Plant Hormone Signal Transduction Research Articles

Characterization and Transcriptome Analysis Reveal Exogenous GA3 Inhibited Rosette Branching via Altering Auxin Approach in Flowering Chinese Cabbage

Branching is an important agronomic trait that is conducive to plant architecture and yield in flowering Chinese cabbage. Plant branching is regulated by a complex network mediated by hormones; gibberellin (GA) is one of the important hormones which is involved in the formation of shoot branching. Research on the regulatory mechanism of GA influencing rosette branch numbers is limited for flowering Chinese cabbage. In this study, the exogenous application of 600 mg/L GA3 effectively inhibited rosette branching and promoted internode elongation in flowering Chinese cabbage. RNA-Seq analysis further found that these DEGs were significantly enriched in ‘the plant hormone signal transduction’ pathways, and auxin-related genes were significantly differentially expressed between MB and MB_GA. The upregulation of auxin (AUX) and the upregulation of auxin/indole-3-acetic acid (AUX/IAA), as well as the downregulation of SMALL AUXIN-UPREGULATED RNA (SAUR), were found in the negative regulation of the rosette branching. The qRT-PCR results showed that the expression of AUX/IAA and SAUR from IAA gene family members were consistent with the results of transcriptome data. Phytohormone profiling by targeted metabolism revealed that endogenous auxin contents were significantly increased in MB_GA. Transcriptome and metabolome analysis clarified the main plant hormones and genes underlying the rosette branching in flowering Chinese cabbage, confirming that auxin could inhibit rosette branching. In this regard, the results present a novel angle for revealing the mechanism of gibberellin acting on the branching architecture in flowering Chinese cabbage.

Physiological, anatomical and transcriptome analyses reveal ‘Huaizhi’ as widely compatible rootstock in Litchi chinensis Sonn. grafting

Litchi chinensis Sonn. cv. ‘Huaizhi’ (HZ) is an ancient cultivar of litchi. It has been used as widely compatible rootstock for litchi grafting for a long time. However, the mechanism of HZ as widely compatible rootstock is still unclear. In the present study, physiology, morphological anatomy, as well as transcriptomics were conducted to reveal the reasons for HZ with wide compatibility in litchi grafting. Field observation were conducted on the grafting combinations of HZ/HZ (homografting as the control), FZX/HZ and MGL/HZ (the scion with good grafting compatibility in production), SYH/HZ, HHDHL/HZ and WHL/HZ (the scion with weak grafting compatibility in production), embodying that HZ as rootstock did show a wide compatibility. The physiological and biochemical indicators of scion new shoot leaves and scion mother tree indicated that nutrients contents (dry matter weight, total soluble sugar, and starch), mineral nutrition (N and P) levels, and antioxidant enzyme (superoxide dismutase and peroxidase) activities, might be related to the wide compatibility of HZ as rootstock. Microscopic observation of the paraffin sections of healing sites at different stages showed that the necrotic layer of three representative litchi grafting combinations of HZ/HZ, WHL/HZ and MGL/HZ basically disappeared from 14 d to 21 d after grafting, and the callus differentiated into a large number of protoxylem cells, indicating a compatible healing dynamics. Subsequently, a total of 14,384 differentially expressed genes (DEGs) were identified by RNA-seq, of which 2,831 DEGs exhibited the same expression trend within three grafting combinations, enriching into phenylpropanoid biosynthesis, plant hormone biosynthesis and signal transduction, sucrose and starch metabolism, MAPK signaling pathway, peroxisome and other metabolic pathways. These results provide a theoretical basis for the adjustment of cultivar structure in litchi production.

