scholarly journals Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Xia ◽  
Xiaosong Ma ◽  
Kai Xu ◽  
Lei Wang ◽  
Hongyan Liu ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Iron Transport ◽  
Ferric Iron ◽  
Temporal Dynamics ◽  
Histone Deacetylation ◽  
System Level ◽  
Biological Processes ◽  
Drought Period ◽  
Recovery Stage ◽  
Rice Genotypes

Abstract Background Drought-tolerance ensures a crop to maintain life activities and protect cell from damages under dehydration. It refers to diverse mechanisms temporally activated when the crop adapts to drought. However, knowledge about the temporal dynamics of rice transcriptome under drought is limited. Results Here, we investigated temporal transcriptomic dynamics in 12 rice genotypes, which varied in drought tolerance (DT), under a naturally occurred drought in fields. The tolerant genotypes possess less differentially expressed genes (DEGs) while they have higher proportions of upregulated DEGs. Tolerant and susceptible genotypes have great differences in temporally activated biological processes (BPs) during the drought period and at the recovery stage based on their DEGs. The DT-featured BPs, which are activated specially (e.g. raffinose, fucose, and trehalose metabolic processes, etc.) or earlier in the tolerant genotypes (e.g. protein and histone deacetylation, protein peptidyl-prolyl isomerization, transcriptional attenuation, ferric iron transport, etc.) shall contribute to DT. Meanwhile, the tolerant genotypes and the susceptible genotypes also present great differences in photosynthesis and cross-talks among phytohormones under drought. A certain transcriptomic tradeoff between DT and productivity is observed. Tolerant genotypes have a better balance between DT and productivity under drought by activating drought-responsive genes appropriately. Twenty hub genes in the gene coexpression network, which are correlated with DT but without potential penalties in productivity, are recommended as good candidates for DT. Conclusions Findings of this study provide us informative cues about rice temporal transcriptomic dynamics under drought and strengthen our system-level understandings in rice DT.

scholarly journals Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 27
Author(s):  
Mahmoud M. Gaballah ◽  
Azza M. Metwally ◽  
Milan Skalicky ◽  
Mohamed M. Hassan ◽  
Marian Brestic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Ssr Markers ◽  
Similarity Index ◽  
Stress Conditions ◽  
Yield Potential ◽  
Drought Tolerant ◽  
Rice Genotypes

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.

scholarly journals Genes Essential to Iron Transport in the Cyanobacterium Synechocystis sp. Strain PCC 6803

2001 ◽  
Vol 183 (9) ◽  
pp. 2779-2784 ◽  
Author(s):  
Hirokazu Katoh ◽  
Natsu Hagino ◽  
Arthur R. Grossman ◽  
Teruo Ogawa
Keyword(s):  
Iron Uptake ◽  
Iron Transport ◽  
Ferric Iron ◽  
Iron Acquisition ◽  
Complete Medium ◽  
Iron Starvation ◽  
Transporter Family ◽  
Genes Encoding ◽  
In Cells ◽  
Pcc 6803

ABSTRACT Genes encoding polypeptides of an ATP binding cassette (ABC)-type ferric iron transporter that plays a major role in iron acquisition inSynechocystis sp. strain PCC 6803 were identified. These genes are slr1295, slr0513, slr0327, and recently reportedsll1878 (Katoh et al., J. Bacteriol. 182:6523–6524, 2000) and were designated futA1, futA2, futB, andfutC, respectively, for their involvement in ferric iron uptake. Inactivation of these genes individually or futA1and futA2 together greatly reduced the activity of ferric iron uptake in cells grown in complete medium or iron-deprived medium. All the fut genes are expressed in cells grown in complete medium, and expression was enhanced by iron starvation. ThefutA1 and futA2 genes appear to encode periplasmic proteins that play a redundant role in iron binding. The deduced products of futB and futC genes contain nucleotide-binding motifs and belong to the ABC transporter family of inner-membrane-bound and membrane-associated proteins, respectively. These results and sequence similarities among the four genes suggest that the Fut system is related to the Sfu/Fbp family of iron transporters. Inactivation of slr1392, a homologue offeoB in Escherichia coli, greatly reduced the activity of ferrous iron transport. This system is induced by intracellular low iron concentrations that are achieved in cells exposed to iron-free medium or in the fut-less mutants grown in complete medium.

scholarly journals Interacting roles of lateral and medial Orbitofrontal cortex in decision-making and learning : A system-level computational model

