Network-based Transcriptome Analysis of Two Maize Genotypes Identified Pathways Associated With Differences in Salt Tolerance

Abstract BackgroundA better understanding of the molecular effects of salinity stress is key to improving salt tolerance in Zea mays. In this study, we combined phenotyping with transcript profiling and network analysis to study genotype-specific differences in salt tolerance in Zea mays. ResultAn extensive phenotypic screening identified two genotypes with an extreme phenotypic difference in tolerance towards salt stress. RNA-seq analysis of the selected salt-tolerant (R9) and salt-sensitive (S46) genotype was performed to unveil the molecular mechanism underlying the difference in salt tolerance. GO enrichment and network analysis on the results of the expression analysis identified phosphorylation-dependent signaling processes, ion transportation, oxidation-reduction, glutathione and tryptophan metabolism as the main processes different between the selected tolerant and sensitive genotypes. Genes belonging to the subnetwork enriched for phosphorylation and kinase activity shared a common regulatory element in their promoter region, which matched the binding site of an Arabidopsis TF with known role in salt-stress response.ConclusionNetwork-based transcriptome analysis of two maize genotypes identified pathways associated with differences in genotype-specific salt tolerance and identified a link between transcriptional and posttranslational regulation of salt tolerance.

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Transcriptome Analysis of Salt Stress Response in Roots of Halophyte Zoysia macrostachya

International Journal of Agriculture and Biology ◽

10.17957/ijab/15.1705 ◽

2021 ◽

Vol 25 (03) ◽

pp. 591-600

Author(s):

Huaguang Hu

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Transcript Abundance ◽

Nacl Stress ◽

Ros Scavenging ◽

Salt Stress Response ◽

Sequencing Platform

Zoysia macrostachya Franch. et Sav. is a halophyte with very strong tolerance to salinity, which can serve as an alternative turfgrass for landscaping in saline-alkali land and provide the salt-tolerance genes for turfgrass breeding. To further illustrate the salt-tolerance mechanisms in this species at molecular level, the roots transcriptome of Z. macrostachya was investigated under salt stress using the Illumina sequencing platform. Altogether 47,325 unigenes were assembled, among which, 32,542 (68.76%) were annotated, and 87.61% clean reads were mapped to the unigenes. Specifically, 14,558 unigenes were shown to be the differentially expressed genes (DEGs) following exposure to 710 mM NaCl stress compared with control, including 7972 up-regulated and 6586 down-regulated DEGs. Among these DEGs, 24 were associated with the reactive oxygen species (ROS) scavenging system, 61 were found to be related to K+ and Na+ transportation, and 16 were related to the metabolism of osmotic adjustment substances. Additionally, 2327 DEGs that encoded the transcription factors (TFs) were also identified. The expression profiles for 10 DEGs examined through quantitative real-time PCR conformed to the individual alterations of transcript abundance verified through RNA-Seq. Taken together, results of transcriptome analysis in this study provided useful insights for salt-tolerance molecular mechanisms of Z. macrostachya. Furthermore, these DEGs under salt stress provided important clues for future salt-tolerance genes cloning of Z. macrostachya. © 2021 Friends Science Publishers

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Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress

PeerJ ◽

10.7717/peerj.12492 ◽

2021 ◽

Vol 9 ◽

pp. e12492

Author(s):

Xun Liu ◽

Xinxia Yang ◽

Bin Zhang

Keyword(s):

Salt Stress ◽

Stress Response ◽

Salt Tolerance ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Differentially Expressed ◽

Rna Seq ◽

Functional Identification ◽

Salt Stress Response ◽

Soybean Seedlings

Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop.

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Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

BMC Genomics ◽

10.1186/s12864-020-07321-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Peng Xu ◽

Qi Guo ◽

Shan Meng ◽

Xianggui Zhang ◽

Zhenzhen Xu ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Genetic Variations ◽

Genome Wide Association ◽

Cotton Production ◽

Fresh Matter ◽

Salt Stress Response ◽

Genome Wide ◽

A Genome

Abstract Background Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

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The Jacalin-Related Lectin HvHorcH Is Involved in the Physiological Response of Barley Roots to Salt Stress

International Journal of Molecular Sciences ◽

10.3390/ijms221910248 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10248

Author(s):

Katja Witzel ◽

Andrea Matros ◽

Uwe Bertsch ◽

Tariq Aftab ◽

Twan Rutten ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Extracellular Fluid ◽

