scholarly journals Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves

2021 ◽  
Vol 22 (15) ◽  
pp. 8155
Author(s):  
Rim Nefissi Ouertani ◽  
Dhivya Arasappan ◽  
Ghassen Abid ◽  
Mariem Ben Chikha ◽  
Rahma Jardak ◽  
...  
Keyword(s):  
Salt Stress ◽  
Signaling Pathways ◽  
Candidate Genes ◽  
Crop Improvement ◽  
Regulation Of Gene Expression ◽  
Ion Homeostasis ◽  
Salt Stress Response ◽  
Salinity Response ◽  
Stress Responsive Genes ◽  
Response Expression

Barley is characterized by a rich genetic diversity, making it an important model for studies of salinity response with great potential for crop improvement. Moreover, salt stress severely affects barley growth and development, leading to substantial yield loss. Leaf and root transcriptomes of a salt-tolerant Tunisian landrace (Boulifa) exposed to 2, 8, and 24 h salt stress were compared with pre-exposure plants to identify candidate genes and pathways underlying barley’s response. Expression of 3585 genes was upregulated and 5586 downregulated in leaves, while expression of 13,200 genes was upregulated and 10,575 downregulated in roots. Regulation of gene expression was severely impacted in roots, highlighting the complexity of salt stress response mechanisms in this tissue. Functional analyses in both tissues indicated that response to salt stress is mainly achieved through sensing and signaling pathways, strong transcriptional reprograming, hormone osmolyte and ion homeostasis stabilization, increased reactive oxygen scavenging, and activation of transport and photosynthesis systems. A number of candidate genes involved in hormone and kinase signaling pathways, as well as several transcription factor families and transporters, were identified. This study provides valuable information on early salt-stress-responsive genes in roots and leaves of barley and identifies several important players in salt tolerance.

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 Understanding the Integrated Pathways and Mechanisms of Transporters, Protein Kinases, and Transcription Factors in Plants under Salt Stress

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Wasifa Hafiz Shah ◽  
Aadil Rasool ◽  
Seerat Saleem ◽  
Naveed Ul Mushtaq ◽  
Inayatullah Tahir ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Protein Kinases ◽  
Stress Responses ◽  
Crop Improvement ◽  
Ion Homeostasis ◽  
Underlying Mechanism ◽  
Regulatory Proteins ◽  
Stress Signalling

Abiotic stress is the major threat confronted by modern-day agriculture. Salinity is one of the major abiotic stresses that influence geographical distribution, survival, and productivity of various crops across the globe. Plants perceive salt stress cues and communicate specific signals, which lead to the initiation of defence response against it. Stress signalling involves the transporters, which are critical for water transport and ion homeostasis. Various cytoplasmic components like calcium and kinases are critical for any type of signalling within the cell which elicits molecular responses. Stress signalling instils regulatory proteins and transcription factors (TFs), which induce stress-responsive genes. In this review, we discuss the role of ion transporters, protein kinases, and TFs in plants to overcome the salt stress. Understanding stress responses by components collectively will enhance our ability in understanding the underlying mechanism, which could be utilized for crop improvement strategies for achieving food security.

scholarly journals The Arabidopsis HY2 Gene Acts as a Positive Regulator of NaCl Signaling during Seed Germination

2021 ◽  
Vol 22 (16) ◽  
pp. 9009
Author(s):  
Mingxin Piao ◽  
Jinpeng Zou ◽  
Zhifang Li ◽  
Junchuan Zhang ◽  
Liang Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Response ◽  
Seed Germination ◽  
Plant Stress ◽  
Ion Homeostasis ◽  
Enrichment Analysis ◽  
Salt Stress Response ◽  
Go Enrichment ◽  
Stress Related Genes ◽  
Go Enrichment Analysis