Analysis of genes related to xylem cell wall development based on transcriptomics in Populus alba ‘Berolinensis’ tension wood

Populus alba ‘Berolinensis’ is a fast-growing, high-yielding species with strong biotic and abiotic stress resistance, and widely planted for timber, shelter belts and aesthetic purposes. In this study, molecular development is explored and the important genes regulating xylem formation in P. alba ‘Berolinensis’ under artificial bending treatments was identified. Anatomical investigation indicated that tension wood (TW) was characterized by eccentric growth of xylem and was enriched in cellulose; the degree of lignification was lower than for normal wood (NW) and opposite wood (OW). RNA-Seq-based transcriptome analysis was performed using developing xylem from three wood types (TW, OW and NW). A large number of differentially expressed genes (DEGs) were screened and 4889 counted. In GO and KEGG enrichment results, genes involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and cell wall and secondary cell wall biogenesis play major roles in xylem development under artificial bending. Eight expansin (PalEXP) genes were identified from the RNA-seq data; four were differentially expressed during tension wood formation. Phylogenetic analysis indicated that PalEXLB1 belongs to the EXPB subfamily and that the other PalEXPs are members of the EXPA subfamily. A transcriptional regulatory network construction showed 10 transcription factors located in the first and second layers upstream of EXP, including WRKY, ERF and bHLH. RT‒qPCR analysis in leaves, stems and roots combined with transcriptome analysis suggests that PalEXPA2, PalEXPA4 and PalEXPA15 play significant regulatory roles in cell wall formation during tension wood development. The candidate genes involved in xylem cell wall development during tension wood formation marks an important step toward identifying the molecular regulatory mechanism of xylem development and wood property improvement in P. alba ‘Berolinensis’.

Wheat response to winter night warming based on physiological and transcriptome analyses

Global warming is primarily characterized by asymmetric temperature increases, with higher temperature rises in winter/spring and at night compared to summer/autumn and daytime. We investigated the impact of winter night warming on wheat leaves using the spring wheat cultivar Yangmai 18 and the semi-winter wheat cultivar Yannong 19 during the 2020–2021 growing season. This study aimed to examine the effect of winter night warming on the top expanded leaf of wheat plants. The results showed that the night mean temperature in the treatment group increased by 1.27°C compared to the ambient temperature and winter night warming increased the yield of both wheat cultivars, the activities of sucrose synthase and sucrose phosphate synthase after anthesis, and the biosynthesis of sucrose and soluble sugars. The differentially expressed genes were identified using P-value<0.05 and fold change>2, and subjected to Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. The genes differentially expressed in wheat leaves treated with night warming were primarily associated with starch and sucrose metabolism, amino acid biosynthesis, carbon metabolism, plant hormone signal transduction, and amino sugar and nucleotide sugar metabolism. Comparison between groups identified 14 differentially expressed genes related to temperature. These results highlight the effects of winter night warming on wheat development from various perspectives. Our results provide new insights into the molecular mechanisms of the wheat response to winter night warming and the candidate genes involved in this process.

Transcriptomic and Metabolomic Analyses Reveal the Response to Short-Term Drought Stress in Bread Wheat (Triticum aestivum L.)

Drought stress, a major abiotic stress, significantly affects wheat (Triticum aestivum L.) production globally. To identify genes and metabolic pathways crucial for responding to short-term drought stress, we conducted transcriptomic and metabolomic analyses of winter wheat cultivar Jimai 418 at four developmental stages: jointing (GS31), booting (GS45), anthesis (GS65), and 8 days after anthesis (DAA8). Transcriptomic analysis identified 14,232 differentially expressed genes (DEGs) under drought stress compared to the control. Specifically, 1387, 4573, 7380, and 892 DEGs were identified at the four developmental stages, respectively. Enriched pathways associated with these DEGs included plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling, galactose metabolism, and starch and sucrose metabolism. Totals of 222, 633, 358, and 38 differentially accumulated metabolites (DAMs) were identified at the four stages, respectively. Correlation analysis of both datasets revealed DEGs and DAMs associated with plant hormone signal transduction, arginine and proline metabolism, ABC transporters, and amino acid biosynthesis. These findings offer significant insights into Jimai 418’s molecular response to short-term drought stress. The identified DEGs, DAMs, and enriched pathways contribute to our understanding of wheat drought tolerance. This research will facilitate further investigations into drought tolerance mechanisms and guide the breeding of wheat varieties with enhanced drought resistance.

Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis.

