scholarly journals Key Cannabis Salt-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Varieties

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2338
Author(s):  
Jiangjiang Zhang ◽  
Cuiping Zhang ◽  
Siqi Huang ◽  
Li Chang ◽  
Jianjun Li ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Plant Hormone ◽  
Signal Transduction Pathway ◽  
Mapk Signaling ◽  
Molecular Networks ◽  
Molecular Response ◽  
Rna Seq ◽  
Physiological Diversity ◽  
Phenylpropanoid Biosynthesis

For the dissection and identification of the molecular response mechanisms to salt stress in cannabis, an experiment was conducted surveying the diversity of physiological characteristics. RNA-seq profiling was carried out to identify differential expression genes and pathway which respond to salt stress in different cannabis materials. The result of physiological diversity analyses showed that it is more sensitive to proline contents in K94 than in W20; 6 h was needed to reach the maximum in K94, compared to 12 h in W20. For profiling 0–72 h after treatment, a total of 10,149 differentially expressed genes were identified, and 249 genes exhibited significantly diverse expression levels in K94, which were clustered in plant hormone signal transduction and the MAPK signaling pathway. A total of 371 genes showed significant diversity expression variations in W20, which were clustered in the phenylpropanoid biosynthesis and plant hormone signal transduction pathway. The pathway enrichment by genes which were identified in K94 and W20 showed a similar trend to those clustered in plant hormone signal transduction pathways and MAPK signaling. Otherwise, there were 85 genes which identified overlaps between the two materials, indicating that these may be underlying genes related to salt stress in cannabis. The 86.67% agreement of the RNA-seq and qRT-PCR indicated the accuracy and reliability of the RNA-seq technique. Additionally, the result of physiological diversity was consistent with the predicted RNA-seq-based findings. This research may offer new insights into the molecular networks mediating cannabis to respond to salt stress.

scholarly journals RNA-Seq And WGCNA Analysis Identifies Salt-Responsive Genes In Pear (Pyrus Ussuriensis Maxim)

2021 ◽  
Author(s):  
Qiming Chen ◽  
Huizhen Dong ◽  
Zhihua Xie ◽  
Kaijie Qi ◽  
Xiaosan Huang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Plant Hormone ◽  
Enrichment Analysis ◽  
Salt Resistance ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Signal Transduction Pathways ◽  
Rna Seq

Abstract Background: Pear is one of the most abundant fruit crops and has been cultivated world-wide. However, the salt injury events caused by increased salinity limited the distribution and sustainable production of pear crops. Therefore, it is needed to take further efforts to understand the genetics and mechanisms of salt tolerance to improved salt resistance and productivity.Results: In this work, we analyzed the dynamic transcriptome of pear (Pyrus ussuriensis Maxim) under salt stress by using RNA-Seq and WGCNA. A total of 3540, 3831, 8374, 6267 and 5381 genes were identified that were differentially expressed after exposure to 200mM NaCl for 4, 6, 12, 24 and 48 hours, respectively, and 1163 genes were shared among the five comparisons. KEGG enrichment analysis of these DEGs (differentially expressed genes) revealed that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly enriched. Meanwhile, 622 DEGs identified from WGCNA were highly correlated with these pathways, and some of them were able to indicate the salt tolerance of pear varieties. In addition, we provide a network to demonstrate the time-sequence of these co-expressed MAPK and hormone related genes.Conclusion: A comprehensive analysis about salt-responsive pear transcriptome were performed by using RNA-Seq and WGCNA. We demonstrated that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly recruited during salt stress, and provided new insights into the metabolism of plant hormones related signaling at transcriptome level underlying salt resistance in pear. The dynamic transcriptome data obtained from this study and these salt-sensitive DEGs may provide potential genes as suitable targets for further biotechnological manipulation to improve pear salt tolerance.

scholarly journals Expression of Genes Related to Plant Hormone Signal Transduction in Jerusalem artichoke (Helianthus tuberosus L.) Seedlings Under Salt Stress