2019 ◽  
Author(s):  
Bhargav Teja Nallapu ◽  
Frédéric Alexandre
Keyword(s):  
Decision Making ◽  
Prefrontal Cortex ◽  
Computational Model ◽  
Orbitofrontal Cortex ◽  
Temporal Dynamics ◽  
System Level ◽  
Interacting Networks ◽  
Cortical Regions ◽  
Experimental Findings

AbstractIn the context of flexible and adaptive animal behavior, the orbitofrontal cortex (OFC) is found to be one of the crucial regions in the prefrontal cortex (PFC) influencing the downstream processes of decision-making and learning in the sub-cortical regions. Although OFC has been implicated to be important in a variety of related behavioral processes, the exact mechanisms are unclear, through which the OFC encodes or processes information related to decision-making and learning. Here, we propose a systems-level view of the OFC, positioning it at the nexus of sub-cortical systems and other prefrontal regions. Particularly we focus on one of the most recent implications of neuroscientific evidences regarding the OFC - possible functional dissociation between two of its sub-regions : lateral and medial. We present a system-level computational model of decision-making and learning involving the two sub-regions taking into account their individual roles as commonly implicated in neuroscientific studies. We emphasize on the role of the interactions between the sub-regions within the OFC as well as the role of other sub-cortical structures which form a network with them. We leverage well-known computational architecture of thalamo-cortical basal ganglia loops, accounting for recent experimental findings on monkeys with lateral and medial OFC lesions, performing a 3-arm bandit task. First we replicate the seemingly dissociate effects of lesions to lateral and medial OFC during decision-making as a function of value-difference of the presented options. Further we demonstrate and argue that such an effect is not necessarily due to the dissociate roles of both the subregions, but rather a result of complex temporal dynamics between the interacting networks in which they are involved.Author summaryWe first highlight the role of the Orbitofrontal Cortex (OFC) in value-based decision making and goal-directed behavior in primates. We establish the position of OFC at the intersection of cortical mechanisms and thalamo-basal ganglial circuits. In order to understand possible mechanisms through which the OFC exerts emotional control over behavior, among several other possibilities, we consider the case of dissociate roles of two of its topographical subregions - lateral and medial parts of OFC. We gather predominant roles of each of these sub-regions as suggested by numerous experimental evidences in the form of a system-level computational model that is based on existing neuronal architectures. We argue that besides possible dissociation, there could be possible interaction of these sub-regions within themselves and through other sub-cortical structures, in distinct mechanisms of choice and learning. The computational framework described accounts for experimental data and can be extended to more comprehensive detail of representations required to understand the processes of decision-making, learning and the role of OFC and subsequently the regions of prefrontal cortex in general.

scholarly journals Evaluation of Drought Tolerance Indices in Rice Genotypes (Oryza Sativa L.)

2018 ◽  
Vol 10 (25) ◽  
pp. 7-18
Author(s):  
Sanam Safaei Chaeikar ◽  
Babak Rabiei ◽  
Mehdi Rahimi ◽  
◽  
◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Drought Tolerance ◽  
Oryza Sativa L ◽  
Rice Genotypes ◽  
Drought Tolerance Indices ◽  
Tolerance Indices

ON MODELING THE GROWTH DYNAMICS OF A STAGE STRUCTURED POPULATION

2013 ◽  
Vol 06 (06) ◽  
pp. 1350039 ◽  
Author(s):  
GIUSEPPE BUFFONI ◽  
SARA PASQUALI
Keyword(s):  
Numerical Simulations ◽  
Temporal Dynamics ◽  
Growth Dynamics ◽  
Biological Processes ◽  
Dispersion Models ◽  
Development Models ◽  
Regression Effects ◽  
Pelagic Copepod ◽  
Structured Population ◽  
Lagrangian Modeling

A Lagrangian modeling approach is applied to the numerical simulation of the temporal dynamics of a stage-structured population. The growth dynamics is determined only by the main biological processes: development of an individual, mortality, reproduction. Different approaches in modeling the development process of an individual are implemented: stochastic advection-diffusion models (backward–forward dispersion models), and stochastic development models where regression effects, defined as negative development on the status of an individual, are forbidden (forward dispersion models). Some properties of the residence times of an individual in a stage are investigated: in particular, their role in the calibration of the development models and in the estimation of some parameters introduced in the model equation. As a study case a multi-stage pelagic copepod population is considered. Trying to separate the effects of the main biological processes on the temporal dynamics, numerical simulations have been carried out in some idealized situations: first only the development of the individuals, neglecting mortality and reproduction, is considered; then the mortality process is introduced, and finally both the mortality and reproduction processes. The results of the numerical simulations, are compared and discussed.

