scholarly journals Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Raheleh Mirdar Mansuri ◽  
Zahra-Sadat Shobbar ◽  
Nadali Babaeian Jelodar ◽  
Mohammadreza Ghaffari ◽  
Seyed Mahdi Mohammadi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Candidate Genes ◽  
Salinity Stress ◽  
Meta Analysis ◽  
Analysis Approach ◽  
Regulation Of Transcription ◽  
Potential Candidate ◽  
Cbs Domain ◽  
Cell Wall Organization

Abstract Background Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. Results A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. Conclusions The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.

scholarly journals Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

2020 ◽  
Author(s):  
Raheleh Mirdar Mansuri ◽  
Zahra-Sadat Shobbar ◽  
Nadali Babaeian Jelodar ◽  
Mohammadreza Ghaffari ◽  
Seyed Mahdi Mohammadi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Candidate Genes ◽  
Salinity Stress ◽  
Meta Analysis ◽  
Analysis Approach ◽  
Regulation Of Transcription ◽  
Potential Candidate ◽  
Cbs Domain ◽  
Cell Wall Organization

Abstract Background: Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. Results: A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. Conclusions: The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.

scholarly journals Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

2020 ◽  
Author(s):  
Raheleh Mirdar Mansuri ◽  
Zahra-Sadat Shobbar ◽  
Nadali Babaeian Jelodar ◽  
Mohammadreza Ghaffari ◽  
Seyed Mahdi Mohammadi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Candidate Genes ◽  
Salinity Stress ◽  
Meta Analysis ◽  
Analysis Approach ◽  
Regulation Of Transcription ◽  
Potential Candidate ◽  
Cbs Domain ◽  
Cell Wall Organization

Abstract Background: Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. Results: A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. Conclusions: The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.

scholarly journals Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

2020 ◽  
Author(s):  
Raheleh Mirdar Mansuri ◽  
Zahra-Sadat Shobbar ◽  
Nadali Babaeian Jelodar ◽  
Mohammadreza Ghaffari ◽  
Seyed Mahdi Mohammadi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Candidate Genes ◽  
Salinity Stress ◽  
Meta Analysis ◽  
Analysis Approach ◽  
Regulation Of Transcription ◽  
Potential Candidate ◽  
Cbs Domain ◽  
Cell Wall Organization

Abstract Background: Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review.Results: A total of 3449 DEGs were detected in 46 meta-QTL positions, while 1286, 86, 1729 and 348 DEGs were observed respectively in root, shoot, seedling and leaves tissues. Moreover, functional annotation of DEGs located in meta-QTLs suggested some involved biological processes (e.g. ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g. transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 20 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein.Conclusions: The obtained results indicate that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and ROS scavenging in response to the salt stress.

A meta-analysis of potential candidate genes associated with salinity stress tolerance in rice

Agri Gene ◽  
2016 ◽  
Vol 1 ◽  
pp. 126-134 ◽  
Author(s):  
Sukhdeep Kaur ◽  
M.A. Iquebal ◽  
Sarika Jaiswal ◽  
Gitanjali Tandon ◽  
R.M. Sundaram ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Candidate Genes ◽  
Salinity Stress ◽  
Meta Analysis ◽  
Potential Candidate ◽  
Salinity Stress Tolerance

scholarly journals GENETICS OF PHOBIC DISORDERS

2021 ◽  
pp. 245-256
Author(s):  
V. Pomohaibo ◽  
O. Berezan ◽  
A. Petrushov
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Meta Analysis ◽  
Molecular Genetic ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Social Phobias ◽  
Phobic Disorders ◽  
Multifactorial Diseases ◽  
Statistical Validity

At present time, on the basis of genome-wide association studies (GWAS), several authors found linkage of phobic disorders with certain regions of chromosomes – 3q26 (agoraphobia), 14q13 (specific phobias), 16q21 (social phobias), 16q22 (social phobias) and 4q31-q34 (phobic disorders). We propose 19 genes that are localized in these regions and are expressed in the brain: PRKCI, CLDN11, EIF5A2, TNIK, CLCN3, CPE, GLRB, GRIA2, NEK1, NPY2R, NPY5R, RAPGEF2,  TRIM2, SMAD1, ADGRG1, BEAN1, CDH8, DOK4 and KATNB1. Therefore, these genes may be investigated as candidate genes of phobic disorders. Various sources propose 26 potential candidate genes of phobic disorders. Finnish geneticist J. Donner carries out a meta-analysis to study the 8 most probable among them and corroborates statistical validity only for 4 genes: ALAD, CDH2, EPB41L4A and GAD1. First three genes are involved in the social phobias, and fourth is involved in whole phobic disorders. Phobias are heterogeneous and multifactorial diseases. To understand the biological mechanisms of such disorders, to create effective methods for their prevention and treatment, there are needed further intensive molecular genetic studies of these disorders on sufficiently large samples and corroborating these results by other authors.

