionally, advancements in understanding shoot-root Pi allocation and a novel technique for studying Pi distribution in plants are discussed. Furthermore, emerging data on the regulation of plant-microorganism interactions by the PS regulatory system, crosstalk between the signaling pathways of phosphate starvation, phytohormones and immunity, and recent studies on natural variation in Pi homeostasis are addressed.

Identification and expression profile analysis of rice CRF gene family

Cytokinin response factors (CRFs), as unique transcription factors in plants, play crucial roles in regulating development, phytohormone signaling pathway, and stress responses. In this study, we identified nine CRF genes from the rice genome by conducting a BLAST analysis using the protein sequences of twelve Arabidopsis AtCRFs. These genes are located on seven different rice chromosomes. We conducted a comprehensive analysis of the conserved domains, physicochemical properties, secondary structures, and phylogenetic relationships of rice CRF proteins using various online tools and local software. Additionally, we analyzed the exon-intron structures and cis-acting elements of OsCRFs, and found an abundance of elements relevant to phytohormone response and stress response on the promoters of rice CRF genes. Spatial-temporal expression pattern analysis revealed that four of the OsCRFs were barely expressed in all tested samples, while the other five were highly expressed in the leaf, panicle, or seed of rice. Microarray data showed that OsCRF genes are regulated to varying degrees by abscisic acid, auxin, cytokinin, and jasmonic acid. Furthermore, through analyzing the RNA-seq data, we found that OsCRFs are primarily involved in plant response to temperature stress (chilling and heat), with several OsCRFs also implicated in drought response, while hardly any respond to salt stress. This study provides an important basis for the functional characterization of rice CRF family genes.

Integrating multi-omics data reveals energy and stress signaling activated by abscisic acid in Arabidopsis.

Phytohormones are essential signaling molecules regulating various processes in growth, development, and stress responses. Genetic and molecular studies, especially using Arabidopsis thaliana (Arabidopsis), have discovered many important players involved in hormone perception, signal transduction, transport, and metabolism. Phytohormone signaling pathways are extensively interconnected with other endogenous and environmental stimuli. However, our knowledge of the huge and complex molecular network governed by a hormone remains limited. Here we report a global overview of downstream events of an abscisic acid (ABA) receptor, REGULATORY COMPONENTS OF ABA RECEPTOR (RCAR) 6 (also known as PYRABACTIN RESISTANCE 1 [PYR1]-LIKE [PYL] 12), by integrating phosphoproteomic, proteomic and metabolite profiles. Our data suggest that the RCAR6 overexpression constitutively decreases the protein levels of its coreceptors, namely clade A protein phosphatases of type 2C, and activates sucrose non-fermenting-1 (SNF1)-related protein kinase 1 (SnRK1) and SnRK2, the central regulators of energy and ABA signaling pathways. Furthermore, several enzymes in sugar metabolism were differentially phosphorylated and expressed in the RCAR6 line, and the metabolite profile revealed altered accumulations of several organic acids and amino acids. These results indicate that energy- and water-saving mechanisms mediated by the SnRK1 and SnRK2 kinases, respectively, are under the control of the ABA receptor-coreceptor complexes.

Sulfate Availability and Hormonal Signaling in the Coordination of Plant Growth and Development.

Sulfur (S), one of the crucial macronutrients, plays a pivotal role in fundamental plant processes and the regulation of diverse metabolic pathways. Additionally, it has a major function in plant protection against adverse conditions by enhancing tolerance, often interacting with other molecules to counteract stresses. Despite its significance, a thorough comprehension of how plants regulate S nutrition and particularly the involvement of phytohormones in this process remains elusive. Phytohormone signaling pathways crosstalk to modulate growth and developmental programs in a multifactorial manner. Additionally, S availability regulates the growth and development of plants through molecular mechanisms intertwined with phytohormone signaling pathways. Conversely, many phytohormones influence or alter S metabolism within interconnected pathways. S metabolism is closely associated with phytohormones such as abscisic acid (ABA), auxin (AUX), brassinosteroids (BR), cytokinins (CK), ethylene (ET), gibberellic acid (GA), jasmonic acid (JA), salicylic acid (SA), and strigolactones (SL). This review provides a summary of the research concerning the impact of phytohormones on S metabolism and, conversely, how S availability affects hormonal signaling. Although numerous molecular details are yet to be fully understood, several core signaling components have been identified at the crossroads of S and major phytohormonal pathways.