Groundnut mutants with end-of-season drought tolerance for the marginal dry lands of North Kordofan State, Sudan.

2021 ◽  
pp. 243-257
Author(s):  
Elgailani Abdalla ◽  
Tarig Ahmed ◽  
Omar Bakhit ◽  
Yasir Gamar ◽  
Salih Elshaikh ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Small Scale ◽  
Mutation Induction ◽  
Total Production ◽  
Drought Period ◽  
Dry Lands ◽  
Terminal Drought ◽  
Drought Tolerant ◽  
Terminal Drought Stress

Abstract Groundnut (Arachis hypogaea L.), produced in the traditional small-scale rainfed sector of Western Sudan, accounts for 80% of the total annual groundnut acreage, producing 70% of the total production. Low productivity of groundnut is a characteristic feature in North Kordofan State, which is characterized as the most vulnerable state to the impact of climate change. Terminal drought stress resulting from reduction in rainfall amount and distribution at the end of the season is the most deleterious drought period, as it coincides with groundnut pod filling and maturation periods. High and stable yields under subsistence farming conditions in North Kordofan State could be realized only by using adapted high-yielding, drought-tolerant genotypes. Mutation induction by gamma-rays of 200 and 300 Gy was utilized to irradiate 500 dry seeds of the Spanish-type groundnut genotypes, Barberton, Sodari, ICGV 89104, ICGV 86743, ICGV 86744 and ICG 221, aiming at increasing the chances of obtaining genotypes with the desired drought-tolerant traits. Mutants were selected from the M3 plants using visual morphological traits. Groundnut mutants at the M4 and M5 generations, advanced by single seed descent, were evaluated for end-of-season drought tolerance. A terminal drought period of 25 days was imposed after 60 days from planting, using a rainout shelter. Mutants that survived 25 days of terminal drought stress were further evaluated for agronomic performance under rainfed field conditions. The groundnut mutant, Barberton-b-30-3-B, produced 1024 kg/ha, a significantly higher mean pod yield over 12 seasons compared with 926 kg/ha for 'Gubeish', the widely grown released check cultivar, showing overall yield advantage of 11%. Under 5 years of participatory research, Barberton-b-30-3-B was ranked the best with yield increment of 21% over 'Gubeish' under the mother trials. The GGE biplot analysis for 12 and five seasons, respectively, showed that Barberton-b-30-3-B was stable and produced a good yield in both high and low rainfall situations. Hence, Barberton-b-30-3-B was found to be a suitable mutant for sustainable profitable yields in the marginal dry lands of North Kordofan State and was officially released as 'Tafra-1' by the National Variety Release Committee during its second meeting of April 2018.

scholarly journals In Vitro Assessment of Kurdish Rice Genotypes in Response to PEG-Induced Drought Stress

2020 ◽  
Vol 10 (13) ◽  
pp. 4471
Author(s):  
Didar Rahim ◽  
Petr Kalousek ◽  
Nawroz Tahir ◽  
Tomáš Vyhnánek ◽  
Petr Tarkowski ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Growth Parameters ◽  
Oryza Sativa L ◽  
Polymorphic Information Content ◽  
Callus Growth ◽  
Antioxidant Systems ◽  
In Vitro Tests ◽  
Rice Genotypes

Rice (Oryza sativa L.) is productively affected by different environmental factors, including biotic and abiotic stress. The objectives of this research were to evaluate the genetic distinction among Kurdish rice genotypes using the simple sequence repeats (SSRs) molecular markers and to perform in vitro tests to characterize the drought tolerance of six local rice genotypes. The polymorphic information content (PIC) varied from 0.38 to 0.84 with an average of 0.56. The genetic distance ranged from 0.33 to 0.88. Drought stress had a significant impact (p ≤ 0.05) on callus growth parameters. Enzymatic antioxidant systems were predicted and exhibited a significant variation. The findings revealed that proline levels increase in proportion to polyethylene glycol (PEG) concentrations. Kalar and Gwll Swr genotypes showed the worst performances in phenotypic and biochemical traits, while Choman and Shawre exhibited the best phenotypic and biochemical performances. A positive and substantial relationship between callus fresh weight (CFW) and callus dry weight (CDW) was found under stressful and optimized conditions. Callus induction (CI) was positively and significantly associated with the catalase activity (CAT) in all stressed treatments. Based on the results for callus growth and the biochemical parameters under stress conditions, a remarkable genotype distinction, based on the tolerance reaction, was noted as follows: PEG resistant > susceptible, Choman > Shawre > White Bazyan > Red Bazyan > Gwll Swr > Kalar. The CI and CAT characteristics were considered as reliable predictors of drought tolerance in rice genotypes.