Phytochromobilin (PΦB) participates in the regulation of plant growth and development as an important synthetase of photoreceptor phytochromes (phy). In addition, Arabidopsis long hypocotyl 2 (HY2) appropriately works as a key PΦB synthetase. However, whether HY2 takes part in the plant stress response signal network remains unknown. Here, we described the function of HY2 in NaCl signaling. The hy2 mutant was NaCl-insensitive, whereas HY2-overexpressing lines showed NaCl-hypersensitive phenotypes during seed germination. The exogenous NaCl induced the transcription and the protein level of HY2, which positively mediated the expression of downstream stress-related genes of RD29A, RD29B, and DREB2A. Further quantitative proteomics showed the patterns of 7391 proteins under salt stress. HY2 was then found to specifically mediate 215 differentially regulated proteins (DRPs), which, according to GO enrichment analysis, were mainly involved in ion homeostasis, flavonoid biosynthetic and metabolic pathways, hormone response (SA, JA, ABA, ethylene), the reactive oxygen species (ROS) metabolic pathway, photosynthesis, and detoxification pathways to respond to salt stress. More importantly, ANNAT1–ANNAT2–ANNAT3–ANNAT4 and GSTU19–GSTF10–RPL5A–RPL5B–AT2G32060, two protein interaction networks specifically regulated by HY2, jointly participated in the salt stress response. These results direct the pathway of HY2 participating in salt stress, and provide new insights for the plant to resist salt stress.

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 Transcriptomic Analysis Reveals Distorted Ion Homeostasis and Responses in the Freshwater Plant Spirodela polyrhiza L. under Salt Stress

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 743 ◽  
Author(s):  
Fu ◽  
Ding ◽  
Sun ◽  
Zhang
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Regulatory Networks ◽  
Starch Content ◽  
Ion Homeostasis ◽  
Atp Synthesis ◽  
Light Reaction ◽  
Salt Stress Response ◽  
Spirodela Polyrhiza

Duckweeds are a family of freshwater angiosperms with morphology reduced to fronds and propagation by vegetative budding. Unlike other angiosperm plants such as Arabidopsis and rice that have physical barriers between their photosynthetic organs and soils, the photosynthetic organs of duckweeds face directly to their nutrient suppliers (waters), therefore, their responses to salinity may be distinct. In this research, we found that the duckweed Spirodela polyrhiza L. accumulated high content of sodium and reduced potassium and calcium contents in large amounts under salt stress. Fresh weight, Rubisco and AGPase activities, and starch content were significantly decreaseded in the first day but recovered gradually in the following days and accumulated more starch than control from Day 3 to Day 5 when treated with 100 mM and 150 mM NaCl. A total of 2156 differentially expressed genes were identified. Overall, the genes related to ethylene metabolism, major CHO degradation, lipid degradation, N-metabolism, secondary metabolism of flavonoids, and abiotic stress were significantly increased, while those involved in cell cycle and organization, cell wall, mitochondrial electron transport of ATP synthesis, light reaction of photosynthesis, auxin metabolism, and tetrapyrrole synthesis were greatly inhibited. Moreover, salt stress also significantly influenced the expression of transcription factors that are mainly involved in abiotic stress and cell differentiation. However, most of the osmosensing calcium antiporters (OSCA) and the potassium inward channels were downregulated, Na+/H+ antiporters (SOS1 and NHX) and a Na+/Ca2+ exchanger were slightly upregulated, but most of them did not respond significantly to salt stress. These results indicated that the ion homeostasis was strongly disturbed. Finally, the shared and distinct regulatory networks of salt stress responses between duckweeds and other plants were intensively discussed. Taken together, these findings provide novel insights into the underlying mechanisms of salt stress response in duckweeds, and can be served as a useful foundation for salt tolerance improvement of duckweeds for the application in salinity conditions.