2021 ◽  
Author(s):  
Yue Yang ◽  
Wang Jueyun ◽  
Ren Wencai ◽  
Zhaosheng Zhou ◽  
Long Xiaohua ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Abscisic Acid ◽  
Salt Stress ◽  
Plant Hormone ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Expression Of Genes ◽  
Gene Functions

Background: Jerusalem artichoke (Helianthus tuberosus L.) is tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, the plant physiology, biochemistry and gene transcription are likely to undergo large changes. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h, 6 h, 12 h, 24 h and 48 h, with 150,129 unigenes and 9023 DEGs (Differentially Expressed Genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among the groups convergence. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belongs to PYL (abscisic acid receptor PYR / PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (Genes such as jasmonate ZIM-domain gene) and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qPCR of 12 randomly selected genes confirmed the accuracy of RNA-seq. Conclusions: Under the impact of high salinity (300mM) environment, Jerusalem artichoke in the seedling stage was difficult to survive for a long time, and the phenotype was severe in the short term. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern.

scholarly journals Expression of Genes Related to Plant Hormone Signal Transduction in Jerusalem Artichoke (Helianthus tuberosus L.) Seedlings under Salt Stress

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 163
Author(s):  
Yang Yue ◽  
Jueyun Wang ◽  
Wencai Ren ◽  
Zhaosheng Zhou ◽  
Xiaohua Long ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Plant Hormone ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Expression Of Genes ◽  
Gene Functions

Background: Jerusalem artichoke (Helianthus tuberosus L.) is moderately tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, gene transcription is likely to undergo large changes. Previous studies have hinted at the importance of temporal expression analysis in plant transcriptome research. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h (hour), 6 h, 12 h, 24 h, and 48 h, with 150 and 129 unigenes and 9023 DEGs (differentially expressed genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among them. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belonging to PYL (abscisic acid receptor PYR/PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (genes such as jasmonate ZIM-domain gene), and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qRT-PCR of 12 randomly selected and function known genes confirmed the accuracy of RNA-seq. Conclusions: Under the influence of high salinity (300 mM) environment, Jerusalem artichoke suffer serious damage in a short period of time. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, and the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern. Research emphasized the regulatory role of hormones under high salt shocks and provided an explorable direction for the study of plant salt tolerance mechanisms.

scholarly journals Comparative transcriptomes and genome-wide identification reveal salt stress-responsive PP2C in Jute (Corchorus capsularis)

2021 ◽  
Author(s):  
Aminu Kurawa Ibrahim ◽  
Yi Xu ◽  
Qingyao He ◽  
Sylvain Niyitanga ◽  
Muhammad Zohaib Afzal ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Abscisic Acid ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Plant Hormone ◽  
Signal Transduction Pathway ◽  
Transduction Pathway ◽  
Salt Tolerant ◽  
Corchorus Capsularis ◽  
Molecular Bases

Abstract Background: The jute plant is of great significance and economic relevance to humanity, but its production has been hindered due to abiotic influences, especially salt stress. Hitherto, the molecular bases for this vital feature await future exploration. The abscisic acid (ABA) signaling pathway comprises many regulated genes and plays a role in plant response to stress, however, a balance between the multiple pathways is always needed for any plant developmental process. In this study, we used a transcriptomic approach to unveil the molecular bases behind this trait. Salt tolerant (J194) and sensitive (J7) germplasms were subjected to sodium chloride (NaCl) stress at a different time point, from which leaf and roots samples were taken for transcriptome analyses. Result: The plant hormone signal transduction pathway was the most abundant observed in the study; the Pyrrolysine (PYL) gene (Cc.03G0016680) was up-regulated, which supports the basic model of abscisic acid (ABA). The quantitative reverse transcription-PCR (qRT –PCR) and the correlation analysis validated the Ribonucleic acid sequence (RNA-seq) results. The candidate genes’ relative expression level was higher in J194, especially in protein phosphate 2C (PP2C). Corchorus capsularis PP2C gene family revealed 38 members, phylogenetic analysis categorized PP2C into 15 based upon conserved domains. Eleven conserved motifs were identified, and most of the genes had the same number of conserved motifs. The exon-intron ranges of (3-21) and (2-20), respectively. Moreover, among the plant hormone signal transduction pathway PP2C genes, Cc.03G0016550 and Cc.07G0028160 were up-regulated in J194 root tissues at 6-hour exposure NaCl, as such recommended to be salt-tolerant candidature genes. It was noted that most of the Corchorus capsularis PP2C genes were involved from segmental duplication, and analysis of the key stress marker salt-tolerant PP2C genes validated the salt tolerance individuals. Conclusion: These results provided valuable insight into salt tolerance transcriptome and indicated that PP2C had provided a stepping-stone to the molecular mechanism in Corchorus capsularis. Furthermore, differentially expressed genes, motifs, gene structure, and the chromosomal location of salt tolerance candidate genes might have experienced functional divergence. As such, their further study will enhance salt tolerance in Corchorus capsularis.