Protein disulfide isomerase (PDI, EC 5.3.4.1) is a thiol-disulfide oxidoreductase that plays a crucial role in catalyzing the oxidation and rearrangement of disulfides in substrate proteins. In plants, PDI is primarily involved in regulating seed germination and development, facilitating the oxidative folding of storage proteins in the endosperm, and also contributing to the formation of pollen. However, the role of PDI in root growth has not been previously studied. This research investigated the impact of PDI gene deficiency in plants by using 16F16 [2-(2-Chloroacetyl)-2,3,4,9-tetrahydro-1-methyl-1H-pyrido[3,4-b]indole-1-carboxylic acid methyl ester], a small-molecule inhibitor of PDI, to remove functional redundancy. The results showed that the growth of Arabidopsis roots was significantly inhibited when treated with 16F16. To further investigate the effects of 16F16 treatment, we conducted expression profiling of treated roots using RNA sequencing and a Tandem Mass Tag (TMT)-based quantitative proteomics approach at both the transcriptomic and proteomic levels. Our analysis revealed 994 differentially expressed genes (DEGs) at the transcript level, which were predominantly enriched in pathways associated with "phenylpropane biosynthesis", "plant hormone signal transduction", "plant-pathogen interaction" and "starch and sucrose metabolism" pathways. Additionally, we identified 120 differentially expressed proteins (DEPs) at the protein level. These proteins were mainly enriched in pathways such as "phenylpropanoid biosynthesis", "photosynthesis", "biosynthesis of various plant secondary metabolites", and "biosynthesis of secondary metabolites" pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network for root shortening in Arabidopsis seedlings under 16F16 treatment, mainly involving phenylpropane biosynthesis and plant hormone signal transduction pathways. This study enhances our understanding of the significant role of PDIs in Arabidopsis root growth and provides insights into the regulatory mechanisms of root shortening following 16F16 treatment.

Physiological and transcriptomic analysis of tomato in response to sub-optimal temperature stress

ABSTRACT Tomato (Solanum lycopersicum L.) is one of the most important economic crops in China. However, its quality and yield are susceptible to the adverse effects of low temperatures. In our study, two tomato cultivars, showing different tolerance to low temperatures, namely the cold-sensitive tomato cultivar (S708) and cold-tolerant tomato cultivar (T722), were grown at optimal (25/18°C) and sub-optimal (15/10°C) temperature conditions for 5 days. Our study aimed to explore the effect of sub-optimal temperature on fresh weight, chlorophyll content and chlorophyll fluorescence, soluble sugars and proline content of two tomato cultivars. Moreover, we employed RNA-Seq to analyze the transcriptomic response of tomato roots to sub-optimal temperature. The results revealed that S708 showed a more significant reduction in fresh weight, chlorophyll content, photochemical efficiency of PSII (YII), maximum quantum yield of PSII (Fv/Fm), photochemical quenching (qP) and electron transport rate (ETR) compared to T722 under the sub-optimal temperature condition. Notably, T722 maintained higher level of soluble sugars and proline in comparison to S708 uner sub-optimal temperature. RNA-seq data showed that up-regulated DEGs in both tomato cultivars were involved in “plant-pathogen interaction”, “MAPK signaling pathway”, “plant hormone signal transduction”, and “phosphatidylinositol signaling system”. Furthermore, “Amino sugar and nucleotide sugar metabolism” pathway was enriched only in T722. Moreover, under sub-optimal temperature, transcription factor genes and osmoregulation genes showed varying degrees of response in both tomato cultivars. Conclusion: In summary, our results offer detailed insights into the response characteristics of tomato to sub-optimal temperature, providing valuable references for the practical management of tomato crops under sub-optimal temperature condition.

Transcriptome analysis of Bipolaris sorokiniana - Hordeum vulgare provides insights into mechanisms of host-pathogen interaction.

