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

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1039 ◽  
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.

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

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.

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

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 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.

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

BMC Genomics ◽  
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.

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

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.

scholarly journals Physiological and Biochemical Responses to Salt Stress of Alfalfa Populations Selected for Salinity Tolerance and Grown in Symbiosis with Salt-Tolerant Rhizobium

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 569
Author(s):  
Annick Bertrand ◽  
Craig Gatzke ◽  
Marie Bipfubusa ◽  
Vicky Lévesque ◽  
Francois P. Chalifour ◽  
...  
Keyword(s):  
Amino Acids ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Water Content ◽  
Salinity Tolerance ◽  
Osmotic Adjustment ◽  
Recurrent Selection ◽  
Aromatic Amino Acids ◽  
Nacl Stress ◽  
Salt Tolerant

Alfalfa and its rhizobial symbiont are sensitive to salinity. We compared the physiological responses of alfalfa populations inoculated with a salt-tolerant rhizobium strain, exposed to five NaCl concentrations (0, 20, 40, 80, or 160 mM NaCl). Two initial cultivars, Halo (H-TS0) and Bridgeview (B-TS0), and two populations obtained after three cycles of recurrent selection for salt tolerance (H-TS3 and B-TS3) were compared. Biomass, relative water content, carbohydrates, and amino acids concentrations in leaves and nodules were measured. The higher yield of TS3-populations than initial cultivars under salt stress showed the effectiveness of our selection method to improve salinity tolerance. Higher relative root water content in TS3 populations suggests that root osmotic adjustment is one of the mechanisms of salt tolerance. Higher concentrations of sucrose, pinitol, and amino acid in leaves and nodules under salt stress contributed to the osmotic adjustment in alfalfa. Cultivars differed in their response to recurrent selection: under a 160 mM NaCl-stress, aromatic amino acids and branched-chain amino acids (BCAAs) increased in nodules of B-ST3 as compared with B-TS0, while these accumulations were not observed in H-TS3. BCAAs are known to control bacteroid development and their accumulation under severe stress could have contributed to the high nodulation of B-TS3.

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

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.

A barley mutant with improved salt tolerance through ion homeostasis and ROS scavenging under salt stress

2017 ◽  
Vol 39 (3) ◽  
Author(s):  
Davood Kiani ◽  
Hassan Soltanloo ◽  
Seyyede Sanaz Ramezanpour ◽  
Ali Asghar Nasrolahnezhad Qumi ◽  
Ahad Yamchi ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Ion Homeostasis ◽  
Ros Scavenging ◽  
Barley Mutant

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

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.

scholarly journals QTL mapping and candidate gene identification in rice using a Kalarata-Azucena population under salt stress

2020 ◽  
Author(s):  
Marjorie P. de Ocampo ◽  
Ho Viet The ◽  
Michael J. Thomson ◽  
Shiro Mitsuya ◽  
Akira Yamauchi ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Evaluation System ◽  
Average Distance ◽  
Chlorophyll Concentration ◽  
Interval Mapping ◽  
Chromosome 1 ◽  
Rice Varieties

Abstract Background Salt stress is a major constraint across large rice production areas in Asia, because of the high sensitivity of modern rice varieties. To identify quantitative trait loci (QTL) associated with salt tolerance in rice, we developed an F2 population from a cross between the salt-tolerant landrace, Kalarata, and the salt-sensitive parent, Azucena. An F2 population was used for DNA extraction, and F2:3 families from this population were screened in a phytotron in a saline nutrient solution at the seedling stage. Results After 2 weeks at an EC of 12 dS m− 1, the F2:3 families were scored for salt tolerance using IRRI’s Standard evaluation system (SES). Growth, biomass, Na+ and K+ concentrations in leaf tissues, and chlorophyll concentration were determined. A genetic linkage map was constructed with 151 SSRs and InDel markers, which cover 1463 cM with an average distance of 9.69 cM between loci. A total of 13 QTL were identified using Composite Interval Mapping for 16 traits. The short arm of chromosome 1 had the highest density of QTL associated with salt tolerance, which coincides with the Saltol locus; emphasizing the importance of this locus for candidate gene discovery and for use in rice breeding. Several novel QTL were identified on other chromosomes. Conclusions The novel QTL identified in this study constitute future targets for molecular breeding, to combine them with other QTLs identified before, for higher and stable performance of rice varieties in salt affected soils. Candidate genes for the large effect QTL on chromosome 3 were found to be involved in diverse biological processes, cellular components, and molecular functions. Several candidate genes in this locus were functionally associated with salt stress tolerance and should further be considered for genetic improvement of rice varieties.

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