Transcriptomic profiling identifies candidate genes involved in salt tolerance of the xerophyte Pugionium cornutum

Abstract Background: Pugionium cornutum is a xerophytic plant that primarily adapts to salt stress by accumulating inorganic ions (e.g., Cl - ) for osmoregulation, improving its reactive oxygen species (ROS)-scavenging ability and maintaining high photosynthetic carbon assimilation efficiency, but the associated molecular mechanisms still remain unclear. Results : Here, we present an analysis of gene responses to salt stress based on the transcriptome of P. cornutum exposed to 50 mM NaCl treatment. The data revealed that, after NaCl treatment for 6 or 24 h, the transcript levels of multiple genes encoding proteins facilitating Cl - accumulation and NO 3 - homeostasis such as SLAH1, CLCg, CCC1, and NPF6.4, as well as the transport of other major inorganic osmoticums were significantly upregulated in roots and shoots, which should be favorable to enhancing osmotic adjustment capacity and maintaining the plant uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which should be beneficial for mitigating salt-induced oxidative damage to the cell metabolism. Meanwhile, many genes encoding components of the photosynthetic electron transport and carbon fixation enzymes were significantly upregulated in shoots after salt treatment, possibly resulting in a high carbon assimilation efficiency in P. cornutum . Additionally, numerous salt-inducible transcription factor genes probably regulating the abovementioned processes were found. Conclusion : Candidate genes involved in salt tolerance of P. cornutum were identified, which lays a preliminary foundation for clarifying the molecular mechanism of the xerophytes adapting to harsh environments.

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Transcriptomic profiling identifies candidate genes involved in salt tolerance of the xerophyte Pugionium cornutum

10.21203/rs.2.14265/v1 ◽

2019 ◽

Author(s):

Yan-Nong Cui ◽

Fang-Zhen Wang ◽

Cheng-Hang Yang ◽

Jian-Zhen Yuan ◽

Huan Guo ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Molecular Mechanisms ◽

Carbon Fixation ◽

Assimilation Efficiency ◽

Carbon Assimilation ◽

Inorganic Ions ◽

Ros Scavenging ◽

Genes Encoding

Abstract Background: Pugionium cornutum is a xerophytic plant that primarily adapts to salt stress by accumulating inorganic ions (e.g., Cl-) for osmoregulation, improving its reactive oxygen species (ROS)-scavenging ability and maintaining high photosynthetic carbon assimilation efficiency, but the associated molecular mechanisms still remain unclear. Results: Here, we present an analysis of gene responses to salt stress based on the transcriptome of P. cornutum exposed to 50 mM NaCl treatment. The data revealed that, after NaCl treatment for 6 or 24 h, the transcript levels of multiple genes encoding proteins facilitating Cl- accumulation and NO3- homeostasis such as SLAH1, CLCg, CCC1, and NPF6.4, as well as the transport of other major inorganic osmoticums were significantly upregulated in roots and shoots, which should be favorable to enhancing osmotic adjustment capacity and maintaining the plant uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which should be beneficial for mitigating salt-induced oxidative damage to the cell metabolism. Meanwhile, many genes encoding components of the photosynthetic electron transport and carbon fixation enzymes were significantly upregulated in shoots after salt treatment, possibly resulting in a high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes probably regulating the abovementioned processes were found. Conclusion: Candidate genes involved in salt tolerance of P. cornutum were identified, which lays a preliminary foundation for clarifying the molecular mechanism of the xerophytes adapting to harsh environments.

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Transcriptomic Profiling Identifies Candidate Genes Involved in the Salt Tolerance of the Xerophyte Pugionium cornutum

Genes ◽

10.3390/genes10121039 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1039 ◽

Cited By ~ 1

Author(s):

Yan-Nong Cui ◽

Fang-Zhen Wang ◽

Cheng-Hang Yang ◽

Jian-Zhen Yuan ◽

Huan Guo ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Osmotic Adjustment ◽