Spot blotch disease incited by Bipolaris sorokiniana severely affects the cultivation of barley. The resistance to B. sorokiniana is quantitative in nature and its interaction with the host is highly complex which necessitates in-depth molecular analysis. Thus, the study aimed to conduct the transcriptome analysis to decipher the mechanisms and pathways involved in interactions between barley and B. sorokiniana in both the resistant (EC0328964) and susceptible (EC0578292) genotypes using the RNA Seq approach. In the resistant genotype, 6,283 genes of Hordeum vulgare were differentially expressed out of which 5,567 genes were upregulated and 716 genes were downregulated. 1,158 genes of Hordeum vulgare were differentially expressed in the susceptible genotype, out of which 654 genes were upregulated and 504 genes were downregulated. Several defense-related genes like resistant gene analogs (RGAs), disease resistance protein RPM1, pathogenesis-related protein PRB1-2-like, pathogenesis-related protein 1, thaumatin-like protein PWIR2 and defensin Tm-AMP-D1.2 were highly expressed exclusively in resistant genotype only. The pathways involved in the metabolism and biosynthesis of secondary metabolites were the most prominently represented pathways in both the resistant and susceptible genotypes. However, pathways involved in MAPK signaling, plant-pathogen interaction, and plant hormone signal transduction were highly enriched in resistant genotype. Further, a higher number of pathogenicity genes of B. sorokiniana was found in response to the susceptible genotype. The pathways encoding for metabolism, biosynthesis of secondary metabolites, ABC transporters, and ubiquitin-mediated proteolysis were highly expressed in susceptible genotype in response to the pathogen. 14 and 11 genes of B. sorokiniana were identified as candidate effectors from susceptible and resistant host backgrounds, respectively. This investigation will offer valuable insights in unraveling the complex mechanisms involved in barley- B. sorokiniana interaction.

DNAL7, a new allele of NAL11, has major pleiotropic effects on rice architecture.

dnal7, a novel allelic variant of the OsHSP40, affects rice plant architecture and grain yield by coordinating auxins, cytokinins, and gibberellic acids. Plant height and leaf morphology are the most important traits of the ideal plant architecture (IPA), and discovering related genes is critical for breeding high-yield rice. Here, a dwarf and narrow leaf 7 (dnal7) mutant was identified from a γ-ray treated mutant population, which exhibits pleiotropic effects, including dwarfing, narrow leaves, small seeds, and low grain yield per plant compared to the wild type (WT). Histological analysis showed that the number of veins and the distance between adjacent small veins (SVs) were significantly reduced compared to the WT, indicating that DNAL7 controls leaf size by regulating the formation of veins. Map-based cloning and transgenic complementation revealed that DNAL7 is allelic to NAL11, which encodes OsHSP40, and the deletion of 2 codons in dnal7 destroyed the His-Pro-Asp (HPD) motif of OsHSP40. In addition, expression of DNAL7 in both WT and dnal7 gradually increased with the increase of temperature in the range of 27-31°C. Heat stress significantly affected the seedling height and leaf width of the dnal7 mutant. A comparative transcriptome analysis of WT and dnal7 revealed that DNAL7 influenced multiple metabolic pathways, including plant hormone signal transduction, carbon metabolism, and biosynthesis of amino acids. Furthermore, the contents of the cytokinins in leaf blades were much higher in dnal7 than in the WT, whereas the contents of auxins were lower in dnal7. The contents of bioactive gibberellic acids (GAs) including GA1, GA3, and GA4 in shoots were decreased in dnal7. Thus, DNAL7 regulates rice plant architecture by coordinating the balance of auxins, cytokinins, and GAs. These results indicate that OsHSP40 is a pleiotropic gene, which plays an important role in improving rice yield and plant architecture.

Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress.

Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study analyzed the transcriptome and metabolome data for Ophiopogon japonicus in the Sichuan region (referred to as CMD) under varying degrees of waterlogging stress: mild, moderate, and severe. The results indicate that the group exposed to flooding stress exhibited a higher number of differentially expressed genes (DEGs) compared to the control group. Notably, most DEGs were downregulated and primarily enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. A total of 5151 differentially accumulated metabolites (DAMs) were identified, with significantly upregulated DAMs annotated to two clusters, namely flavonoids such as apiin, pelargonin, and others. Furthermore, our study revealed significant upregulation in the expression of C2H2 (C2H2 zinc finger proteins) and AP2/ERF-ERF (the subfamily ERF proteins of APETALA2/ethylene-responsive element binding factors) transcription factors in CMD under flooding stress, suggesting their critical roles in enabling CMD to adapt to these conditions. In conclusion, this research provides insights into the intricate molecular mechanisms underlying CMD's response to flooding stress and reports valuable genetic data for the development of transgenic plants with improved waterlogging tolerance.