scholarly journals Transcriptome-Based Analysis of Phosphite-Induced Resistance against Pathogens in Rice

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1334
Author(s):  
Yuqing Huang ◽  
Shengguan Cai ◽  
Guoping Zhang ◽  
Songlin Ruan
Keyword(s):  
Signal Transduction ◽  
Molecular Mechanism ◽  
Differentially Expressed Genes ◽  
Induced Resistance ◽  
Plant Hormone ◽  
Xanthomonas Oryzae ◽  
Pyricularia Grisea ◽  
Protection Effect ◽  
Phenylpropanoid Biosynthesis ◽  
Xanthomonas Oryzae Pv.Oryzae

Phosphite (PHI) has been used in the management of Phytophthora diseases since the 1970s.We assessed the effect of PHI on controlling the incidence of Xanthomonas oryzae pv.oryzae and Pyricularia grisea. As a result, PHI application significantly inhibited the incidence of the diseases. To clarify the molecular mechanism underlying this, a transcriptome study was employed. In total, 2064 differentially expressed genes (DEGs) were identified between control and PHI treatment. The key DEGs could be classified into phenylpropanoid biosynthesis (ko00940), starch and sucrose metabolism (ko00500), and plant hormone signal transduction (ko04075). The expressions of defense-related genes had a higher expression lever upon PHI treatment. This study provides new insights into the mechanism of protection effect of PHI against pathogens.

Illumina Sequencing Reveals Conserved and Novel MicroRNAs of Dendrobium nobile Protocorm Involved in Synthesizing Dendrobine, a Potential Nanodrug

2021 ◽  
Vol 17 (3) ◽  
pp. 416-425
Author(s):  
Xu Qian ◽  
Jieying Zhu ◽  
Qingjun Yuan ◽  
Qi Jia ◽  
Hui Jin ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Illumina Sequencing ◽  
Plant Hormone ◽  
Signal Transduction Pathway ◽  
Perennial Herb ◽  
Transduction Pathway ◽  
Biological Regulation ◽  
Dendrobium Nobile ◽  
Short Period ◽  
Post Transcriptional Regulation

Emergency of nanoparticulate drug delivery systems has improved the target, bioavailability, and curative effect of traditional Chinese medicine (TCM). However, the application of nano-preparation has been limited owing to the low content of active ingredients in part TCM. MicroRNAs (miRNAs) regulate plant growth, development, and response to environmental stresses at post-transcriptional regulation level by cleavage or translational inhibition. The molecular functions of miRNAs playing a role in synthesizing active comportments at medicinal plants have been widely researched. Dendrobium nobile is a perennial herb in the orchidaceae family. D. nobile protocorm can produce plant-specific metabolites at a short period. Therefore, it is a good substitute for producing metabolites. To understand the functions of miRNAs in D. nobile protocorm, Illumina sequencing of D. nobile protocorm (Dnp), D. officinale protocorm (Dcp), and D. nobile leaf (Dnl) were carried out. A total of 439, 412, and 432 miRNAs were identified from Dnp, Dcp, and Dnl, respectively. Some specific miRNAs were identified among them. Through combing GO and KEGG function annotation, miRNAs mainly involved metabolic pathways, plant hormone signal transduction, biological regulation, and protein binding. Acetyl-CoA acetyltransferase (AACT), mevalonate kinase (MK), 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), and 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (HDS), synthesizing basic precursor isoprene pyrophosphate (IPP) in terpenoid backbone biosynthesis pathway, were predicted as potential targets of 6 different miRNAs. Twenty-six miRNAs participated in auxin, cytokinin, abscisic acid, jasmonic acid, and salicylic acid signal transduction pathway. This report provided valuable candidate genes in Dnp involved in terpenoid biosynthesis and plant hormone signal transduction pathway. At the same time, it can help accelerate the use of dendrobine into nano preparation.

