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

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.

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

Agronomy ◽

10.3390/agronomy12010163 ◽

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.

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

Agronomy ◽

10.3390/agronomy11112338 ◽

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.

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

10.21203/rs.3.rs-847089/v1 ◽

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.

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

10.21203/rs.3.rs-190737/v1 ◽

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.

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Drought tolerance molecular responses of two cultivated varieties Jerusalem artichoke (Helianthus tuberosus L.) as revealed by RNA-Seq

10.21203/rs.3.rs-124586/v1 ◽

2020 ◽

Author(s):

Shipeng Yang ◽

Lihui Wang ◽

Qiwen Zhong ◽

Guangnan Zhang ◽

Haiwang Zhang ◽

...

Keyword(s):

Drought Stress ◽

Drought Resistance ◽

Metabolic Pathways ◽

Jerusalem Artichoke ◽

Tibet Plateau ◽

Helianthus Tuberosus ◽

Rna Seq ◽

Concentration Gradients ◽

Light Reaction ◽

Metabolic Activities

Abstract Background Jerusalem artichoke (Helianthus tuberosus L.) is a highly stress-resistant crop, especially it grows normally in the desertified land of Qinghai-Tibet Plateau in the past two years, and has become a crop with agricultural, industrial and ecological functions. However, there are few studies on drought resistance of Jerusalem artichoke at present, and studies on the mechanisms of stress resistance of Jerusalem artichoke breeding and fructan are seriously lagging behind. In this study, we selected two differentially resistant cultivars for drought stress experiments with different concentration gradients, the aim was finding DEGs and metabolic pathways associated with drought stress. Results Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. It was suggested that flavonoids could help Jerusalem artichoke to resist drought stress and maintain normal metabolic activities. In addition, the gene analysis of the abscisic acid (ABA) key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1, but QY1 had more genes in response to drought stress as a whole. By combining RNA-Seq and WGCNA, a weighted gene co-expression network was constructed and divided into modules. By analyzing specifically the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase had the highest significance in these pathways. Conclusions These findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the excavation of related genes.

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Salt stress induced differential metabolic responses in the sprouting tubers of Jerusalem artichoke (Helianthus tuberosus L.)

PLoS ONE ◽

10.1371/journal.pone.0235415 ◽

2020 ◽

Vol 15 (6) ◽

pp. e0235415

Author(s):

Hui-Xi Zou ◽

Dongsheng Zhao ◽

Haihong Wen ◽

Nan Li ◽

Weiguo Qian ◽

...

Keyword(s):

Salt Stress ◽

Jerusalem Artichoke ◽

Metabolic Responses ◽

Helianthus Tuberosus

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

BMC Plant Biology ◽

10.1186/s12870-020-02753-1 ◽

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.

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Melatonin Improves Cotton Salt Tolerance by Regulating ROS Scavenging System and Ca2 + Signal Transduction

Frontiers in Plant Science ◽

10.3389/fpls.2021.693690 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuexin Zhang ◽

Yapeng Fan ◽

Cun Rui ◽

Hong Zhang ◽

Nan Xu ◽

...

Keyword(s):

Signal Transduction ◽

Salt Stress ◽

Salt Tolerance ◽

Signal Molecules ◽

Protective Mechanism ◽

Rna Seq ◽

Ros Scavenging ◽

Exogenous Melatonin ◽

Endogenous Melatonin

As one of the cash crops, cotton is facing the threat of abiotic stress during its growth and development. It has been reported that melatonin is involved in plant defense against salt stress, but whether melatonin can improve cotton salt tolerance and its molecular mechanism remain unclear. We investigated the role of melatonin in cotton salt tolerance by silencing melatonin synthesis gene and exogenous melatonin application in upland cotton. In this study, applicating of melatonin can improve salt tolerance of cotton seedlings. The content of endogenous melatonin was different in cotton varieties with different salt tolerance. The inhibition of melatonin biosynthesis related genes and endogenous melatonin content in cotton resulted in the decrease of antioxidant enzyme activity, Ca2+ content and salt tolerance of cotton. To explore the protective mechanism of exogenous melatonin against salt stress by RNA-seq analysis. Melatonin played an important role in the resistance of cotton to salt stress, improved the salt tolerance of cotton by regulating antioxidant enzymes, transcription factors, plant hormones, signal molecules and Ca2+ signal transduction. This study proposed a regulatory network for melatonin to regulate cotton’s response to salt stress, which provided a theoretical basis for improving cotton’s salt tolerance.

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Transcriptome changes induced by drought stress in Jerusalem artichoke (Helianthus tuberosus L.) and weighted gene co-expression network analysis (WGCNA)

10.21203/rs.3.rs-25678/v1 ◽

2020 ◽

Author(s):

Shipeng Yang ◽

Lihui Wang ◽

Qiwen Zhong ◽

Guangnan Zhang ◽

Dengshan Zhang ◽

...

Keyword(s):

Drought Stress ◽

Drought Resistance ◽

Jerusalem Artichoke ◽

Northern China ◽

Qinghai Lake ◽

Helianthus Tuberosus ◽

Rna Seq ◽

Light Reaction ◽

Qinghai Province ◽

Watering Treatment

Abstract Background: Jerusalem artichoke (Helianthus tuberosus L.) is strongly resistant to stress and an important plant used for ecological management in northern China in recent years. Currently, Jerusalem artichoke has been widely planted in the area around Qinghai Lake in Qinghai Province, China. Jerusalem artichoke can not only prevent land desertification but also has maintain most of its level of production. However, there is little research on the mechanism of drought resistance of Jerusalem artichoke.Results: We conducted transcriptome sequencing under drought stress and normal watering treatment for two varieties, QY1 and QY3, with differing degrees of drought tolerance. In the three stress periods of QY1 and QY3, 5,613, 12,985 and 24,923 differentially expressed genes (DEGs) were identified, respectively. GO analysis showed that there were more DEGs in QY1 than in QY3, but there were more up-regulated genes in QY3 than in QY1. Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. The up-regulated genes in QY3 were significantly more prevalent than those in QY1 and were primarily concentrated in flavor IDS, phenylpropanoids, and the shikimate and terpenoids pathway. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. In addition, the gene analysis of the ABA key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1. A weighted gene co-expression network was constructed and divided into modules. By specifically analyzing the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase were the most significant in these pathways.Conclusions: In summary, these findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the unearthing of related genes.

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