De Novo Transcriptome Analysis by PacBio SMRT-Seq and Illumina RNA-Seq Provides New Insights into Polyphenol Biosynthesis in Chinese Olive Fruit

Polyphenols play a crucial role in fruit flavor. To elucidate the mechanism of fruit polyphenol metabolism, we constructed a transcriptome atlas through PacBio single-molecule real-time (SMRT) sequencing and Illumina next-generation sequencing (NGS) using Canarium album (Lour.) Raeusch., which is a fantastic fruit rich in polyphenolic compounds. In this work, PacBio full-length transcriptome assembly generated 135,439 isoforms with an average length of all isoforms of 2687.94 bp and an N50 length of 3224 bp. To gain deeper insights into the molecular mechanisms of polyphenol biosynthesis in C. album, we constructed twelve RNA-Seq libraries from four developmental stages of the fruits. We identified a total of 28,658 differentially expressed genes (DEGs). We found that many DEGs were involved in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of antibiotics, starch and sucrose metabolism, and plant hormone signal transduction. Here, we report the expression profiles of 215 DEGs encoding 27 enzymes involved in the polyphenol biosynthesis pathway in C. album. In addition, 285 differentially expressed transcription factors (TFs) continuously down-regulated in four developmental periods of C. album fruit, which may indicate their potential role in the response to polyphenol metabolism and phenylpropanoid biosynthesis pathways. This report will help us understand polyphenol biosynthesis’s functions and metabolic mechanism in C. album. The transcriptome data provide a valuable resource for genetic and genomics research. They will facilitate future work exploiting C. album and other fruits used as medicine and food.

Transcriptomic Analysis of Self-Incompatibility in Alfalfa

Alfalfa (Medicago sativa L.) is an important forage crop worldwide, but molecular genetics and breeding research in this species are hindered by its self-incompatibility (SI). Although the mechanisms underlying SI have been extensively studied in other plant families, SI in legumes, including alfalfa, remains poorly understood. Here, we determined that self-pollinated pollen tubes could germinate on the stigma of alfalfa, grow through the style, and reach the ovarian cavity, but the ovules collapsed ~48 h after self-pollination. A transcriptomic analysis of dissected pistils 24 h after self-pollination identified 941 differently expressed genes (DEGs), including 784 upregulated and 157 downregulated genes. A gene ontology (GO) analysis showed that the DEGs were highly enriched in functions associated with the regulation of pollen tube growth and pollen germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that pentose and glucuronate interconversion, plant hormone signal transduction, the spliceosome, and ribosomes might play important roles in SI. Our co-expression analysis showed that F-box proteins, serine/threonine protein kinases, calcium-dependent protein kinases (CDPKs), bHLHs, bZIPs, and MYB-related family proteins were likely involved in the SI response. Our study provides a catalog of candidate genes for further study to understand SI in alfalfa and related legumes.

Integrative Phytohormone and Transcriptome Analyses Reveal the Inhibitory Mechanism of Ethylene on Potato Tuber Sprouting at Room Temperature

As a commercial potato sprout suppressant, ethylene (Eth) is usually used under a low temperature for long-term storage of potato tubers. However, in many cases, potato tubers are usually transferred from a refrigeration house and sold at room temperature. In the present research, Eth’s inhibitory effects on tuber sprouting at room temperature were investigated. The potential molecular mechanisms of Eth-induced sprout suppression were revealed by phytohormone and transcriptome analyses. Results showed that exogenous Eth significantly suppressed sprout growth in potato tubers during two weeks of storage. The endogenous plant hormone levels of abscisic acid (ABA) and auxin (Aux) were markedly reduced by Eth treatment. Transcriptomic analysis revealed that more transcriptional changes occurred in the early stage of sprouting. The differentially expressed genes (DEGs) assigned to the pathways of plant hormone signal transduction, photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis, which were closely associated with sprouting, were extensively down-regulated by Eth treatment. In addition, the heat map of six hormone signal transduction pathways showed that the expression of most DEGs annotated into the Aux signal transduction pathway was suppressed by Eth treatment, while the expression of many DEGs annotated as ETR (Eth receptor) and ERF1/2 (Eth-responsive transcription factor 1 and 2) in the Eth signal transduction pathway was enhanced by Eth treatment. Taken together, our results indicated that Eth-induced sprout inhibition might be closely related to the suppression of internal Aux production and signal transduction and the activation of Eth signal transduction.