Root Tip ◽

Salinity Treatment ◽

Root Tips ◽

Salt Stress Response ◽

Cdna Sequences ◽

Barley Cultivars ◽

Protein Levels

Salt stress tolerance of crop plants is a trait with increasing value for future food production. In an attempt to identify proteins that participate in the salt stress response of barley, we have used a cDNA library from salt-stressed seedling roots of the relatively salt-stress-tolerant cv. Morex for the transfection of a salt-stress-sensitive yeast strain (Saccharomyces cerevisiae YSH818 Δhog1 mutant). From the retrieved cDNA sequences conferring salt tolerance to the yeast mutant, eleven contained the coding sequence of a jacalin-related lectin (JRL) that shows homology to the previously identified JRL horcolin from barley coleoptiles that we therefore named the gene HvHorcH. The detection of HvHorcH protein in root extracellular fluid suggests a secretion under stress conditions. Furthermore, HvHorcH exhibited specificity towards mannose. Protein abundance of HvHorcH in roots of salt-sensitive or salt-tolerant barley cultivars were not trait-specific to salinity treatment, but protein levels increased in response to the treatment, particularly in the root tip. Expression of HvHorcH in Arabidopsis thaliana root tips increased salt tolerance. Hence, we conclude that this protein is involved in the adaptation of plants to salinity.

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Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

10.21203/rs.3.rs-66236/v3 ◽

2020 ◽

Author(s):

Peng Xu ◽

Qi Guo ◽

Shan Meng ◽

Xianggui Zhang ◽

Zhenzhen Xu ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Genetic Variations ◽

Genome Wide Association ◽

Cotton Production ◽

Fresh Matter ◽

Salt Stress Response ◽

Genome Wide ◽

A Genome

Abstract Background: Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results: In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on two years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (-log10p>4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions: These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

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Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud.

10.21203/rs.2.16313/v3 ◽

2020 ◽

Author(s):

Jingjing Wang ◽

Cong An ◽

Hailin Guo ◽

Xiangyang Yang ◽

Jingbo Chen ◽

...

Keyword(s):

Signal Transduction ◽

Salt Stress ◽

Stress Response ◽

Salt Tolerance ◽

Molecular Mechanisms ◽

Salt Tolerant ◽

Zoysia Japonica ◽

Salt Stress Response ◽

Leaves And Roots ◽

Time Point

Abstract Background: Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown. Results: The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K+/Na+ ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family. Conclusions: Z011 may have improved salt tolerance by reducing Na+ transport from the roots to the leaves, increasing K+ absorption in the roots and reducing K+ secretion from the leaves to maintain a significantly greater K+/Na+ ratio. Twenty-four hours might be a relatively important time point for the salt-stress response of zoysiagrass. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation. This study provides fundamental information concerning the salt-stress response of Zoysia and improves the understanding of molecular mechanisms in salt-tolerant plants.

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Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii

International Journal of Molecular Sciences ◽

10.3390/ijms19113359 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3359 ◽

Cited By ~ 18

Author(s):

Ning Wang ◽

Zhixin Qian ◽

Manwei Luo ◽

Shoujin Fan ◽

Xuejie Zhang ◽

...

Keyword(s):

Salt Stress ◽

Chlamydomonas Reinhardtii ◽

Green Alga ◽

Transcriptome Analysis ◽

Stress Responses ◽

Electron Flow ◽

Saline Stress ◽

Alternative Source ◽

Salt Stress Response ◽

Stress Responding

Salinity is one of the most important abiotic stresses threatening plant growth and agricultural productivity worldwide. In green alga Chlamydomonas reinhardtii, physiological evidence indicates that saline stress increases intracellular peroxide levels and inhibits photosynthetic-electron flow. However, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge. In this study, the transcriptome analysis of short-term acclimation to salt stress (200 mM NaCl for 24 h) was performed in C. reinhardtii. A total of 10,635 unigenes were identified as being differently expressed by RNA-seq, including 5920 up- and 4715 down-regulated unigenes. A series of molecular cues were screened for salt stress response, including maintaining the lipid homeostasis by regulating phosphatidic acid, acetate being used as an alternative source of energy for solving impairment of photosynthesis, and enhancement of glycolysis metabolism to decrease the carbohydrate accumulation in cells. Our results may help understand the molecular and genetic underpinnings of salt stress responses in green alga C. reinhardtii.

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Morphological and Genetic Diversity within Salt Tolerance Detection in Eighteen Wheat Genotypes

Plants ◽

10.3390/plants9030287 ◽

2020 ◽

Vol 9 (3) ◽

pp. 287 ◽

Cited By ~ 4

Author(s):

Ibrahim Al-Ashkar ◽

Ali Alderfasi ◽

Walid Ben Romdhane ◽

Mahmoud F. Seleiman ◽

Rania A. El-Said ◽

...