Sirt1 regulates the expression of critical metabolic genes in chicken hepatocytes

2020 ◽  
Vol 60 (11) ◽  
pp. 1381
Author(s):  
Jianfeng Yu ◽  
Jie Li ◽  
Sai He ◽  
Lu Xu ◽  
Yanping Zhang ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Quantitative Polymerase Chain Reaction ◽  
Histone Deacetylation ◽  
Chicken Liver ◽  
Biological Processes ◽  
Metabolic Genes ◽  
Carbohydrate And Lipid Metabolism ◽  
Expression Of Genes ◽  
And Control ◽  
Identify Gene Expression

Context Studies in mammals show that SIRT1 plays an important role in many biological processes including liver metabolism through histone and non-histone deacetylation. Little is known about the function of Sirt1 in the chicken. Aims The current study investigated the expression pattern of Sirt1 mRNA in the chicken and its functions in the chicken liver. Methods In this work, we used real-time quantitative polymerase chain reaction to quantify the expression levels of Sirt1 mRNA in major chicken organs and tissue types, siRNA to knock down Sirt1 expression in primary chicken hepatocytes, RNA sequencing to identify gene-expression changes induced by Sirt1 knockdown, and analysed the function of the differentially expressed genes (DEGs) through gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes ontology analysis. Key results In total, 86 DEGs were found between Sirt1 knockdown and control chicken hepatocytes, of which 63 genes were downregulated and 23 genes were upregulated by Sirt1 knockdown. The Kyoto Encyclopedia of Genes and Genomes analysis showed that 24 DEGs were involved in metabolism. Seven DEGs were involved in carbohydrate and lipid metabolism. Conclusions The present study showed that Sirt1 regulates the expression of genes involved in carbohydrate and lipid metabolism and many other biological processes in the chicken liver. Implications The results of the present study imply that Sirt1 has various functions in the chicken liver and that Sirt1 plays a potentially important role in hepatic carbohydrate and lipid metabolism in the chicken.

scholarly journals A System-Level Investigation into the Mechanisms of Apigenin Against Inflammation

2019 ◽  
Vol 14 (9) ◽  
pp. 1934578X1987860 ◽  
Author(s):  
Ying Xie ◽  
Dongdong Liang ◽  
Qingke Wu ◽  
Xuemei Chen ◽  
Manal Ali Buabeid ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Biological Activities ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Mitogen Activated Protein Kinase ◽  
System Level ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Biological Processes ◽  
Go Terms

Apigenin is a natural flavone that possesses excellent biological activities especially against aging and cancer. However, the underlying mode of its action is not yet revealed. The purpose of this study was to examine the pharmacological mechanisms of apigenin using the knowledge of network pharmacology, protein-protein interaction (PPI) databases and biological processes analysis through Cytoscape. Apigenin targets were retrieved through PASS Prediction and STITCH database and the interactive associations between these targets were studied using STITCH, followed by GO (gene ontology) and pathway enrichment analysis. As a result of target search, 125 protein targets were retrieved. Moreover, 216 GO terms related to various biological processes, 16 GO terms for various molecular processes, 5 GO terms for the cellular components, and 52 Kyoto Encyclopedia of Genes and Genomes pathway terms were achieved by analyzing gene functional annotation clusters and abundance values of these targets. Most of these terms are strongly associated with inflammation through various pathways, for example, FOXO, mammalian target of rapamycin, tumor necrosis factor, p53, AMP-activated protein kinase, p13K-AKT, and mitogen-activated protein kinase, which play an important role in inflammation, aging and cancer. Apigenin can be used to treat inflammation, aging, and cancer with an underlying mechanism of inflammation suppression. This study contributed excellent information for a better understanding of the modes of action of apigenin. However, further studies such as docking and MD simulation are required to understand the therapeutic and toxicological roles of these targets of apigenin.

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