Transcriptomic profiling of Poa pratensis L. under treatment of various phytohormones.

Poa pratensis L. (Poaceae) is a valuable grass across the north hemisphere, inhabiting diverse environments with wide altitudinal span, where ubiquitous various kinds of stresses. Phytohormones would be helpful to improve tolerance to abiotic and biotic stresses, but the responses of transcriptome regulation of P. pratensis to exogenous phytohormones application remain unclear. In this study, we explored the alteration of plant physiological responses by the application of phytohormones. Aiming to achieve this knowledge, we got full-length transcriptome data 42.76 Gb, of which 74.9% of transcripts were completed. Then used 27 samples representing four treatments conducted at two time points (1 h and 6 h after application) to generate RNA-seq data. 371 and 907 common DEGs were identified in response to four phytohormones application, respectively, these DEGs were involved in "plant hormone signal transduction", "carbon metabolism" and "plant-pathogen interaction". Finally, P. pratensis basic research can gain valuable information regarding the responses to exogenous application of phytohormones in physiological indicators and transcriptional regulations in order to facilitate the development of new cultivars.

Comparative transcriptomic analysis of rubber (Hevea brasiliensis) clones differing in disease tolerance provides novel insights into the disease response associated with abnormal leaf fall disease caused by Phytophthora meadii

Rubber is an important industrial commodity and Hevea brasiliensis is the commercial source of natural rubber (NR). Abnormal Leaf Fall (ALF) disease caused by Phytophthora meadii is one of the major diseases affecting yield of NR. Understanding Hevea-Phytophthora interaction mechanism is essential to manage this devastating disease. Transcriptome analysis was employed to gain an understanding on the molecular mechanisms that confer resistance to Phytophthora that would facilitate development of disease-tolerant Hevea clones. As our current understanding of Hevea-Phytophthora interaction is limited, an attempt was made to analyze and compare the transcriptomes of tolerant and susceptible clones of H. brasiliensis in response to P. meadii infection (in healthy and Phytophthora challenge-inoculated condition) during early, middle and late phases of infection by using the RNA-Seq technology. The transcriptome sequencing generated an average of 19,000 differentially expressed genes (DEGs) in both clones. When comparing the tolerant clone to the susceptible clone, there was an overall increase in the number of DEGs and a progression in the number of DEGs, indicating a more active engagement of transcriptional activity in the tolerant clone. Functional annotation, KEGG analysis and enrichment analysis revealed that the major pathways enriched for the DEGs were involved in plant hormone signal transduction and plant-pathogen interaction. An analysis of DEGs during each phase showed that the most active transcripts involved in defense mechanisms were activated during mid-phase and in the case of susceptible clone least transcripts were induced during mid-phase than in any other phase in both the clones. Many DEGs belonging to the MYB, NAC, WRKY and AP2/ERF transcription factor families were observed in both clones. Comparative studies revealed their differential involvement in tolerant and susceptible clones against Phytophthora infection. These findings may facilitate further exploration of Hevea-Phytophthora interaction and in cloning for defense related genes.

Transcriptome analysis reveals regulatory mechanisms of different drought-tolerant Gleditsia sinensis seedlings under drought stress