scholarly journals Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)

2019 ◽  
Vol 20 (17) ◽  
pp. 4303 ◽  
Author(s):  
Hongyou Li ◽  
Qiuyu Lv ◽  
Jiao Deng ◽  
Juan Huang ◽  
Fang Cai ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Seed Development ◽  
Seed Size ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Fagopyrum Esculentum ◽  
Rna Seq ◽  
Common Buckwheat ◽  
Size Change ◽  
Key Genes

Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.

scholarly journals Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Pibiao Shi ◽  
Minfeng Gu
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Plant Hormone ◽  
Stress Factors ◽  
Soil Conditions ◽  
Regulation Mechanism

Abstract Background Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance. Results The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

scholarly journals Differential Gene Expression Analysis of Resistant and Susceptible Flax Cultivars in Response to Fusarium oxysporum Stress

2021 ◽  
Author(s):  
He Rui ◽  
Chang Yin Dong ◽  
Wang Jian Ming
Keyword(s):  
Signal Transduction ◽  
Disease Resistance ◽  
Fusarium Oxysporum ◽  
Signaling Pathway ◽  
Plant Hormone ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Resistant Cultivar ◽  
Susceptible Cultivar ◽  
Significant Difference

A plant’s early response to pathogen stress is a vital indicator of its disease resistance. In order to study the response mechanism of resistant and susceptible flax cultivars to Fusarium oxysporum f. sp. lini (Foln), we applied RNA-sequencing to analyze transcriptomes of flax with Foln 0.5, 2 and 8 hours post inoculation (hpi). We found a significant difference in the number of differential expression genes (DEGs) between resistant and susceptible flax clutivars. The number of DEGs in the Fusarium-resistant cultivar increased dramatically at 2 hpi, and a large number of DEGs participated in the Fusarium-susceptible cultivar response to Foln infection 0.5 hpi. GO enrichment analysis determined that the up-regulated DEGs of both flax cultivars were enriched such as oxidoreductase activity and oxidation-reduction process. At the same time, the genes involved in diterpenoid synthesis were up-regulated in resistant cultivar, while those involved in extracellular region, cell wall and organophosphate ester transport were down-regulated in susceptible cultivar. KEGG enrichment analysis showed the genes encoded WRKY 22 and WRKY33 which involved in MAPK signaling pathway were up-regulated expressed in S-29 and down-regulated expressed in R-7, negatively regulated the disease resistance of flax; The genes encoded Hsp 90 family which in involved in plant pathogen interaction pathway were up-regulated in R-7 and down-regulated in S-29, which positively regulated the disease resistance of flax; The genes encoded MYC2 transcription factor and TIFY proteins which involved in plant hormone signaling pathway were up-regulated in R-7, and regulated the jasmonic acid metabolism of flax and the signal transduction of plant hormones. Meanwhile seven regulatory genes with the most correlation were screened out, Among Lus10025000.g and Lus10026447.g regulated other genes expressed both in plant hormone signal transduction pathway and MAPK signal pathway. In conclusion, these findings will facilitate further studies on the function of these candidate genes in flax of response to Fusarium stress, and the breeding of disease-resistant flax cultivar.

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