Assimilation Efficiency ◽

Carbon Assimilation ◽

Ros Scavenging ◽

Transport Pathway ◽

Genes Encoding ◽

Assimilation Capacity

The xerophyte Pugionium cornutum adapts to salt stress by accumulating inorganic ions (e.g., Cl−) for osmotic adjustment and enhancing the activity of antioxidant enzymes, but the associated molecular basis remains unclear. In this study, we first found that P. cornutum could also maintain cell membrane stability due to its prominent ROS-scavenging ability and exhibits efficient carbon assimilation capacity under salt stress. Then, the candidate genes associated with the important physiological traits of the salt tolerance of P. cornutum were identified through transcriptomic analysis. The results showed that after 50 mM NaCl treatment for 6 or 24 h, multiple genes encoding proteins facilitating Cl− accumulation and NO3− homeostasis, as well as the transport of other major inorganic osmoticums, were significantly upregulated in roots and shoots, which should be favorable for enhancing osmotic adjustment capacity and maintaining the uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which might be beneficial for mitigating salt-induced oxidative damage to the cells. Meanwhile, many genes encoding components of the photosynthetic electron transport pathway and carbon fixation enzymes were significantly upregulated in shoots, possibly resulting in high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes that probably regulate the abovementioned processes were found. This work lays a preliminary foundation for clarifying the molecular mechanism underlying the adaptation of xerophytes to harsh environments.

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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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Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and Salt Stress

Plants ◽

10.3390/plants10112281 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2281

Author(s):

Qian Ma ◽

Chunxue Su ◽

Chun-Hai Dong

Keyword(s):

Cell Wall ◽

Salt Stress ◽

Molecular Mechanisms ◽

Plant Hormone ◽

Structural Protein ◽

Ros Scavenging ◽

Glutathione S Transferase ◽

Tandem Mass Tag ◽

Genes Encoding ◽

Plant Hormone Signaling

Quinoa (Chenopodiumquinoa Willd.), originated from the Andean region of South America, shows more significant salt tolerance than other crops. To reveal how the plant hormone ethylene is involved in the quinoa responses to salt stress, 4-week-old quinoa seedlings of ‘NL-6′ treated with water, sodium chloride (NaCl), and NaCl with ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were collected and analyzed by transcriptional sequencing and tandem mass tag-based (TMT) quantitative proteomics. A total of 9672 proteins and 60,602 genes was identified. Among them, the genes encoding glutathione S-transferase (GST), peroxidase (POD), phosphate transporter (PT), glucan endonuclease (GLU), beta-galactosidase (BGAL), cellulose synthase (CES), trichome birefringence-like protein (TBL), glycine-rich cell wall structural protein (GRP), glucosyltransferase (GT), GDSL esterase/lipase (GELP), cytochrome P450 (CYP), and jasmonate-induced protein (JIP) were significantly differentially expressed. Further analysis suggested that the genes may mediate through osmotic adjustment, cell wall organization, reactive oxygen species (ROS) scavenging, and plant hormone signaling to take a part in the regulation of quinoa responses to ethylene and salt stress. Our results provide a strong foundation for exploration of the molecular mechanisms of quinoa responses to ethylene and salt stress.

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Transcriptome Changes Reveal the Molecular Mechanisms of Humic Acid-Induced Salt Stress Tolerance in Arabidopsis

Molecules ◽

10.3390/molecules26040782 ◽

2021 ◽

Vol 26 (4) ◽

pp. 782

Author(s):

Joon-Yung Cha ◽

Sang-Ho Kang ◽

Myung Geun Ji ◽

Gyeong-Im Shin ◽

Song Yi Jeong ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Humic Acid ◽

Stress Tolerance ◽

Plant Development ◽

Molecular Mechanisms ◽

Abiotic Stress Tolerance ◽

Principal Component ◽

Salt Stress Tolerance ◽

Genes Encoding

Humic acid (HA) is a principal component of humic substances, which make up the complex organic matter that broadly exists in soil environments. HA promotes plant development as well as stress tolerance, however the precise molecular mechanism for these is little known. Here we conducted transcriptome analysis to elucidate the molecular mechanisms by which HA enhances salt stress tolerance. Gene Ontology Enrichment Analysis pointed to the involvement of diverse abiotic stress-related genes encoding HEAT-SHOCK PROTEINs and redox proteins, which were up-regulated by HA regardless of salt stress. Genes related to biotic stress and secondary metabolic process were mainly down-regulated by HA. In addition, HA up-regulated genes encoding transcription factors (TFs) involved in plant development as well as abiotic stress tolerance, and down-regulated TF genes involved in secondary metabolic processes. Our transcriptome information provided here provides molecular evidences and improves our understanding of how HA confers tolerance to salinity stress in plants.

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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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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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Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa (Medicago sativa L.)

International Journal of Molecular Sciences ◽

10.3390/ijms21093361 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3361

Author(s):

Cesar Augusto Medina ◽

Charles Hawkins ◽

Xiang-Ping Liu ◽

Michael Peel ◽

Long-Xi Yu

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Prediction Models ◽

Genome Wide Association ◽

Support Vector ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Allele Dosage ◽

Mean Square Errors

Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.

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