Interspecific grafting promotes poplar growth and drought resistance via regulating phytohormone signaling and secondary metabolic pathways

Populus cathayana (C) grafted onto P. deltoides (D) (C/D) can promote growth better than self-grafting (C/C and D/D). However, the mechanisms underlying growth and resistance to drought stress are not clear. In this study, we performed physiological and RNA-seq analysis on the different grafted combinations. It was found that C/D plants exhibited higher growth, net photosynthetic rate, IAA content and intrinsic water use efficiency (WUEi) than C/C and D/D plants under both well-watered and drought-stressed conditions. However, most growth, photosynthetic indices, and IAA content were decreased less in C/D, whereas ABA content, WUEi and root characteristics (e.g., root length, volume, surface area and vitality) were increased more in C/D than in other grafting combinations under drought-stressed conditions. Transcriptomic analysis revealed that the number of differentially expressed genes (DEGs) in leaves of C/D vs C/C (control, 181; drought, 121) was much lower than that in the roots of C/D vs D/D (control, 1639; drought, 1706), indicating that the rootstocks were more responsive to drought resistance. KEGG and GO functional enrichment analysis showed that the enhanced growth and drought resistance of C/D were mainly related to DEGs involved in the pathways of ABA and IAA signaling, and secondary metabolite biosynthesis, especially the pathways for lignin and dopamine synthesis and metabolism. Therefore, our results further demonstrated the dominant role of rootstock in drought resistance, and enriched our knowledge on the mechanism of how interspecific grafting enhanced the growth and drought resistance in poplar.

The maize ZmCPK39-ZmKnox2 module regulates plant height

AbstractPlant height is an important agronomic trait that affects high-density tolerance and lodging resistance. However, the regulators and their underlying molecular mechanisms controlling plant height in maize remain understudied. Here, we report that knockout mutants of the calcium-dependent protein kinase gene ZmCPK39 (ZmCPK39-KO) exhibit dramatically reduced plant height, characterized by shorter internodes and a slight decrease in node numbers. Furthermore, we identified a ZmCPK39-interacting protein, the knotted-related homeobox (ZmKnox2), and observed that plant height was also significantly reduced in a mutator transposon-inserted mutant of ZmKnox2 (ZmKnox2-Mu). Combined analysis of transcriptomic and metabonomic data indicates that multiple phytohormone signaling and photosynthesis pathways are disrupted in both ZmCPK39-KO and ZmKnox2-Mu mutants. Taken together, these results provide new insights into the function of ZmCPK39 and identify potential targets for breeding lodging-resistant and high-density tolerant maize cultivars.

Exploring the allelopathic autotoxicity mechanism of ginsenosides accumulation under ginseng decomposition based on integrated analysis of transcriptomics and metabolomics.

Continuous cropping obstacles seriously constrained the sustainable development of the ginseng industry. The allelopathic autotoxicity of ginsenosides is the key "trigger" of continuous cropping obstacles in ginseng. During harvest, the ginseng plants could be broken and remain in the soil. The decomposition of ginseng residue in soil is one of the important release ways of ginsenosides. Therefore, the allelopathic mechanism of ginsenosides through the decomposed release pathway needs an in-depth study. To investigate this allelopathic regulation mechanism, the integrated analysis of transcriptomics and metabolomics was applied. The prototype ginsenosides in ginseng were detected converse to rare ginsenosides during decomposition. The rare ginsenosides caused more serious damage to ginseng hairy root cells and inhibited the growth of ginseng hairy roots more significantly. By high-throughput RNA sequencing gene transcriptomics study, the significantly differential expressed genes (DEGs) were obtained under prototype and rare ginsenoside interventions. These DEGs were mainly enriched in the biosynthesis of secondary metabolites and metabolic pathways, phytohormone signal transduction, and protein processing in endoplasmic reticulum pathways. Based on the functional enrichment of DEGs, the targeted metabolomics analysis based on UPLC-MS/MS determination was applied to screen endogenous differential metabolized phytohormones (DMPs). The influence of prototype and rare ginsenosides on the accumulation of endogenous phytohormones was studied. These were mainly involved in the biosynthesis of diterpenoid, zeatin, and secondary metabolites, phytohormone signal transduction, and metabolic pathways. After integrating the transcriptomics and metabolomics analysis, ginsenosides could regulate the genes in phytohormone signaling pathways to influence the accumulation of JA, ABA, and SA. The conclusion was that the prototype ginsenosides were converted into rare ginsenosides by ginseng decomposition and released into the soil, which aggravated its allelopathic autotoxicity. The allelopathic mechanism was to intervene in the response regulation of genes related to the metabolic accumulation of endogenous phytohormones in ginseng. This result provides a reference for the in-depth study of continuous cropping obstacles of ginseng.