Keyword(s):

Genetic Variation ◽

Salt Stress ◽

Salt Tolerance ◽

Dry Matter ◽

Phenotypic Trait ◽

Salinity Treatment ◽

Salt Tolerant ◽

Salt Stress Response ◽

Wheat Genotypes ◽

Relative Change

Salinity is a major obstacle to wheat production worldwide. Salt-affected soils could be used by improving salt-tolerant genotypes depending upon the genetic variation and salt stress response of adapted and donor wheat germplasm. We used a comprehensive set of morpho-physiological and biochemical parameters and simple sequence repeat (SSR) marker technique with multivariate analysis to accurately demonstrate the phenotypic and genetic variation of 18 wheat genotypes under salinity stress. All genotypes were evaluated without NaCl as a control and with 150 mM NaCl, until the onset of symptoms of death in the sensitive plant (after 43 days of salinity treatment). The results showed that the relative change of the genetic variation was high for all parameters, heritability (>60%), and genetic gain (>20%). Stepwise regression analysis, noting the importance of the root dry matter, relative turgidity, and their respective contributions to the shoot dry matter, indicated their relevance in improving and evaluating the salt-tolerant genotypes of breeding programs. The relative change of the genotypes in terms of the relative turgidity and shoot dry matter during salt stress was verified using clustering methods. For cluster analysis, the genotypes were classified into three groups: tolerant, intermediate, and sensitive, representing five, six, and seven genotypes, respectively. The morphological and genetic distances were significantly correlated based on the Mantel test. Of the 23 SSR markers that showed polymorphism, 17 were associated with almost all examined parameters. Therefore, based on the observed molecular marker-phenotypic trait association, the markers were highly useful in detecting tolerant and sensitive genotypes. Thus, it considers a helpful tool for salt tolerance through marker-assisted selection.

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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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Transcriptome Profiling of the Salt Stress Response in the Leaves and Roots of Halophytic Eutrema salsugineum

Frontiers in Genetics ◽

10.3389/fgene.2021.770742 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chuanshun Li ◽

Yuting Qi ◽

Chuanzhi Zhao ◽

Xingjun Wang ◽

Quan Zhang

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Soluble Sugars ◽

Lignin Biosynthesis ◽

Sugar Metabolism ◽

Transcriptome Profiling ◽

Salt Stress Response ◽

Salt Shock ◽

Eutrema Salsugineum ◽

Leaves And Roots

Eutrema salsugineum can grow in natural harsh environments; however, the underlying mechanisms for salt tolerance of Eutrema need to be further understood. Herein, the transcriptome profiling of Eutrema leaves and roots exposed to 300 mM NaCl is investigated, and the result emphasized the role of genes involved in lignin biosynthesis, autophagy, peroxisome, and sugar metabolism upon salt stress. Furthermore, the expression of the lignin biosynthesis and autophagy-related genes, as well as 16 random selected genes, was validated by qRT-PCR. Notably, the transcript abundance of a large number of lignin biosynthesis genes such as CCoAOMT, C4H, CCR, CAD, POD, and C3′H in leaves was markedly elevated by salt shock. And the examined lignin content in leaves and roots demonstrated salt stress led to lignin accumulation, which indicated the enhanced lignin level could be an important mechanism for Eutrema responding to salt stress. Additionally, the differentially expressed genes (DEGs) assigned in the autophagy pathway including Vac8, Atg8, and Atg4, as well as DEGs enriched in the peroxisome pathway such as EsPEX7, EsCAT, and EsSOD2, were markedly induced in leaves and/or roots. In sugar metabolism pathways, the transcript levels of most DEGs associated with the synthesis of sucrose, trehalose, raffinose, and xylose were significantly enhanced. Furthermore, the expression of various stress-related transcription factor genes including WRKY, AP2/ERF-ERF, NAC, bZIP, MYB, C2H2, and HSF was strikingly improved. Collectively, the increased expression of biosynthesis genes of lignin and soluble sugars, as well as the genes in the autophagy and peroxisome pathways, suggested that Eutrema encountering salt shock possibly possess a higher capacity to adjust osmotically and facilitate water transport and scavenge reactive oxidative species and oxidative proteins to cope with the salt environment. Thus, this study provides a new insight for exploring the salt tolerance mechanism of halophytic Eutrema and discovering new gene targets for the genetic improvement of crops.

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