Pinpointing Genomic Regions Associated with Root System Architecture in Rice Through an Integrative Meta-Analysis Approach

2021 ◽  
Author(s):  
Parisa Daryani ◽  
Hadi Darzi Ramandi ◽  
Sara Dezhsetan ◽  
Raheleh Mirdar Mansuri ◽  
Ghasem Hosseini Salekdeh ◽  
...  
Keyword(s):  
Drought Stress ◽  
Root System ◽  
Candidate Genes ◽  
System Architecture ◽  
Meta Analysis ◽  
Root System Architecture ◽  
Stress Conditions ◽  
Yield Potential ◽  
Analysis Approach ◽  
Genomic Regions

Abstract Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA related MQTLs were detected, and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA) and lignification (e.g. C4H, PAL, PRX and CAD). The genes located both in the SNP peak positions and in the high-overview-index MQTLs for root architecture traits are suggested as novel candidate genes for further functional analysis.. The promising candidate genes and MQTLs would be applicable to genetic engineering and MQTL-assisted breeding of root phenotypes aimed at improving yield potential, stability and performance in a water-stressed environment.

scholarly journals Integrity transcriptome and proteome analyses provide new insights into the mechanisms regulating peel cracking in Akebia trifoliata fruit

2019 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candidate Genes ◽  
Fruit Ripening ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Sugar Metabolism ◽  
Potential Candidate ◽  
Proteomics Data ◽  
Galactose Metabolism ◽  
Fruit Cracking

Abstract Background Akebia trifoliata (Thunb.) Koidz, can be used as a new potential candidate biofuel and bioenergy crop due to its high productivity, adaptability and tolerance to cultivation conditions. However, the pericarp of A. trifoliata cracks open longitudinally and disperses its seeds along the ventral suture during fruit ripening, which is a serious problem that limits the usefulness of its biofuel feedstocks and causes significant losses of yield and commercial value. However, there have been no known previous investigations of the fruit cracking and its molecular mechanisms in A. trifoliata.Results The dynamic structural changes of the fruit peels were observed. In the non-cracking stage of growth, the exocarp was dense, had an orderly arrangement, and the cuticle was complete and distributed continuously. However, the cells became thinner, had reduced integrity, lost cell wall structures, and there was cell wall break down, in the fruit cracking stage. Moreover, analysis of the complementary RNA sequencing based transcriptomes and tandem mass tag based proteomes at different development stages of the fruit ripening, were performed to detect the genes and proteins related to the fruit cracking in A. trifoliata. A total of 20 differentially expressed genes and 17 differentially abundant proteins were identified from the transcriptomics and proteomics data that contribute to the fruit cracking, by participating in the biosynthesis of the phenylpropanoid pathway, galactose metabolism, pentose, and glucuronate interconversions, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Several candidate genes and proteins related to pentose and glucuronate interconversions (pectate lyases and pectinesterase) and galactose metabolism (β-galactosidases 1 and β-galactosidases 2) may play key roles in A. trifoliata fruit cracking.Conclusions Complementary transcriptome and proteome level analyses indicated that a complex molecular network was controlling the fruit cracking process. This study provides new insights into the molecular basis of fruit cracking in A. trifoliata fruits. The candidate genes/proteins identified in this study may be useful for the genetic improvement of A. trifoliata and other crops.

scholarly journals Meta-analysis of Drought-tolerant Genotypes inOryza sativa: A Network-based Approach

2018 ◽  
Author(s):  
Sanchari Sircar ◽  
Nita Parekh
Keyword(s):  
Cluster Analysis ◽  
Cell Wall ◽  
Candidate Genes ◽  
Computational Approach ◽  
External Information ◽  
Potential Candidate ◽  
Aba Signaling ◽  
Cell Wall Metabolism ◽  
Drought Tolerant ◽  
Tightly Coupled

AbstractBackgroundDrought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress.ResultsCo-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as, resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as ‘seed’ genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up-and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signaling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signaling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signaling, calcium signaling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions.ConclusionCurrently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.

Calcium effects on root cell wall composition and ion contents in two soybean cultivars under salinity stress

2014 ◽  
Vol 94 (4) ◽  
pp. 733-740 ◽  
Author(s):  
Ping An ◽  
Xiangjun Li ◽  
Yuanrun Zheng ◽  
A. Egrinya Eneji ◽  
Shinobu Inanaga
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Root Growth ◽  
Salinity Stress ◽  
Cell Wall Composition ◽  
Root Cell ◽  
Soybean Cultivars ◽  
Ion Contents ◽  
Calcium Effects ◽  
Root Cell Wall

An, P., Li, X., Zheng, Y., Eneji, A. E. and Inanaga, S. 2014. Calcium effects on root cell wall composition and ion contents in two soybean cultivars under salinity stress. Can. J. Plant Sci. 94: 733–740. It has been widely suggested that calcium (Ca) application ameliorates salt stress, but characteristic changes in root cell wall due to Ca application under saline conditions are poorly documented. Our objectives were: (1) to determine the effect of Ca on root cell wall composition, using two soybean cultivars differing in sensitivity to salt stress and (2) to understand the relationship between the internal effects of sodium–calcium interaction on the root cell wall. Uniform seedlings were transplanted into mixed solutions of NaCl (0, 40 mM,) and CaCl2 (0, 0.5, 2 mM). Root lengths were measured after an exposure of 14, 24 and 40 h to the treatments and cell wall analysis performed for total sugars, uronic acid and ion contents. Without salinity stress, Ca application caused no significant changes in root growth and cell wall constituents in both cultivars. However, it did ameliorate the decrease in the amount of cell wall under stress, especially the pectin fraction. Both cell wall and cellular Ca2+ and K+ contents were significantly increased by additional Ca2+ under saline condition. Therefore, by applying Ca2+, the maintenance of pectin level and increase in cell wall Ca2+ may contribute to the restoration of root growth under salinity. Calcium application significantly increased the pectin level under salinity and soybean root growth also showed notable restoration. One way Ca ameliorates salt toxicity may be by maintaining the composition of the cell wall. This ameliorative effect was more conspicuous in the salt-tolerant cultivar, Dare, than the salt-sensitive cultivar, Touzan 69.

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