Combined transcriptomics and metabolomics to analyse the response of Cuminum cyminum L. under Pb stress

Lead (Pb) can disrupt plant gene expression, modify metabolite contents, and influence the growth of plants. Cuminum cyminum L. is highly adaptable to adversity, but molecular mechanism by which it responds to Pb stress is unknown. For this study, transcriptomic and metabolomic sequencing was performed on root tissues of C. cyminum under Pb stress. Our results showed that high Pb stress increased the activity of peroxidase (POD), the contents of malondialdehyde (MDA) and proline by 80.03 %, 174.46 % and 71.24 %, respectively. Meanwhile, Pb stress decreased the activities of superoxide dismutase (SOD) and catalase (CAT) as well as contents of soluble sugars and GSH, which thus affected the growth of C. cyminum. In addition, Pb stress influenced the accumulation and transport of Pb in C. cyminum. Metabolomic results showed that Pb stress affected eight metabolic pathways involving 108 differentially expressed metabolites, primarily amino acids, organic acids, and carbohydrates. The differentially expressed genes identified through transcriptome analysis were mainly involved the oxidation reductase activity, transmembrane transport, phytohormone signaling, and MAPK signaling pathway. The results of this study will help to understand the molecular mechanisms of C. cyminum response to Pb stress, and provide a basis for screening seeds with strong resistance to heavy metals.

Enhancing lipid production and sedimentation of Chlorella pyrenoidosa in saline wastewater through the addition of agricultural phytohormones

In this study, the effect of external agricultural phytohormones (mixed phytohormones) addition (1.0, 5.0, 10.0, and 20.0 mg L−1) on the growth performance, lipid productivity, and sedimentation efficiency of Chlorella pyrenoidosa cultivated in saline wastewater was investigated. Among the different concentrations evaluated, the highest biomass (1.00 g L−1) and lipid productivity (11.11 mg L−1 d−1) of microalgae were obtained at 10.0 mg L−1 agricultural phytohormones addition. Moreover, exogenous agricultural phytohormones also improved the sedimentation performance of C. pyrenoidosa, which was conducive to the harvest of microalgae resources, and the improvement of sedimentation performance was positively correlated with the amount of agricultural phytohormones used. The promotion of extracellular polymeric substances synthesis by phytohormones in microalgal cells could be considered as the reason for its promotion of microalgal sedimentation. Transcriptome analysis revealed that the addition of phytohormones upregulated the expression of genes related to the mitogen-activated protein kinase (MAPK)-mediated phytohormone signaling pathway and lipid synthesis, thereby improving salinity tolerance and lipid production in C. pyrenoidosa. Overall, agricultural phytohormones provide an effective and inexpensive strategy for increasing the lipid productivity and sedimentation efficiency of microalgae cultured in saline wastewater.

Nanopore Direct RNA Sequencing Reveals the Short-Term Salt Stress Response in Maize Roots