BackgroundGleditsia sinensis is a significant tree species from both ecological and economic perspectives. However, its growth is hampered by temporary droughts during the seedling stage, thereby impeding the development of the G. sinensis industry. Drought stress and rehydration of semi-annual potted seedlings using an artificial simulated water control method. RNA sequencing (RNA-seq) analyses were conducted on leaves collected from highly resistant (HR) and highly susceptible (HS) seedling families at five different stages during the process of drought stress and rehydration to investigate their gene expression patterns.ResultsThe differentially expressed genes (DEGs) were predominantly enriched in pathways related to “chloroplast” (GO:0009507), “photosynthesis” (GO:0015979), “plant hormone signal transduction” (map04075), “flavonoid biosynthesis” (map00941), “stress response”, “response to reactive oxygen species (ROS)” (GO:0000302), “signal transduction” (GO:0007165) in G. sinensis HR and HS families exposed to mild and severe drought stress. Additionally, the pathways related to “plant hormone signal transduction” (map04075), and osmoregulation were also enriched. The difference in drought tolerance between the two families of G. sinensis may be associated with “transmembrane transporter activity” (GO:0022857), “stress response”, “hormones and signal transduction” (GO:0007165), “cutin, suberine and wax biosynthesis” (map00073), “ribosome” (map03010), “photosynthesis” (map00195), “sugar metabolism”, and others. An enrichment analysis of DEGs under severe drought stress suggests that the drought tolerance of both families may be related to “water-soluble vitamin metabolic process” (GO:0006767), “photosynthesis” (map00195), “plant hormone signal transduction” (map04075), “starch and sucrose metabolism” (map00500), and “galactose metabolism” (map00052). Osmoregulation-related genes such as delta-1-pyrroline-5-carboxylate synthase (P5CS), Amino acid permease (AAP), Amino acid permease 2 (AAP2) and Trehalose-phosphate synthase (TPS), as well as the antioxidant enzyme L-ascorbate peroxidase 6 (APX6), may be significant genes involved in drought tolerance in G. sinensis. Five genes were selected randomly to validate the RNA-seq results using quantitative real-time PCR (RT-qPCR) and they indicated that the transcriptome data were reliable.ConclusionsThe study presents information on the molecular regulation of the drought tolerance mechanism in G. sinensis and provides a reference for further research on the molecular mechanisms involved in drought tolerance breeding of G. sinensis.

Integrated analysis of the transcriptome and metabolome reveals the molecular mechanism regulating cotton boll abscission under low light intensity

BackgroundCotton boll shedding is one of the main factors adversely affecting the cotton yield. During the cotton plant growth period, low light conditions can cause cotton bolls to fall off prematurely. In this study, we clarified the regulatory effects of low light intensity on cotton boll abscission by comprehensively analyzing the transcriptome and metabolome.ResultsWhen the fruiting branch leaves were shaded after pollination, all of the cotton bolls fell off within 5 days. Additionally, H2O2 accumulated during the formation of the abscission zone. Moreover, 10,172 differentially expressed genes (DEGs) and 81 differentially accumulated metabolites (DAMs) were identified. A KEGG pathway enrichment analysis revealed that the identified DEGs and DAMs were associated with plant hormone signal transduction and flavonoid biosynthesis pathways. The results of the transcriptome analysis suggested that the expression of ethylene (ETH) and abscisic acid (ABA) signaling-related genes was induced, which was in contrast to the decrease in the expression of most of the IAA signaling-related genes. A combined transcriptomics and metabolomics analysis revealed that flavonoids may help regulate plant organ abscission. A weighted gene co-expression network analysis detected two gene modules significantly related to abscission. The genes in these modules were mainly related to exosome, flavonoid biosynthesis, ubiquitin-mediated proteolysis, plant hormone signal transduction, photosynthesis, and cytoskeleton proteins. Furthermore, TIP1;1, UGT71C4, KMD3, TRFL6, REV, and FRA1 were identified as the hub genes in these two modules.ConclusionsIn this study, we elucidated the mechanisms underlying cotton boll abscission induced by shading on the basis of comprehensive transcriptomics and metabolomics analyses of the boll abscission process. The study findings have clarified the molecular basis of cotton boll abscission under low light intensity, and suggested that H2O2, phytohormone, and flavonoid have the potential to affect the shedding process of cotton bolls under low light stress.