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 ◽  
Genome Wide Association Study ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Cotton Production ◽  
Salt Stress Response ◽  
Genome Wide ◽  
A Genome

Abstract Background: As a pioneer industrial crop in saline-alkali lands, cotton is more resistant to salt and drought stresses. However, abiotic stresses still have significant negative effects on its growth and development. 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 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 platform. A total of 51,060 polymorphic SNPs unevenly distributed in 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 RPH, A07 for RSFW, A08 and A13 for RSDW were expressed in both two environments, indicating that they were likely to be stable 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 to conduct 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 accelerate the improvement of salt tolerance in cotton.

Reduced expression of a vesicle trafficking-related ATPase SKD1 decreases salt tolerance in Arabidopsis

2010 ◽  
Vol 37 (10) ◽  
pp. 962 ◽  
Author(s):  
Li-Wei Ho ◽  
Ting-Ting Yang ◽  
Shyan-Shu Shieh ◽  
Gerald E. Edwards ◽  
Hungchen E. Yen
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Higher Plants ◽  
Lateral Roots ◽  
Ion Homeostasis ◽  
Normal Activity ◽  
Growth Defect ◽  
Naphthaleneacetic Acid ◽  
Wild Type ◽  
Salinity Response

In this study we present the functional characterisation of SKD1 (suppressor of K+ transport growth defect) in salt tolerance of higher plants. SKD1 participates in endosome-mediated protein sorting and expression of SKD1 is salt-induced in Na+ storage cells of halophyte ice plant. Transgenic Arabidopsis with reduced SKD1 expression were generated by expressing AtSKD1 in antisense orientation. Relative root growth rate of antisense seedlings was slower than that of wild-type seedlings under salt treatment. The Na+/K+ ratio doubled in the antisense seedlings compared with the wild-type seedlings indicating a loss in Na+/K+ homeostasis. The PSII activity dropped following one week of salt-stress in antisense plants whereas wild-type plants maintained normal activity. Upon germination, transgenic seedlings developed multiple roots where each root had lower density of lateral roots. Application of 1-naphthaleneacetic acid restored the ability of transgenic seedlings to form lateral roots. Expression profiling analyses revealed that expressions of one stress-related kinase, several salt-induced transcription factors and one auxin efflux transporter were altered in antisense seedlings. With decreased expression of SKD1, plants experience a reduced salinity response and altered root development indicating the importance of intracellular vesicular trafficking in both auxin-mediated plant growth and in maintaining ion homeostasis under salt stress.

scholarly journals Adaptation of Plants to Salt Stress: Characterization of Na+ and K+ Transporters and Role of CBL Gene Family in Regulating Salt Stress Response

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 687 ◽  
Author(s):  
Toi Ketehouli ◽  
Kue Foka Idrice Carther ◽  
Muhammad Noman ◽  
Fa-Wei Wang ◽  
Xiao-Wei Li ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Ion Homeostasis ◽  
Transport Systems ◽  
Physiological Disorder ◽  
Salt Stress Response ◽  
Aerial Parts ◽  
Lower Productivity ◽  
Ion Imbalance

Salinity is one of the most serious factors limiting the productivity of agricultural crops, with adverse effects on germination, plant vigor, and crop yield. This salinity may be natural or induced by agricultural activities such as irrigation or the use of certain types of fertilizer. The most detrimental effect of salinity stress is the accumulation of Na+ and Cl− ions in tissues of plants exposed to soils with high NaCl concentrations. The entry of both Na+ and Cl− into the cells causes severe ion imbalance, and excess uptake might cause significant physiological disorder(s). High Na+ concentration inhibits the uptake of K+, which is an element for plant growth and development that results in lower productivity and may even lead to death. The genetic analyses revealed K+ and Na+ transport systems such as SOS1, which belong to the CBL gene family and play a key role in the transport of Na+ from the roots to the aerial parts in the Arabidopsis plant. In this review, we mainly discuss the roles of alkaline cations K+ and Na+, Ion homeostasis-transport determinants, and their regulation. Moreover, we tried to give a synthetic overview of soil salinity, its effects on plants, and tolerance mechanisms to withstand stress.

Sign in / Sign up

Export Citation Format

Share Document