Transcriptome analysis, relying on the cutting-edge sequencing of cDNA libraries, has become increasingly prevalent within functional genome studies. However, the dependence on cDNA in most RNA sequencing technologies restricts their ability to detect RNA base modifications. To address this limitation, the latest Oxford Nanopore Direct RNA Sequencing (ONT DRS) technology was employed to investigate the transcriptome of maize seedling roots under salt stress. This approach aimed to unveil both the RNA transcriptional profiles and alterations in base modifications. The analysis of the differential expression revealed a total of 1398 genes and 2223 transcripts that exhibited significant variation within the maize root system following brief exposure to salt stress. Enrichment analyses, such as the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway assessments, highlighted the predominant involvement of these differentially expressed genes (DEGs) in regulating ion homeostasis, nitrogen metabolism, amino acid metabolism, and the phytohormone signaling pathways. The protein–protein interaction (PPI) analysis showed the participation of various proteins related to glycolytic metabolism, nitrogen metabolism, amino acid metabolism, abscisic acid signaling, and the jasmonate signaling pathways. It was through this intricate molecular network that these proteins collaborated to safeguard root cells against salt-induced damage. Moreover, under salt stress conditions, the occurrence of variable shear events (AS) in RNA modifications diminished, the average length of poly(A) tails underwent a slight decrease, and the number of genes at the majority of the variable polyadenylation (APA) sites decreased. Additionally, the levels of N5-methylcytosine (m5C) and N6-methyladenosine (m6A) showed a reduction. These results provide insights into the mechanisms of early salt tolerance in maize.

Physiological and transcriptional analyses reveal the resistance mechanisms of kiwifruit (Actinidia chinensis) mutant with enhanced heat tolerance

High temperature is an environmental stressor that severely threatens plant growth, development, and yield. In this study, we obtained a kiwifruit mutant (MT) of ‘Hongyang’ (WT) through 60Co-γ irradiation. The MT possessed different leaf morphology and displayed prominently elevated heat tolerance compared to the WT genotype. When exposure to heat stress, the MT plants exhibited stabler photosynthetic capacity and accumulated less reactive oxygen species, along with enhanced antioxidant capacity and higher expression levels of related genes in comparison with the WT plants. Moreover, global transcriptome profiling indicated that an induction in genes related to stress-responsive, phytohormone signaling, and transcriptional regulatory pathways, which might contribute to the upgrade of thermotolerance in the MT genotype. Collectively, the significantly enhanced thermotolerance of MT might be mainly attributed to profitable leaf structure variations, improved photosynthetic and antioxidant capacities, as well as extensive transcriptome reprogram. These findings would be insightful in elucidating the sophisticated mechanisms of kiwifruit response to heat stress, and suggest the MT holds great potential for future kiwifruit improvement with enhanced heat tolerance.

The Molecular Mechanism of Relatively Low-Temperature-Induced Broccoli Flower Bud Differentiation Revealed by Transcriptomic Profiling

Broccoli (Brassica oleracea L. var. italica) has a large, edible green flower head, which is one of its critical economic traits. A prerequisite of broccoli flower head formation is flower bud differentiation (FBD). Low-temperature treatment is an effective way to induce FBD in broccoli. However, the molecular mechanism underlying low-temperature-induced broccoli FBD remains largely unclear. In this study, using broccoli cultivar Zhongqing 10 as the experimental material, we investigated the effects of low-temperature treatment on FBD by comparing the plants grown at low temperatures (17 °C/9 °C, 16 h/8 h) with the control plants grown under normal temperature conditions (25 °C/17 °C, 16 h/8 h). After 15 days of different temperature treatments, the flower buds of the plants growing under the low-temperature condition started to differentiate. However, the control plants remained in the vegetative growth stage, indicating that low temperature successfully induced flower bud formation. Subsequently, a global transcriptomic analysis was conducted to detect the differentially expressed genes (DEGs) during low-temperature-induced FBD in broccoli. A total of 14 DEGs in five phytohormone signaling pathways, 42 DEGs in nine transcription factor families, and 16 DEGs associated with the floral development pathways were identified. More DEGs were present in the auxin signaling pathway than in other phytohormone signaling pathways, which indicated that the auxin signaling pathway played a critical role in modulating low-temperature-induced FBD in broccoli. Furthermore, four TF classes, including bZIP, GCM domain factors, MADS-box factors, and C2H2 zinc finger factors, possessed enriched motifs, indicating that their closely related DETFs ABI5, HY5L, WRKY11, WRKY15, WRKY22, SOC1, AGL8, FLC, SPL8, and SPL15 may be directly involved in the transcription regulation of broccoli FBD. This study provides an important basis for further investigation of the molecular regulatory mechanism of broccoli flower development under low temperatures.