Comparative Transcript Profiling of Resistant and Susceptible Tea Plants in Response to Gray Blight Disease

Gray blight disease stands as one of the most destructive ailments affecting tea plants, causing significant damage and productivity losses. However, the dynamic roles of defense genes during the infection of gray blight disease remain largely unclear, particularly concerning their distinct responses in resistant and susceptible cultivars. In the pursuit of understanding the molecular interactions associated with gray blight disease in tea plants, a transcriptome analysis unveiled that 10,524, 17,863, and 15,178 genes exhibited differential expression in the resistant tea cultivar (Yingshuang), while 14,891, 14,733, and 12,184 genes showed differential expression in the susceptible tea cultivar (Longjing 43) at 8, 24, and 72 h post-inoculation (hpi), respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses highlighted that the most up-regulated genes were mainly involved in secondary metabolism, photosynthesis, oxidative phosphorylation, and ribosome pathways. Furthermore, plant hormone signal transduction and flavonoid biosynthesis were specifically expressed in resistant and susceptible tea cultivars, respectively. These findings provide a more comprehensive understanding of the molecular mechanisms underlying tea plant immunity against gray blight disease.

Transcriptomics Reveal an Integrated Gene Regulation Network of Early Flowering Development in an Oil Sunflower Mutant Induced by Heavy Ion Beam

The oil sunflower is an important oil crop and ornamental plant. Flowering time affects the environmental adaptability and final yield of oil sunflowers. Floral induction is one of the important events that determines subsequent reproductive growth and seed setting, but there has been no systematic study on the regulation of gene expression during the transition from vegetative growth to reproductive growth in oil sunflowers. In this study, an oil sunflower mutant displaying early flowering (ef) was obtained by heavy ion beam irradiation. This mutant had a stable genetic trait, and its flowering time was 15 days earlier than the wild type (WT) in the field. The histology result showed that the ef mutant induced floral meristem at 6-leaf stage earlier than WT. The shoot apical meristems (SAMs) of the ef mutant and WT at 4-leaf, 6-leaf, 8-leaf, 10-leaf and budding periods were collected for RNA sequencing. The results showed that the transition from the leaf meristem to the floral meristem resulted in significant changes in the transcriptional landscape. Overall, 632, 1825, 4549, 5407 and 2164 differentially expressed genes (DEGs) were identified at 4-leaf, 6-leaf, 8-leaf, 10-leaf and budding periods, respectively. These DEGs were mainly enriched in biological pathways, including plant hormone signal transduction, carbon metabolism, protein processing in endoplasmic reticulum, secondary metabolism, and photosynthesis. We also found significant differences in the expression levels of starch and sucrose metabolism-related genes in the ef mutant and WT, indicating that sugar signaling plays an important role in the early flowering of oil sunflowers, especially SUC9 and sugar synthesis and degradation enzyme genes. In addition to hormone and sugar signals, flowering integration genes SOC1, AP1, FUL and LFY were upregulated in the ef mutant, and genes in photoperiod, aging, autonomous and temperature pathways were also involved in the regulation of floral transition. The results showed that plant hormones, sucrose metabolism, and flowering genes synergistically cause the early flowering of oil sunflowers. Our study provided important information for understanding flowering and is helpful for the genetic improvement of sunflowers.

Comparative stigmatic transcriptomics reveals self and cross pollination responses to heteromorphic incompatibility in Plumbago auriculata Lam.

"Heteromorphic self-incompatibility" (HetSI) in plants is a mechanism of defense to avoid self-pollination and promote outcrossing. However, the molecular mechanism underlying HetSI remains largely unknown. In this study, RNA-seq was conducted to explore the molecular mechanisms underlying self-compatible (SC, "T × P" and "P × T") and self-incompatible (SI, "T × T" and "P × P") pollination in the two types of flowers of Plumbago auriculata Lam. which is a representative HetSI plant. By comparing "T × P" vs. "T × T", 3773 (1407 upregulated and 2366 downregulated) differentially expressed genes (DEGs) were identified, 1261 DEGs between "P × T" and "P × P" (502 upregulated and 759 downregulated). The processes in which these DEGs were significantly enriched were "MAPK (Mitogen-Activated Protein Kinases-plant) signaling pathway", "plant-pathogen interaction","plant hormone signal transduction", and "pentose and glucuronate interconversion" pathways. Surprisingly, we discovered that under various pollination conditions, multiple notable genes that may be involved in HetSI exhibited distinct regulation. We can infer that the HetSI strategy might be unique in P. auriculata. It was similar to "sporophytic self-incompatibility" (SSI) but the HetSI mechanisms in pin and thrum flowers are diverse. In this study, new hypotheses and inferences were proposed, which can provide a reference for crop production and breeding.